├── .gitattributes ├── .gitignore ├── CMakeLists.txt ├── CTestConfig.cmake ├── GSM ├── CMakeLists.txt ├── GitSHA1.cpp.in ├── GitSHA1.h ├── ase.cpp ├── ase.h ├── bmat.cpp ├── cmake │ └── Dependencies.cmake ├── constants.h ├── eckart.cpp ├── eckart.h ├── gaussian.cpp ├── gaussian.h ├── grad.cpp ├── grad.h ├── grad.py ├── gstring.cpp ├── gstring.h ├── icoord.cpp ├── icoord.h ├── knnr.cpp ├── knnr.h ├── main.cpp ├── mem.cpp ├── mm_grad.cpp ├── molpro.cpp ├── molpro.h ├── mopac.cpp ├── mopac.h ├── optic.cpp ├── orca.cpp ├── orca.h ├── pTable.cpp ├── pTable.h ├── print.cpp ├── qchem.cpp ├── qchem.h ├── qchem.h.in ├── qchemsf.cpp ├── qchemsf.h ├── stringtools.cpp ├── stringtools.h ├── turbomole.cpp ├── turbomole.h ├── utils.cpp ├── utils.h ├── xtb.cpp └── xtb.h ├── GetGitRevisionDescription.cmake ├── GetGitRevisionDescription.cmake.in ├── LICENSE ├── Makefile ├── PackagesList.cmake ├── ProjectName.cmake ├── README.md ├── TEST ├── ASE │ └── diels │ │ ├── grad.py │ │ ├── inpfileq │ │ └── stringfile.standard ├── CMakeLists.txt ├── alanineDipeptideIsomerization │ ├── mopac │ │ └── de-gsm │ │ │ ├── gscreate │ │ │ ├── inpfileq │ │ │ ├── scratch │ │ │ └── initial0001.xyz │ │ │ └── stringfile.standard │ └── qchem │ │ ├── .q002.product.inp.9354.qcin.1 │ │ └── de-gsm │ │ ├── gscreate │ │ ├── inpfileq │ │ ├── qend │ │ ├── qstart │ │ └── scratch │ │ ├── gsmdone1 │ │ ├── initial0001.xyz │ │ ├── paragsm0001 │ │ ├── stringfile.xyz0001g │ │ ├── stringfile.xyz0001g1 │ │ └── tsq0001.xyz ├── ammoniaBorane │ ├── mopac │ │ └── de-gsm │ │ │ ├── inpfileq │ │ │ ├── scratch │ │ │ └── initial0001.xyz │ │ │ ├── stringfile.standard │ │ │ └── stringfile.standard.fr │ └── qchem │ │ └── de-gsm │ │ ├── gscreate │ │ ├── inpfileq │ │ ├── qend │ │ ├── qstart │ │ ├── scratch │ │ └── initial0001.xyz │ │ └── stringfile.standard ├── compare.py ├── dielsAlder │ ├── gaussian │ │ ├── de-gsm │ │ │ ├── ggrad │ │ │ ├── gscreate │ │ │ ├── gstart │ │ │ ├── inpfileq │ │ │ ├── scratch │ │ │ │ └── initial0001.xyz │ │ │ ├── stringfile.intel │ │ │ └── stringfile.standard │ │ ├── ggrad │ │ ├── gstart │ │ └── se-gsm │ │ │ ├── ISOMERS0001 │ │ │ ├── ggrad │ │ │ ├── gscreate │ │ │ ├── gstart │ │ │ ├── inpfileq │ │ │ ├── scratch │ │ │ └── initial0001.xyz │ │ │ ├── stringfile.intel │ │ │ └── stringfile.standard │ ├── mopac │ │ ├── de-gsm │ │ │ ├── inpfileq │ │ │ ├── scratch │ │ │ │ ├── initial0001.xyz │ │ │ │ └── paragsm0001 │ │ │ └── stringfile.standard │ │ └── se-gsm │ │ │ ├── ISOMERS0001 │ │ │ ├── inpfileq │ │ │ ├── scratch │ │ │ ├── initial0001.xyz │ │ │ └── paragsm0001 │ │ │ └── stringfile.standard │ ├── orca │ │ ├── de-gsm │ │ │ ├── inpfileq │ │ │ ├── ograd │ │ │ ├── scratch │ │ │ │ ├── initial0001.xyz │ │ │ │ ├── paragsm0001 │ │ │ │ ├── stringfile.xyz0001g │ │ │ │ ├── stringfile.xyz0001g1 │ │ │ │ └── tsq0001.xyz │ │ │ ├── slurm_orca_gsm.sbatch │ │ │ ├── stringfile.xyz0001 │ │ │ └── stringfile.xyz0001fr │ │ └── se-gsm │ │ │ ├── ISOMERS0001 │ │ │ ├── inpfileq │ │ │ ├── ograd │ │ │ └── scratch │ │ │ ├── initial0001.xyz │ │ │ ├── paragsm0001 │ │ │ └── tsq0001.xyz │ ├── qchem │ │ ├── de-gsm │ │ │ ├── gscreate │ │ │ ├── inpfileq │ │ │ ├── qend │ │ │ ├── qstart │ │ │ ├── scratch │ │ │ │ └── initial0001.xyz │ │ │ └── stringfile.standard │ │ └── se-gsm │ │ │ ├── ISOMERS0001 │ │ │ ├── gscreate │ │ │ ├── inpfileq │ │ │ ├── qend │ │ │ ├── qstart │ │ │ ├── scratch │ │ │ └── initial0001.xyz │ │ │ ├── stringfile.intel │ │ │ └── stringfile.standard │ └── turbomole │ │ ├── de-gsm-nowrapper │ │ ├── TM │ │ │ ├── auxbasis │ │ │ ├── basis │ │ │ ├── control │ │ │ ├── coord │ │ │ ├── coord.xyz │ │ │ └── mos │ │ ├── gscreate │ │ ├── inpfileq │ │ ├── scratch │ │ │ └── initial0001.xyz │ │ └── stringfile.standard │ │ └── de-gsm-wrapper │ │ ├── gscreate │ │ ├── run_mgsm.py │ │ ├── scratch │ │ └── initial0001.xyz │ │ └── stringfile.standard ├── ethyleneRotation │ ├── mopac │ │ └── de-gsm │ │ │ ├── gscreate │ │ │ ├── inpfileq │ │ │ ├── scratch │ │ │ └── initial0001.xyz │ │ │ └── stringfile.standard │ └── qchem │ │ └── de-gsm │ │ ├── gscreate │ │ ├── inpfileq │ │ ├── qend │ │ ├── qstart │ │ ├── scratch │ │ └── initial0001.xyz │ │ └── stringfile.standard └── methanolFormaldehydeHydTransfer │ ├── mopac │ └── de-gsm │ │ ├── inpfileq │ │ ├── scratch │ │ └── initial0001.xyz │ │ ├── stringfile.standard │ │ └── stringfile.standard.fr │ └── qchem │ └── de-gsm │ ├── gscreate │ ├── inpfileq │ ├── qend │ ├── qstart │ ├── scratch │ └── initial0001.xyz │ └── stringfile.standard ├── TPLsList.cmake ├── Version.cmake ├── athena.pbs ├── cmake ├── FindMKL.cmake ├── TPLS │ └── FindMKL.cmake └── tribits ├── docs ├── CMakeLists.txt ├── Doxyfile.in └── assets │ └── project_logo.png ├── flux.pbs ├── pixi-build.sh ├── pixi.lock ├── pixi.toml └── tutorial └── geometryOptimization ├── getOptEnergy ├── makeXYZ ├── q001.template.inp └── submitall.qsh /.gitattributes: -------------------------------------------------------------------------------- 1 | # SCM syntax highlighting & preventing 3-way merges 2 | pixi.lock merge=binary linguist-language=YAML linguist-generated=true 3 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | *.o[0-9]* 2 | *.e[0-9]* 3 | *.exe 4 | *.log 5 | tags 6 | example.tgz 7 | gstring.cpp_1 8 | build*/ 9 | BUILD/ 10 | BUILD2/ 11 | getOptEnergy 12 | makeXYZ 13 | *.qsh 14 | gfstringq.exe 15 | *.qsh.* 16 | gsmdone 17 | qmaked 18 | qmakeg 19 | reset 20 | status 21 | tmp/ 22 | r 23 | fort* 24 | mxyzfile* 25 | test_output 26 | gsmdone1 27 | stringfile.xyz0001* 28 | compare_output 29 | TEST/**/scratch/* 30 | # pixi environments 31 | .pixi 32 | *.egg-info 33 | -------------------------------------------------------------------------------- /CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # Declare minimum required CMake version before anything to avoid problems. 2 | CMAKE_MINIMUM_REQUIRED(VERSION 3.15) 3 | 4 | # Define project name and set up major options 5 | INCLUDE(${CMAKE_SOURCE_DIR}/ProjectName.cmake) 6 | 7 | ADD_SUBDIRECTORY(GSM) 8 | #ADD_SUBDIRECTORY(TEST) 9 | -------------------------------------------------------------------------------- /CTestConfig.cmake: -------------------------------------------------------------------------------- 1 | ## Gives access to SET_DEFAULT_AND_FROM_ENV function 2 | ## This is file defined in TriBITS. Like a header file in C. 3 | #INCLUDE(SetDefaultAndFromEnv) 4 | # 5 | ## Settings for CTest/CDash 6 | #IF(NOT DEFINED CTEST_DROP_METHOD) 7 | # SET_DEFAULT_AND_FROM_ENV(CTEST_DROP_METHOD "https") 8 | #ENDIF() 9 | # 10 | #IF(CTEST_DROP_METHOD STREQUAL "https") 11 | # # The normal default is ${HOST_TYPE}-${COMPUTER_VERSION}-${BUILD_DIR} 12 | # # We are over-riding it by using set. 13 | # SET(CTEST_BUILD_NAME "Linux-HW2-mjafari") 14 | # 15 | # # To learn more about this function look at the TriBits documentation 16 | # SET_DEFAULT_AND_FROM_ENV(CTEST_PROJECT_NAME "GSM") 17 | # SET_DEFAULT_AND_FROM_ENV(CTEST_TRIGGER_SITE "") 18 | # 19 | # # CDash server hostname 20 | # SET_DEFAULT_AND_FROM_ENV(CTEST_DROP_SITE "cdash-ners590.aura.arc-ts.umich.edu") 21 | # 22 | # # The rest of the web address 23 | # SET_DEFAULT_AND_FROM_ENV(CTEST_DROP_LOCATION "/submit.php?project=GSM") 24 | # 25 | # # YES SUBMIT RESULTS! I WANT MY 10 POINTS! 26 | # SET_DEFAULT_AND_FROM_ENV(CTEST_DROP_SITE_CDASH TRUE) 27 | #ENDIF() 28 | -------------------------------------------------------------------------------- /GSM/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # setting different energy calculators that GSM will use 2 | file(GLOB GSM_SRC "*.h" "*.cpp") 3 | add_executable(gsm ${GSM_SRC}) 4 | 5 | if(NOT DEFINED GSM_ENABLE_QCHEM) 6 | SET(GSM_ENABLE_QCHEM 0) 7 | else() 8 | set(CALCULATOR "qchem" CACHE STRING "Calculator") 9 | set(CALCULATOR_FLAG "-DGSM_ENABLE_QCHEM=1 -DQCHEM=1") 10 | 11 | endif() 12 | 13 | if(NOT DEFINED GSM_ENABLE_QCHEM_SF) 14 | SET(GSM_ENABLE_QCHEM_SF 0) 15 | else() 16 | set(CALCULATOR "qchem_sf" CACHE STRING "Calculator") 17 | set(CALCULATOR_FLAG "-DGSM_ENABLE_QCHEM_SF=1 -DQCHEMSF=1") 18 | endif() 19 | 20 | if(NOT DEFINED GSM_ENABLE_MOLPRO) 21 | SET(GSM_ENABLE_MOLPRO 0) 22 | else() 23 | set(CALCULATOR "molpro" CACHE STRING "Calculator") 24 | set(CALCULATOR_FLAG "-DGSM_ENABLE_MOLPRO=1 -DUSE_MOLPRO=1") 25 | endif() 26 | 27 | if(NOT DEFINED GSM_ENABLE_ASE) 28 | SET(GSM_ENABLE_ASE 0) 29 | else() 30 | set(CALCULATOR "ase" CACHE STRING "Calculator") 31 | set(CALCULATOR_FLAG "-DGSM_ENABLE_ASE=1 -DUSE_ASE=1") 32 | endif() 33 | 34 | if(NOT DEFINED GSM_ENABLE_GAUSSIAN) 35 | SET(GSM_ENABLE_GAUSSIAN 0) 36 | else() 37 | set(CALCULATOR "gaussian" CACHE STRING "Calculator") 38 | set(CALCULATOR_FLAG "-DGSM_ENABLE_GAUSSIAN=1 -DUSE_GAUSSIAN") 39 | endif() 40 | 41 | if(NOT DEFINED GSM_ENABLE_ORCA) 42 | SET(GSM_ENABLE_ORCA 0) 43 | else() 44 | set(CALCULATOR "orca" CACHE STRING "Calculator") 45 | set(CALCULATOR_FLAG "-DGSM_ENABLE_ORCA=1 -DUSE_ORCA=1") 46 | endif() 47 | 48 | if(NOT DEFINED GSM_ENABLE_TURBOMOLE) 49 | SET(GSM_ENABLE_TURBOMOLE 0) 50 | else() 51 | set(CALCULATOR "turbomole" CACHE STRING "Calculator") 52 | set(CALCULATOR_FLAG "-DGSM_ENABLE_TURBOMOLE=1") 53 | endif() 54 | 55 | 56 | if( NOT(GSM_ENABLE_QCHEM EQUAL 1 OR GSM_ENABLE_QCHEM_SF EQUAL 1 OR GSM_ENABLE_MOLPRO EQUAL 1 OR GSM_ENABLE_ASE EQUAL 1 OR GSM_ENABLE_GAUSSIAN EQUAL 1 OR GSM_ENABLE_ORCA EQUAL 1 OR GSM_ENABLE_TURBOMOLE EQUAL 1)) 57 | set(CALCULATOR "mopac" CACHE STRING "Calculator") 58 | endif() 59 | 60 | set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CALCULATOR_FLAG}") 61 | 62 | # source files 63 | file(GLOB GSM_SRC 64 | "qchem.h" 65 | "*.h" 66 | "*.cpp" 67 | ) 68 | 69 | list(APPEND GSM_SRC "${CMAKE_CURRENT_BINARY_DIR}/GitSHA1.cpp" GitSHA1.h) 70 | 71 | # set up libraries 72 | find_package(BLAS REQUIRED) 73 | 74 | message("${BLAS_LIBRARIES} ${BLAS_LINKER_FLAGS}") 75 | 76 | find_package(BLAS REQUIRED) 77 | set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${BLAS_LINKER_FLAGS}") 78 | target_include_directories(gsm PUBLIC "$ENV{MKLROOT}/include") 79 | 80 | FIND_PACKAGE( OpenMP REQUIRED) 81 | if(OPENMP_FOUND) 82 | message("OPENMP FOUND") 83 | set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") 84 | set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") 85 | set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}") 86 | endif() 87 | 88 | MESSAGE("-- Calculator is ${CALCULATOR}") 89 | target_link_libraries(gsm PUBLIC ${BLAS_LIBRARIES}) 90 | 91 | # Install the gsm executable to the bin directory when `make install` is run 92 | install(TARGETS gsm DESTINATION bin) 93 | -------------------------------------------------------------------------------- /GSM/GitSHA1.cpp.in: -------------------------------------------------------------------------------- 1 | #include "GitSHA1.h" 2 | #define GIT_SHA1 "@GIT_SHA1@" 3 | const char g_GIT_SHA1[] = GIT_SHA1; 4 | -------------------------------------------------------------------------------- /GSM/GitSHA1.h: -------------------------------------------------------------------------------- 1 | extern const char g_GIT_SHA1[]; 2 | -------------------------------------------------------------------------------- /GSM/ase.h: -------------------------------------------------------------------------------- 1 | #ifndef ASE_H 2 | #define ASE_H 3 | 4 | #include 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include 10 | #include 11 | 12 | #include "stringtools.h" 13 | #include "pTable.h" 14 | #include "constants.h" 15 | #include "utils.h" 16 | 17 | class ASE 18 | { 19 | private: 20 | 21 | int nscffail; 22 | int firstrun; 23 | 24 | int runNum; 25 | int runend; 26 | string aseoutfile; 27 | string scrdir; 28 | string scrBaseDir; 29 | string runName; 30 | string runName0; 31 | string fileloc; 32 | 33 | int natoms; 34 | int* anumbers; 35 | string* anames; 36 | 37 | double get_energy_grad(string file, double* grad, int natoms); 38 | 39 | public: 40 | 41 | int CHARGE; 42 | int MULT; 43 | 44 | double grads(double* coords, double* grads); 45 | void alloc(int natoms); 46 | void init(string infilename, int natoms, int* anumbers, string* anames, int run, int rune); 47 | void freemem(); 48 | void write_xyz_grad(double* coords, double* grad, string filename); 49 | 50 | int ncpu; 51 | int gradcalls; 52 | 53 | double energy0; 54 | double energy; 55 | 56 | }; 57 | 58 | #endif 59 | -------------------------------------------------------------------------------- /GSM/cmake/Dependencies.cmake: -------------------------------------------------------------------------------- 1 | TRIBITS_PACKAGE_DEFINE_DEPENDENCIES( 2 | 3 | ) 4 | -------------------------------------------------------------------------------- /GSM/constants.h: -------------------------------------------------------------------------------- 1 | #ifndef CONSTANTS_H 2 | #define CONSTANTS_H 3 | 4 | // unir conversions 5 | 6 | const double ECHARGE=1.60217646e-19; // unit = C 7 | const double EMASS=9.10938188e-31; // mass of electron kg 8 | const double AMU=1.66053886e-27; // mass of proton kg 9 | 10 | const double SPEEDc=299792458; // m/s light speed 11 | const double HPLANCK=6.626068e-34; // h, Joule*sec 12 | 13 | const double HARTREEtoKCAL=627.5095; 14 | const double HARTREEtoEV=27.2116; 15 | const double BOHRtoANG=0.52917720859; 16 | const double ANGtoBOHR =1.0000000/BOHRtoANG; 17 | 18 | const double NAVOGAD=6.0221415e+23; // mol^(-1) 19 | const double RGAS=8.314472 ; // J/mol/K 20 | const double KBOLTZ=RGAS/NAVOGAD; //boltzmann J/K 21 | 22 | const double radToDegree =180.000/3.14159265; 23 | const double degreetorad =3.14159/180.000; 24 | const double ZERO = 0.00000000; 25 | const double ONE = 1.00000000; 26 | const double PI = 3.14159265; 27 | 28 | const double CALtoJOULE=4.18400; 29 | 30 | // omega^2 comes in units of Hartree/bohr/bohr/mass_og_hydrogen 31 | // need to divide by 2*pi*c to get cm_inverse 32 | //const define OMEGAtoCMINV= 1/200/PI/SPEEDc*sqrt(627.5*4184/(0.52918*0.52819)/1e-20*1.0e-3); 33 | // AMU*Nav=1e-3 34 | const double OMEGAtoCMINV= 5137.02; 35 | 36 | #endif 37 | -------------------------------------------------------------------------------- /GSM/eckart.h: -------------------------------------------------------------------------------- 1 | /*************************************************************************** 2 | Contians small array and other math functions from baron's code 3 | ***************************************************************************/ 4 | 5 | #ifndef ECKART_H 6 | #define ECKART_H 7 | 8 | #include 9 | #include 10 | #include 11 | #include 12 | #include 13 | #include 14 | 15 | #include "constants.h" 16 | #include "utils.h" 17 | 18 | using namespace std; 19 | 20 | namespace Eckart 21 | { 22 | 23 | void centroid_to_origin(double* structure, int natoms); 24 | double d2grad(double* grad, double* initial, double* final, int natoms); 25 | void d2hessian(double** hess, double* initial, double* final, int natoms); 26 | void Eckart_align(double* xyzreact, double* xyzprod, double tol, double* total_thetas, int max_iter, double* masses, int natoms); 27 | void Eckart_align(double* xyzreact, double* xyzprod, double* masses, int natoms); 28 | void Eckart_align(double* xyzreact, double* xyzprod, double tol, double* total_thetas, int max_iter, double* masses, int natoms, double rfrac); 29 | void Eckart_align(double* xyzreact, double* xyzprod, double* masses, int natoms, double rfrac); 30 | 31 | void Eckart_align_string(double** angs, int nstring, double* masses, int natoms); 32 | 33 | // void Eckart_align_string_and_gradients(double** angs, double** ang_gradients, double** ang_gradients_perp, double** dangsds, int nstring, double* masses, int natoms); 34 | 35 | void Eckart_align_with_grads(double* anchor_struct, double* structure, double* grad, double** rot_mat, double* masses, int natoms); 36 | 37 | void Eckart_align_string_and_gradients(double** angs, double** ang_gradients, int nstring, double* masses, int natoms); 38 | 39 | 40 | }; 41 | 42 | #endif 43 | 44 | 45 | 46 | 47 | -------------------------------------------------------------------------------- /GSM/gaussian.h: -------------------------------------------------------------------------------- 1 | #ifndef GAUSSIAN_H 2 | #define GAUSSIAN_H 3 | 4 | #include 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include 10 | #include 11 | 12 | #include "stringtools.h" 13 | #include "pTable.h" 14 | #include "constants.h" 15 | #include "utils.h" 16 | 17 | class GAUSSIAN 18 | { 19 | private: 20 | 21 | int nscffail; 22 | int firstrun; 23 | 24 | int runNum; 25 | int runend; 26 | string outfile; 27 | string scrdir; 28 | string scrBaseDir; 29 | string runName; 30 | string runName0; 31 | string fileloc; 32 | 33 | int natoms; 34 | int* anumbers; 35 | string* anames; 36 | 37 | double get_energy_grad(string file, double* grad, int natoms); 38 | 39 | public: 40 | 41 | int CHARGE; 42 | int MULT; 43 | 44 | double grads(double* coords, double* grads); 45 | void alloc(int natoms); 46 | void init(string infilename, int natoms, int* anumbers, string* anames, int run, int rune); 47 | void freemem(); 48 | void write_xyz_grad(double* coords, double* grad, string filename); 49 | 50 | int ncpu; 51 | int gradcalls; 52 | 53 | double energy0; 54 | double energy; 55 | 56 | }; 57 | 58 | #endif 59 | -------------------------------------------------------------------------------- /GSM/grad.h: -------------------------------------------------------------------------------- 1 | #ifndef GRAD_H 2 | #define GRAD_H 3 | 4 | #include 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include 10 | #include 11 | 12 | #include "stringtools.h" 13 | #include "qchem.h" 14 | #include "gaussian.h" 15 | #include "ase.h" 16 | #include "knnr.h" 17 | #include "orca.h" 18 | #include "molpro.h" 19 | #include "qchemsf.h" 20 | #include "turbomole.h" 21 | 22 | class Gradient 23 | { 24 | 25 | private: 26 | 27 | int runNum; 28 | int runend; 29 | string runends; 30 | string runName; 31 | string runName0; 32 | 33 | int natoms; 34 | int N3; 35 | string* anames; 36 | int* anumbers; 37 | int CHARGE; //total system charge 38 | int MULT; //multiplicity 39 | 40 | QChem qchem1; 41 | QChemSF qchemsf1; 42 | GAUSSIAN gaus1; 43 | ASE ase1; 44 | ORCA orca1; 45 | Molpro mp1; 46 | Turbomole turbol; 47 | 48 | int knn_k; 49 | KNNR knnr1; 50 | int knnr_inited; 51 | 52 | int nforce; 53 | int* fa; 54 | double* fv; 55 | double* fk; 56 | 57 | int read_nstates(); 58 | void read_molpro_settings(int& nstates, int& nclosed, int& nocc, int& nelec, string& basis); 59 | int read_molpro_init(string* &hf_lines); 60 | int force_init(string ffile); 61 | 62 | 63 | public: 64 | 65 | int hessian(double* H); 66 | double grads(double* coords, double* grad, double* Ut, int type); 67 | void add_force(double* coords, double* grad); 68 | void init(string infilename, int natoms, int* anumbers, string* anames, double* coords, int run, int rune, int ncpu, int use_knnr, int q1); 69 | void update_knnr(); 70 | void freemem(); 71 | void write_xyz_grad(double* coords, double* grad, string filename); 72 | int external_grad(double* coords, double* grads); 73 | 74 | int knnr_active; 75 | int always_do_exact; 76 | int write_on; 77 | int wrote_grad; 78 | int xyz_grad; 79 | int gradcalls; 80 | int nscffail; 81 | double V0; 82 | double fdE; //force * distance energy 83 | 84 | double energy0; 85 | double energy; 86 | 87 | //for molpro 88 | int nstates; 89 | int wstate; 90 | int wstate2; 91 | int wstate3; 92 | double** grada; //multistate gradients 93 | double* E; //for multiple states 94 | 95 | int seedType; 96 | 97 | int res_t; //restart found files 98 | 99 | }; 100 | 101 | #endif 102 | -------------------------------------------------------------------------------- /GSM/grad.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | 3 | from ase import Atoms 4 | from ase.visualize import view 5 | from ase.calculators.emt import EMT 6 | from ase.constraints import FixAtoms 7 | from ase.io import write 8 | from ase.io import read 9 | import sys 10 | 11 | nargs = len(sys.argv) 12 | argv = sys.argv[1] 13 | print 'argv: ',argv 14 | fname = 'structure'+argv 15 | slab = read(fname) 16 | slab.set_calculator(EMT()) 17 | energy = slab.get_potential_energy() 18 | grads = slab.get_forces() 19 | #print grads 20 | f = open('GRAD'+argv, 'w') 21 | f.write(str(energy)) 22 | f.write('\n') 23 | f.write(str(grads)) 24 | f.write('\n') 25 | f.close() 26 | 27 | -------------------------------------------------------------------------------- /GSM/knnr.h: -------------------------------------------------------------------------------- 1 | #ifndef KNNR_H 2 | #define KNNR_H 3 | 4 | #include 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include 10 | #include 11 | 12 | #include "stringtools.h" 13 | #include "pTable.h" 14 | #include "constants.h" 15 | #include "utils.h" 16 | //pointers only 17 | class ICoord; 18 | 19 | class KNNR { 20 | 21 | private: 22 | 23 | string file0; 24 | int runnum; 25 | string* filesxyz; 26 | string* filesgrad; 27 | string* fileshess; 28 | 29 | int natoms; 30 | double** xyz; 31 | int* anumbers; 32 | string* anames; 33 | 34 | int* id; 35 | double* distances; 36 | double* distancesu; 37 | double* energies; 38 | double** grads; 39 | double** hess; 40 | int* useH; 41 | 42 | int nic; 43 | int nbonds; int nangles; int ntor; 44 | 45 | 46 | int read_ics(int& nbonds, int** bonds, int& nangles, int** angles, int& ntor, int** torsions, string filename); 47 | int read_xyzs(double* energies, double** xyz, string* filenames); 48 | double read_one_xyz(int n, string filename, double* coords); 49 | 50 | void xyz_read(string* anames, double* coords, string xyzfile); 51 | 52 | int read_hess(int nic, string* filenames); 53 | void read_one_hess(int n, int nic, string filename); 54 | int get_files(string fileprefix, string filesuffix, string* files); 55 | 56 | void get_distances(int npts, double** xyz, ICoord& ic1, ICoord& ic2); 57 | double get_distance(double* xyz1, double* xyz2, ICoord& ic1, ICoord& ic2); 58 | void get_distances_u(int npts, int pt, ICoord& ic1, ICoord& ic2); 59 | double get_distance_u(double* xyz1, double* xyz2, ICoord& ic1, ICoord& ic2); 60 | void get_dqpic(double* dq1, ICoord& ic1, ICoord& ic2); 61 | 62 | void setup_ic(ICoord& ic1, ICoord& ic2); 63 | void release_ic(ICoord& ic1, ICoord& ic2); 64 | 65 | //prototyping functions 66 | int find_knn(int pt, int k, int* knn, double* knnd, int type); 67 | double predict_point(int pt, int k, ICoord& ic1, ICoord& ic2); 68 | 69 | //for unknown structures 70 | int find_knn_xyz(double* coords, int k, int* knn, double* knnd, ICoord& ic1, ICoord& ic2); 71 | 72 | int compare_add_files(int npts1, string* filesxyz1, string* filesgrad1, string* fileshess1, string* newfilesxyz, string* newfilesgrad, string* newfileshess); 73 | void reassign_mem(int npts1); 74 | 75 | public: 76 | 77 | int npts; 78 | int printl; 79 | 80 | int begin(int runnum, int natoms0); 81 | double test_points(int k0); 82 | double grad_knnr(double* coords, double &E1, double* grads, double* Ut, int k); 83 | int add_extra_points(); 84 | void add_point(double energy, double* xyz, double* grad, double* hess); 85 | void freemem(); 86 | 87 | 88 | }; 89 | 90 | #endif 91 | -------------------------------------------------------------------------------- /GSM/mem.cpp: -------------------------------------------------------------------------------- 1 | #include "icoord.h" 2 | 3 | void ICoord::freemem(){ 4 | 5 | delete [] grad; 6 | 7 | for (int i=0;i 6 | #include 7 | #include 8 | 9 | #include "stringtools.h" 10 | #include "utils.h" 11 | 12 | class Molpro 13 | { 14 | 15 | private: 16 | 17 | string infile; 18 | string outfile; 19 | string scratchname; 20 | 21 | int nhf_lines; 22 | string* hf_lines; 23 | 24 | string basis; 25 | 26 | int nclosed; 27 | int nocc; 28 | int nelec; 29 | 30 | int nstates; 31 | int natoms; 32 | 33 | int tstate; 34 | 35 | string* anames; 36 | double* E; 37 | double* xyz; 38 | double* grad; 39 | double* dvec; 40 | 41 | int read_E(); 42 | 43 | int NPROCS; 44 | 45 | public: 46 | 47 | void init(int nstates0, int nclosed0, int nocc0, int nelec0, int natoms0, string* anames0, double* xyz0, int NPROCS0, string basis0); 48 | void init_hf(int nhf_lines1, string* hf_lines1); 49 | void reset(double* xyz); 50 | void runname(string name); 51 | int seed(); //run RHF to get initial orbitals 52 | int run(int n, int m); // n is current state, m is target state for derivative coupling 53 | double getE(int n); 54 | int getGrad(double* grads); 55 | int getDVec(double* D); 56 | void clean_scratch(); 57 | 58 | void freemem(); 59 | 60 | int nrun; 61 | 62 | }; 63 | 64 | 65 | #endif 66 | -------------------------------------------------------------------------------- /GSM/mopac.h: -------------------------------------------------------------------------------- 1 | #ifndef MOPAC_H 2 | #define MOPAC_H 3 | 4 | #include "stringtools.h" 5 | #include "pTable.h" 6 | #include "icoord.h" 7 | 8 | #define SKIPMOPAC 0 9 | 10 | class Mopac { 11 | 12 | private: 13 | 14 | int natoms; 15 | int* anumbers; 16 | string* anames; 17 | int nfrz; //total frozen atoms 18 | int nfrz0; //total "moved" frozen atoms 19 | int* frzlist; 20 | int* frzlistb; 21 | 22 | int gradcalls; 23 | int rnum; 24 | string id; 25 | 26 | void opt_header(ofstream& inpfile); 27 | void grad_header(ofstream& inpfile); 28 | void write_ic_input(ofstream& inpfile, int anum, ICoord icoords); 29 | double read_output(string filename); 30 | double read_grad(string filename); 31 | void xyz_read(string filename); 32 | void xyz_save(string filename); 33 | 34 | public: 35 | 36 | double opt(); 37 | double opt(string filename); 38 | double opt(string filename, ICoord icoords); 39 | double grads(string filename); 40 | void alloc(int natoms); 41 | void init(int natoms, int* anumbers, string* anames, double* xyz); 42 | void reset(int natoms, int* anumbers, string* anames, double* xyz); 43 | void reset(double* xyz_i); 44 | void freemem(); 45 | void write_xyz_grad(string filename); 46 | 47 | void freeze(int* frzlist, int nfrz, int nfrz0); 48 | 49 | double energy0; 50 | double energy; 51 | 52 | double* xyz0; 53 | double* xyz; 54 | double* grad; 55 | 56 | }; 57 | 58 | #endif 59 | -------------------------------------------------------------------------------- /GSM/orca.h: -------------------------------------------------------------------------------- 1 | #ifndef ORCA_H 2 | #define ORCA_H 3 | 4 | #include 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include 10 | #include 11 | 12 | #include "stringtools.h" 13 | #include "pTable.h" 14 | #include "constants.h" 15 | #include "utils.h" 16 | 17 | class ORCA 18 | { 19 | private: 20 | 21 | int nscffail; 22 | int firstrun; 23 | 24 | int runNum; 25 | int runend; 26 | string outfile; 27 | string scrdir; 28 | string scrBaseDir; 29 | string runName; 30 | string runName0; 31 | string fileloc; 32 | 33 | int natoms; 34 | int* anumbers; 35 | string* anames; 36 | 37 | double get_energy_grad(string file, double* grad, int natoms); 38 | 39 | public: 40 | 41 | double grads(double* coords, double* grads); 42 | void alloc(int natoms); 43 | void init(string infilename, int natoms, int* anumbers, string* anames, int run, int rune); 44 | void freemem(); 45 | void write_xyz_grad(double* coords, double* grad, string filename); 46 | 47 | int ncpu; 48 | int gradcalls; 49 | 50 | double energy0; 51 | double energy; 52 | 53 | }; 54 | 55 | #endif 56 | -------------------------------------------------------------------------------- /GSM/pTable.h: -------------------------------------------------------------------------------- 1 | /*************************************************************************** 2 | pTable.h - description 3 | ------------------- 4 | copyright : (C) 2004 by Shaji Chempath 5 | University of California Berkeley 6 | ***************************************************************************/ 7 | 8 | /*************************************************************************** 9 | * * 10 | * This program is free software; you can redistribute it and/or modify * 11 | * it under the terms of the GNU General Public License as published by * 12 | * the Free Software Foundation; either version 2 of the License, or * 13 | * (at your option) any later version. * 14 | * * 15 | ***************************************************************************/ 16 | 17 | #ifndef PTABLE_H 18 | #define PTABLE_H 19 | 20 | #include 21 | #include 22 | #include 23 | #include 24 | #include 25 | 26 | 27 | using namespace std; 28 | 29 | namespace PTable 30 | { 31 | int atom_number(string &aName); 32 | 33 | string atom_name(int aNumber); 34 | 35 | double atom_mass(int aNumber); 36 | } 37 | #endif 38 | 39 | -------------------------------------------------------------------------------- /GSM/qchem.h: -------------------------------------------------------------------------------- 1 | #ifndef QCHEM_H 2 | #define QCHEM_H 3 | 4 | // Default to using threaded qchem 5 | #ifndef THREADS_ON 6 | #define THREADS_ON 1 7 | #endif 8 | 9 | #define WRITE_FILES 0 10 | #define USE_KNNR 0 11 | #define KNN_K 3 12 | #define KNNR_MAX_DIST 0.3 13 | 14 | #include 15 | #include 16 | #include 17 | #include 18 | #include 19 | #include 20 | #include 21 | 22 | #include "stringtools.h" 23 | #include "pTable.h" 24 | #include "constants.h" 25 | #include "utils.h" 26 | 27 | class QChem { 28 | 29 | private: 30 | 31 | int nscffail; 32 | int firstrun; 33 | 34 | int runNum; 35 | int runend; 36 | string qcinfile; 37 | string inpfile; 38 | string qcoutfile; 39 | string qcoutfileh; 40 | string scrdir; 41 | string scrBaseDir; 42 | string runName; 43 | string runName0; 44 | string fileloc; 45 | 46 | int natoms; 47 | int* anumbers; 48 | string* anames; 49 | 50 | double read_output(string filename); 51 | double read_grad(string filename); 52 | void xyz_read(string filename); 53 | void xyz_save(string filename); 54 | double get_energy(string filename); 55 | int scangradient(string file, double* grad, int natoms); 56 | 57 | public: 58 | 59 | int read_hess(double* hess); 60 | double grads(double* coords, double* grads); 61 | void alloc(int natoms); 62 | void init(string infilename, int natoms, int* anumbers, string* anames, int run, int rune); 63 | void freemem(); 64 | void write_xyz_grad(double* coords, double* grad, string filename); 65 | 66 | int ncpu; 67 | int gradcalls; 68 | 69 | double energy0; 70 | double energy; 71 | 72 | }; 73 | 74 | #endif 75 | -------------------------------------------------------------------------------- /GSM/qchem.h.in: -------------------------------------------------------------------------------- 1 | #ifndef QCHEM_H 2 | #define QCHEM_H 3 | 4 | #define QCHEM ${GSM_ENABLE_QCHEM} 5 | #define QCHEMSF ${GSM_ENABLE_QCHEM_SF} 6 | #define USE_MOLPRO ${GSM_ENABLE_MOLPRO} 7 | #define USE_ASE ${GSM_ENABLE_ASE} 8 | #define USE_GAUSSIAN ${GSM_ENABLE_GAUSSIAN} 9 | #define USE_ORCA ${GSM_ENABLE_ORCA} 10 | #define THREADS_ON 0 11 | #define WRITE_FILES 0 12 | #define USE_KNNR 0 13 | #define KNN_K 3 14 | #define KNNR_MAX_DIST 0.3 15 | 16 | #include 17 | #include 18 | #include 19 | #include 20 | #include 21 | #include 22 | #include 23 | 24 | #include "stringtools.h" 25 | #include "pTable.h" 26 | #include "constants.h" 27 | #include "utils.h" 28 | 29 | class QChem { 30 | 31 | private: 32 | 33 | int nscffail; 34 | int firstrun; 35 | 36 | int runNum; 37 | int runend; 38 | string qcinfile; 39 | string inpfile; 40 | string qcoutfile; 41 | string qcoutfileh; 42 | string scrdir; 43 | string scrBaseDir; 44 | string runName; 45 | string runName0; 46 | string fileloc; 47 | 48 | int natoms; 49 | int* anumbers; 50 | string* anames; 51 | 52 | double read_output(string filename); 53 | double read_grad(string filename); 54 | void xyz_read(string filename); 55 | void xyz_save(string filename); 56 | double get_energy(string filename); 57 | int scangradient(string file, double* grad, int natoms); 58 | 59 | public: 60 | 61 | int read_hess(double* hess); 62 | double grads(double* coords, double* grads); 63 | void alloc(int natoms); 64 | void init(string infilename, int natoms, int* anumbers, string* anames, int run, int rune); 65 | void freemem(); 66 | void write_xyz_grad(double* coords, double* grad, string filename); 67 | 68 | int ncpu; 69 | int gradcalls; 70 | 71 | double energy0; 72 | double energy; 73 | 74 | }; 75 | 76 | #endif 77 | -------------------------------------------------------------------------------- /GSM/qchemsf.h: -------------------------------------------------------------------------------- 1 | #ifndef QCHEMSF_H 2 | #define QCHEMSF_H 3 | 4 | #include 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include 10 | #include 11 | 12 | #include "qchem.h" 13 | #include "stringtools.h" 14 | #include "pTable.h" 15 | #include "constants.h" 16 | #include "utils.h" 17 | 18 | class QChemSF { 19 | 20 | private: 21 | 22 | int nscffail; 23 | int firstrun; 24 | 25 | int runNum; 26 | int runend; 27 | string qcinfile; 28 | string inpfile; 29 | string qcoutfile; 30 | string qcoutfileh; 31 | string scrdir; 32 | string scrBaseDir; 33 | string runName; 34 | string runName0; 35 | string fileloc; 36 | 37 | int natoms; 38 | int* anumbers; 39 | string* anames; 40 | 41 | 42 | int nstates; 43 | double* grad1; 44 | double* grad2; 45 | double* grad3; 46 | double* grad4; 47 | double* E; 48 | 49 | double read_output(string filename); 50 | double read_grad(string filename); 51 | void xyz_read(string filename); 52 | void xyz_save(string filename); 53 | double get_energy(); 54 | void get_grads(); 55 | int scangradient(string file, double* grad, int natoms); 56 | 57 | public: 58 | 59 | int read_hess(double* hess); 60 | double calc_grads(double* coords); 61 | double getE(int ws); 62 | void getGrad(int ws, double* grad); 63 | void alloc(int natoms); 64 | void init(string infilename, int natoms, int* anumbers, string* anames, int run, int rune); 65 | void freemem(); 66 | void write_xyz_grad(double* coords, double* grad, string filename); 67 | 68 | int ncpu; 69 | int gradcalls; 70 | 71 | double energy0; 72 | double energy; 73 | 74 | }; 75 | 76 | #endif 77 | -------------------------------------------------------------------------------- /GSM/stringtools.h: -------------------------------------------------------------------------------- 1 | /*************************************************************************** 2 | stringtools.h - description 3 | ------------------- 4 | begin : Mon Dec 10 2001 5 | copyright : (C) 2001 by André Simon 6 | email : andre.simon1@gmx.de 7 | ***************************************************************************/ 8 | 9 | /*************************************************************************** 10 | * * 11 | * This program is free software; you can redistribute it and/or modify * 12 | * it under the terms of the GNU General Public License as published by * 13 | * the Free Software Foundation; either version 2 of the License, or * 14 | * (at your option) any later version. * 15 | * * 16 | ***************************************************************************/ 17 | 18 | #ifndef STRINGTOOLS_H 19 | #define STRINGTOOLS_H 20 | 21 | #include 22 | #include 23 | #include 24 | #include 25 | #include 26 | #include 27 | #include 28 | #include 29 | #include 30 | 31 | 32 | #define WS_CHARS " \n\r\t" 33 | 34 | #ifdef _WIN32 35 | #define PATH_SEPARATOR_CHAR '\\' 36 | #define PATH_SEPARATOR_STR "\\" 37 | #else 38 | #define PATH_SEPARATOR_CHAR '/' 39 | #define PATH_SEPARATOR_STR "/" 40 | #endif 41 | 42 | using namespace std; 43 | 44 | /**Methoden zur Stringbearbeitung 45 | *@author Andre Simon 46 | */ 47 | 48 | namespace StringTools 49 | { 50 | 51 | string genfilename(const string& pref, const string &suff, 52 | int nfields, int nxyz); 53 | 54 | 55 | /** \param s String 56 | \returns lowercase string */ 57 | string lowerCase(const string &s); 58 | double atod(const string &s); 59 | 60 | /** \param String 61 | \returns Integer value */ 62 | int str2int(string &s); 63 | 64 | /** gibt integer als String zurueck */ 65 | string int2str(int integer, int size=0, const string spaceStr= " "); 66 | 67 | string double2str(double val, int precision); 68 | 69 | /** gibt True zurueck, falls c ein Buchstabe ist */ 70 | bool isAlpha(unsigned char c); 71 | 72 | /** wandelt String s in Integer um */ 73 | int str2int(unsigned char *s); 74 | 75 | /* entfernt whitespace von stringende*/ 76 | string trimRight(const string &); 77 | 78 | /** gibt naechsten Character der Zeile zurck, der kein Whitespace ist*/ 79 | unsigned char getNextNonWs(const string &line, int index=0); 80 | 81 | unsigned int getNextNonWsPos(const string &line, int index=0); 82 | 83 | string validateDirPath(const string & path); 84 | 85 | int cleanstring(string& line); 86 | string newCleanString(string line); 87 | 88 | vector tokenize(string str, string delims); 89 | bool findstr(ifstream &fstr, string tag); 90 | bool findstr(ifstream &fstr, string tag, string & outstring); 91 | bool contains(string s1, string s2); 92 | bool iscomment(string s); 93 | 94 | }; 95 | 96 | #endif 97 | 98 | 99 | 100 | 101 | -------------------------------------------------------------------------------- /GSM/turbomole.h: -------------------------------------------------------------------------------- 1 | #ifndef TURBOMOLE_H 2 | #define TURBOMOLE_H 3 | 4 | #include 5 | #include 6 | #include 7 | #include 8 | #include 9 | #include 10 | #include 11 | 12 | #include "stringtools.h" 13 | #include "pTable.h" 14 | #include "constants.h" 15 | #include "utils.h" 16 | 17 | class Turbomole { 18 | 19 | private: 20 | 21 | int nscffail; 22 | int firstrun; 23 | 24 | int runNum; 25 | int runend; 26 | string turboinfile; 27 | string inpfile; 28 | string turbooutfile; 29 | string turbooutfileh; 30 | string scrdir; 31 | string scrBaseDir; 32 | string runName; 33 | string runName0; 34 | string fileloc; 35 | 36 | int natoms; 37 | int* anumbers; 38 | string* anames; 39 | 40 | double read_output(string filename); 41 | double read_grad(string filename); 42 | void xyz_read(string filename); 43 | void xyz_save(string filename); 44 | double get_energy(string filename); 45 | int scangradient(string file, double* grad, int natoms); 46 | 47 | public: 48 | 49 | int read_hess(double* hess); 50 | double grads(double* coords, double* grads); 51 | void alloc(int natoms); 52 | void init(string infilename, int natoms, int* anumbers, string* anames, int run, int rune); 53 | void freemem(); 54 | void write_xyz_grad(double* coords, double* grad, string filename); 55 | 56 | int ncpu; 57 | int gradcalls; 58 | 59 | double energy0; 60 | double energy; 61 | 62 | bool RI; 63 | bool COSMO; 64 | string turboDIR; 65 | 66 | }; 67 | 68 | #endif 69 | -------------------------------------------------------------------------------- /GSM/utils.h: -------------------------------------------------------------------------------- 1 | /*************************************************************************** 2 | Contians small array and other math functions from baron's code 3 | ***************************************************************************/ 4 | 5 | #ifndef UTILS_H 6 | #define UTILS_H 7 | 8 | #include 9 | #include 10 | #include 11 | #include 12 | #include 13 | #include 14 | #include 15 | #include 16 | #include 17 | 18 | #include "constants.h" 19 | 20 | using namespace std; 21 | 22 | void trans(double* A, double* B, int m, int n); 23 | int Diagonalize(double* A, double* eigen, int size); 24 | int SVD(double* A, double* Ut, double* eigen, int size1, int size2); 25 | int Invert(double* A, int m); 26 | 27 | int mat_root(double* A, int size); 28 | int mat_root_inv(double* A, int size); 29 | 30 | int mat_times_mat(double* C, double* A, double* B, int size); //square matrices 31 | int mat_times_mat_bt(double* C, double* A, double* B, int size); //square matrices 32 | int mat_times_mat_at_bt(double* C, double* A, double* B, int size); //square matrices 33 | int mat_times_mat(double* C, double* A, double* B, int N, int M, int K); //rectangular 34 | int mat_times_mat_bt(double* C, double* A, double* B, int N, int M, int K); //rectangular 35 | 36 | int sign(double x); 37 | void cross(double* x, double* r1, double* r2); 38 | int close_val(double x1, double x2, double diff); 39 | int check_array(int size, double* A); 40 | 41 | namespace Utils 42 | { 43 | 44 | void normalize_string_step_direc(double** a, int nstring, int LEN); 45 | 46 | double step_direc_overlap(double** a, double** b, int nstring, int LEN); 47 | 48 | void display_matrix(double** a, int LEN); 49 | 50 | void eigen_decomp(double** mat, double** evecs, double* evals, int n); 51 | 52 | void matrix_times_matrix(double** A, double** B, double** C, int LEN); 53 | 54 | void display_structure_nonames(double* a, int natoms); 55 | void display_structure(double* a, int natoms, string* anames); 56 | 57 | void jacobi(float **a, int n, float d[], float **v, int *nrot); 58 | void eigsrt(float d[], float **v, int n); 59 | 60 | void S_straight_line_in_angs(double** string_angs, double* S, int nstring, int natoms); 61 | 62 | void subtract_arrays(double* a, double* b, double* diff, int LEN); 63 | 64 | void vector_outer_prod(double* vec1, double* vec2, int LEN, double** output); 65 | void copy_2D_array(double** pointer1, double** pointer2, int LEN1, int LEN2); 66 | 67 | void copy_structure(double* structure1, double* structure2, int natoms); 68 | void alloc_dpointer_1D(double* pointer_name, int LEN); 69 | void alloc_dpointer_2D(double** pointer_name, int LEN1, int LEN2); 70 | void alloc_dpointer_3D(double*** pointer_name, int LEN1, int LEN2, int LEN3); 71 | 72 | void get_rotation_matrix(double** rotMat, double* thetas); 73 | void Rotate_structure(double** RotMat, double* structure, int natoms); 74 | void Rotate_hessian(double** Rot_mat, double** hessian, int natoms); 75 | 76 | void Rot_around_vec(double* vec, double* structure, int natoms); 77 | 78 | void mwc_to_ang(double** angs, double** mwc, int nstring, int natoms, double* amasses); 79 | void mwc_to_ang(double* angs, double* mwc, int natoms, double* amasses); 80 | void ang_to_mwc(double** mwc, double** ang, int nstring, int natoms, double* amasses); 81 | void ang_to_mwc(double* mwc, double* ang, int natoms, double* amasses); 82 | 83 | void mwcgrad_to_anggrad(double** ang_grad, double** mwc_grad, int nstring, int natoms, double* amasses); 84 | void mwcgrad_to_anggrad(double* ang_grad, double* mwc_grad, int natoms, double* amasses); 85 | void anggrad_to_mwcgrad(double** mwc_grad, double** ang_grad, int nstring, int natoms, double* amasses); 86 | void anggrad_to_mwcgrad(double* mwc_grad, double* ang_grad, int natoms, double* amasses); 87 | void diagonalize3x3(double** hmwc, double** smwc, 88 | double* w2, int ndiag); 89 | 90 | void projectfrommatrix3x3(double* vector, double** hmwc); 91 | double randomf(double a, double b); 92 | 93 | void Mat_times_vec(double** d2S_1, double* dS, double* prod, int LEN); 94 | void normalize(double* u, int LEN); 95 | void invertNxN(double** Mat, double** Inverse, int n); 96 | void ludcmp(double **a, int n, int *indx, double *d); 97 | void lubksb(double **a, int n, int *indx, double b[]); 98 | 99 | 100 | double det3x3(double A[1+3][1+3]); 101 | void adjoint3x3(double A[4][4], double Aadj[4][4]); 102 | double det2x2(double A[3][3]); 103 | void gramschmidt(int LEN, double* v_out, double* u_in, double* v_in); 104 | void splineTangents(int LEN, double* x, double* y, double* y2, double* y1); 105 | void getSpline(int LEN, double* x, double* y, double* y2); 106 | double evalSpline(int LEN, double x, double* xa, double* ya, double* y2a); 107 | void S_from_angs(double** angs, double* S, double* masses, int LEN, int natoms); 108 | void Rmat_from_lincart(double** r, double* xyz, int natoms); 109 | void normalize_S(double* normalized_s, double* S, int LEN); 110 | void angs_to_mwcs(double** temparray, int nn, int natoms, double* amasses); 111 | void anggrads_to_mwcgrads(double** temparray, int nn, int natoms, double* amasses); 112 | double dotProd(double* v, double* u, int LEN); 113 | double vecMag(double* u, int LEN); 114 | 115 | void generate_Project_RT_tan(double** Proj, double* structure, double* tangent); 116 | void generate_Project_RT(double** Proj, double* structure); 117 | 118 | 119 | }; 120 | 121 | #endif 122 | 123 | 124 | 125 | 126 | -------------------------------------------------------------------------------- /GSM/xtb.h: -------------------------------------------------------------------------------- 1 | #ifndef XTB_H 2 | #define XTB_H 3 | 4 | #include 5 | #include "stringtools.h" 6 | #include "pTable.h" 7 | #include "icoord.h" 8 | 9 | class XTB { 10 | 11 | private: 12 | 13 | int natoms; 14 | int* anumbers; 15 | string* anames; 16 | int charge; 17 | int nfrz; //total frozen atoms 18 | int nfrz0; //total "moved" frozen atoms 19 | int* frzlist; 20 | int* frzlistb; 21 | 22 | int nskip; 23 | int* skip; 24 | 25 | void write_ic_input(ofstream& inpfile, int anum, ICoord icoords); 26 | 27 | public: 28 | 29 | string sdir; 30 | 31 | double grads(string filename); 32 | double opt(); 33 | double opt(string filename); 34 | double opt_check(string filename); 35 | double opt(string filename, ICoord icoords); 36 | void opt_write(); 37 | void opt_write(string filename); 38 | void opt_write(string filename, ICoord icoords); 39 | 40 | double read_grad(string filename); 41 | double read_output(string filename); 42 | void xyz_read(string filename); 43 | void xyz_read_aux(string filename); 44 | void xyz_save(string filename); 45 | 46 | 47 | void set_charge(int c0); 48 | 49 | void alloc(int natoms); 50 | void init(int natoms, int* anumbers, string* anames, double* xyz); 51 | void reset(int natoms, int* anumbers, string* anames, double* xyz); 52 | void freemem(); 53 | 54 | void freeze(int* frzlist, int nfrz, int nfrz0); 55 | void freeze_d(int* frzlist); 56 | 57 | double energy0; 58 | double energy; 59 | 60 | double* xyz0; 61 | double* xyz; 62 | double* grad; 63 | 64 | }; 65 | 66 | #endif 67 | -------------------------------------------------------------------------------- /GetGitRevisionDescription.cmake.in: -------------------------------------------------------------------------------- 1 | # 2 | # Internal file for GetGitRevisionDescription.cmake 3 | # 4 | # Requires CMake 2.6 or newer (uses the 'function' command) 5 | # 6 | # Original Author: 7 | # 2009-2010 Ryan Pavlik 8 | # http://academic.cleardefinition.com 9 | # Iowa State University HCI Graduate Program/VRAC 10 | # 11 | # Copyright Iowa State University 2009-2010. 12 | # Distributed under the Boost Software License, Version 1.0. 13 | # (See accompanying file LICENSE_1_0.txt or copy at 14 | # http://www.boost.org/LICENSE_1_0.txt) 15 | 16 | set(HEAD_HASH) 17 | 18 | file(READ "@HEAD_FILE@" HEAD_CONTENTS LIMIT 1024) 19 | 20 | string(STRIP "${HEAD_CONTENTS}" HEAD_CONTENTS) 21 | if(HEAD_CONTENTS MATCHES "ref") 22 | # named branch 23 | string(REPLACE "ref: " "" HEAD_REF "${HEAD_CONTENTS}") 24 | if(EXISTS "@GIT_DIR@/${HEAD_REF}") 25 | configure_file("@GIT_DIR@/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY) 26 | else() 27 | configure_file("@GIT_DIR@/packed-refs" "@GIT_DATA@/packed-refs" COPYONLY) 28 | file(READ "@GIT_DATA@/packed-refs" PACKED_REFS) 29 | if(${PACKED_REFS} MATCHES "([0-9a-z]*) ${HEAD_REF}") 30 | set(HEAD_HASH "${CMAKE_MATCH_1}") 31 | endif() 32 | endif() 33 | else() 34 | # detached HEAD 35 | configure_file("@GIT_DIR@/HEAD" "@GIT_DATA@/head-ref" COPYONLY) 36 | endif() 37 | 38 | if(NOT HEAD_HASH) 39 | file(READ "@GIT_DATA@/head-ref" HEAD_HASH LIMIT 1024) 40 | string(STRIP "${HEAD_HASH}" HEAD_HASH) 41 | endif() 42 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | The MIT License (MIT) 2 | 3 | Copyright (c) 2016 ZimmermanGroup 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 1 | # Use this Makefile with make 2 | 3 | # Executable name 4 | CMD = gfstringq.exe 5 | 6 | # -------- description of DFLAGS --------------- 7 | 8 | # -------- Define environmental variable C_COMPILER ----------- 9 | # Make sure it is defined 10 | # ifeq ($(strip$(FORTRAN_COMPILER)),) 11 | # Otherwise you can define it here also by uncommenting next line 12 | #FC = icpc -openmp -I$(MKLROOT)/include 13 | FC = g++ -fopenmp -I$(MKLROOT)/include 14 | 15 | GIT_VERSION := $(shell git describe --abbrev=4 --dirty --always --tags) 16 | 17 | 18 | DFLAGS = -DVERSION=\"$(GIT_VERSION)\" 19 | OFLAGS = # optimization 20 | F95ROOT = $(MKLROOT) 21 | 22 | #Intel Linkers 23 | 24 | #LINKERFLAGS = -L$(MKLROOT)/lib/em64t $(F95ROOT)/lib/em64t/libmkl_lapack95_lp64.a -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm 25 | 26 | #Intel parallel openmp (only w/icpc compiler) 27 | #LINKERFLAGS = -L$(MKLROOT)/lib/em64t -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lm 28 | 29 | # this one works for icpc 30 | #LINKERFLAGS = -L$(MKLROOT)/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread -lm 31 | # MAC OS linkers 32 | #LINKERFLAGS = -lm -framework Accelerate 33 | # this one works with g++ 34 | LINKERFLAGS = -Wl,--no-as-needed -L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lm 35 | 36 | 37 | # 38 | # Implicit rules for handling src files 39 | # ( uses static pattern rules, see info for make ) 40 | .c.o: 41 | $(FC) -c -g $(DFLAGS) -Wimplicit $< 42 | .cpp.o: 43 | $(FC) -c -g $(DFLAGS) $< 44 | 45 | OBJECTS = gstring.o main.o pTable.o stringtools.o qchem.o utils.o eckart.o mem.o bmat.o print.o icoord.o mm_grad.o optic.o mopac.o grad.o knnr.o ase.o gaussian.o orca.o molpro.o qchemsf.o 46 | 47 | $(CMD) : $(OBJECTS) 48 | $(FC) $(DEBUG_FLAGS) $(OFLAGS) $(OBJECTS) $(LINKERFLAGS) -o ./$(CMD) 49 | 50 | clean: 51 | /bin/rm -f *.o *.i *.mod *.exe a.out make.log 52 | 53 | cleano: 54 | rm -f *.o *.i 55 | 56 | depend : 57 | g++ -MM *.cpp *.c >> Makefile 58 | 59 | # DO NOT DELETE created with g++ -MM *.cpp *.c 60 | LST.o: LST.cpp LST.h constants.h utils.h 61 | eckart.o: eckart.cpp eckart.h constants.h utils.h 62 | gstring.o: gstring.cpp gstring.h utils.h constants.h stringtools.h pTable.h qchem.h eckart.h icoord.h qchem.h ase.h grad.h 63 | mem.o: mem.cpp icoord.h qchem.h 64 | bmat.o: bmat.cpp icoord.h qchem.h 65 | icoord.o: icoord.cpp icoord.h qchem.h 66 | main.o: main.cpp gstring.h utils.h constants.h stringtools.h pTable.h qchem.h eckart.h 67 | mopac.o: mopac.cpp mopac.h qchem.h 68 | mm_grad.o: mm_grad.cpp icoord.h 69 | optimize.o: optimize.cpp optimize.h utils.h constants.h eckart.h stringtools.h pTable.h qchem.h 70 | optic.o: optic.cpp icoord.h 71 | pTable.o: pTable.cpp pTable.h 72 | print.o: print.cpp icoord.h 73 | qchem.o: qchem.cpp qchem.h stringtools.h pTable.h utils.h constants.h 74 | stringtools.o: stringtools.cpp stringtools.h 75 | utils.o: utils.cpp utils.h constants.h 76 | grad.o: mopac.h qchem.h knnr.h grad.h grad.cpp ase.h gaussian.h orca.h 77 | knnr.o: icoord.h utils.h knnr.h knnr.cpp qchem.h 78 | ase.o: ase.h ase.cpp utils.h 79 | gaussian.o: gaussian.h gaussian.cpp constants.h utils.h stringtools.h pTable.h 80 | orca.o: orca.h orca.cpp constants.h utils.h stringtools.h pTable.h 81 | molpro.o: molpro.h molpro.cpp utils.h 82 | qchemsf.o: qchemsf.cpp qchemsf.h utils.h stringtools.h qchem.h 83 | -------------------------------------------------------------------------------- /PackagesList.cmake: -------------------------------------------------------------------------------- 1 | TRIBITS_REPOSITORY_DEFINE_PACKAGES( 2 | gsm GSM PT 3 | ) 4 | -------------------------------------------------------------------------------- /ProjectName.cmake: -------------------------------------------------------------------------------- 1 | SET(PROJECT_NAME GSM) 2 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | ## Questions? 2 | Contact Liz Doty: lizdoty@umich.edu 3 | 4 | ## Overview 5 | The growing string method is a reaction path and transition state finding method developed in c++. 6 | 7 | For more information, check out the wiki page: 8 | https://github.com/ZimmermanGroup/molecularGSM/wiki 9 | 10 | Sample tutorial files can be found under the tutorial folder: 11 | https://github.com/ZimmermanGroup/molecularGSM/tree/master/tutorial 12 | 13 | Running GSM with the XTB package (from the Grimme lab): 14 | https://github.com/grimme-lab/xtb_docs/blob/master/source/gsm.rst 15 | 16 | ## Installation 17 | This code can be built using CMake. To do so: 18 | 19 | 1. Load/install CMake 20 | 2. Load MKL (On Athena use `intel/oneapi/mkl/2021.1.1` and GCC, e.g. `gcc/12.1.0`) 21 | 3. Clone this repository, use master branch 22 | 23 | ```bash 24 | $ git clone https://github.com/ZimmermanGroup/molecularGSM.git 25 | $ cd molecularGSM 26 | ``` 27 | 28 | 4. Create a BUILD directory at the same level as GSM 29 | ```bash 30 | $ mkdir BUILD 31 | $ cd BUILD 32 | ``` 33 | 34 | 5. Configure using CMake 35 | ```bash 36 | $ cmake -D GSM_ENABLE_QCHEM=1 ../ 37 | ``` 38 | - other options: 39 | - GSM_ENABLE_QCHEM_SF=1 40 | - GSM_ENABLE_ORCA=1 41 | - GSM_ENABLE_GAUSSIAN=1 42 | - GSM_ENABLE_MOLPRO=1 43 | - GSM_ENABLE_ASE=1 44 | - If no option is specified, the code will use MOPAC as its energy calculator. Check mopac.cpp to make sure charge/multiplicity is correct, since that is hard-coded. 45 | 46 | 6. After successful configuration. To compile: 47 | ```bash 48 | $make -j8 49 | ``` 50 | 51 | 7. An executable named `gsm` will be created in `BUILD/GSM` directory. 52 | 53 | To run gsm, copy the executable to the working directory (where the input files are) or reference it using the full path. 54 | 55 | ## CTest 56 | 57 | There are five test examples: alanine dipeptide isomerization, ammonia borane reactions, diels alder reaction, ethylene rotation, and methanol formaldehyde reaction. After building the executable you can use type $ ctest to run the tests. When each test is complete, the output will be compared with the standard output in each test directory. If the difference in coordinates of a each atom is more than 0.001, the test will fail. 58 | 59 | -------------------------------------------------------------------------------- /TEST/ASE/diels/grad.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | 3 | import shutil 4 | from ase import Atoms # pip install ase if it fails 5 | from ase.visualize import view 6 | from ase.calculators.emt import EMT 7 | from ase.calculators.qchem import QChem 8 | from ase.constraints import FixAtoms 9 | from ase.io import write 10 | from ase.io import read 11 | import sys 12 | import os 13 | 14 | nargs = len(sys.argv) 15 | argv1 = sys.argv[1] 16 | argv2 = sys.argv[2] 17 | os.system("cp scratch/structure"+argv1+" scratch/structure"+argv1+".xyz") 18 | fname = 'scratch/structure'+argv1+'.xyz' 19 | atoms = read(fname) 20 | folder = 'scratch/qchem'+argv1 21 | 22 | #atoms.set_calculator(EMT()) 23 | calc = QChem( 24 | jobtype='FORCE', 25 | method='B3LYP', 26 | basis='6-31G*', 27 | nt=8, 28 | ) 29 | 30 | atoms.calc = calc 31 | 32 | atoms.calc.label = 'scratch/qchem'+argv1 33 | inputfile = 'qchem'+argv1+'.inp' 34 | outputfile = 'qchem'+argv1+'.out' 35 | atoms.calc.command = f'cd scratch; qchem -nt 8 '+inputfile+' > '+outputfile 36 | print('QChem command: ',atoms.calc.command) 37 | 38 | atoms.calc.reset() 39 | 40 | cwd = os.getcwd() 41 | 42 | if not os.path.exists(folder): 43 | os.mkdir(folder) 44 | os.chdir(folder) 45 | 46 | energy = - atoms.get_potential_energy() 47 | grads = - atoms.get_forces() 48 | #print grads 49 | f = open('scratch/GRAD'+argv1, 'w') 50 | f.write(str(energy)) 51 | f.write('\n') 52 | f.write(str(grads)) 53 | f.write('\n') 54 | f.close() 55 | 56 | shutil.copy2('scratch/GRAD'+argv1, cwd+'/scratch') 57 | os.chdir(cwd) 58 | 59 | # comment out the following lines for debugging to be able to see the qchem output 60 | os.system('rm -rf '+folder) 61 | os.system('rm -f scratch/structure'+argv1) 62 | os.system('rm -f '+fname) 63 | -------------------------------------------------------------------------------- /TEST/ASE/diels/inpfileq: -------------------------------------------------------------------------------- 1 | 2 | # FSM/GSM/SSM inpfileq 3 | 4 | ------------- QCHEM Scratch Info ------------------------ 5 | $QCSCRATCH/ # path for scratch dir. end with "/" 6 | GSM_go1q # name of run 7 | --------------------------------------------------------- 8 | 9 | ------------ String Info -------------------------------- 10 | SM_TYPE GSM # SSM, FSM or GSM 11 | RESTART 0 # read restart.xyz 12 | MAX_OPT_ITERS 80 # maximum iterations 13 | STEP_OPT_ITERS 30 # for FSM/SSM 14 | CONV_TOL 0.0005 # perp grad 15 | ADD_NODE_TOL 0.1 # for GSM 16 | SCALING 1.0 # for opt steps 17 | SSM_DQMAX 0.8 # add step size 18 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 19 | INT_THRESH 2.0 # intermediate detection 20 | MIN_SPACING 5.0 # node spacing SSM 21 | BOND_FRAGMENTS 1 # make IC's for fragments 22 | INITIAL_OPT 0 # opt steps first node 23 | FINAL_OPT 150 # opt steps last SSM node 24 | PRODUCT_LIMIT 100.0 # kcal/mol 25 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 26 | NNODES 9 # including endpoints 27 | --------------------------------------------------------- 28 | -------------------------------------------------------------------------------- /TEST/ASE/diels/stringfile.standard: -------------------------------------------------------------------------------- 1 | 16 2 | 0.000000 3 | C -1.060017 -1.517146 0.052887 4 | C -1.829554 -0.594086 -0.539688 5 | C -2.012604 0.793709 -0.089780 6 | C -1.097406 1.540951 0.541104 7 | C 3.018414 -0.332740 0.534205 8 | C 2.482680 0.169904 -0.576610 9 | H -2.400633 -0.882356 -1.423216 10 | H -0.513652 -1.303832 0.968289 11 | H -0.966890 -2.521220 -0.351177 12 | H 3.891712 0.112541 1.005362 13 | H 2.608491 -1.215917 1.019022 14 | H 1.608060 -0.276406 -1.043738 15 | H 2.895264 1.050961 -1.063014 16 | H -1.320890 2.556285 0.856673 17 | H -0.094545 1.173901 0.744815 18 | H -2.981424 1.238281 -0.320708 19 | 16 20 | 0.503226 21 | C -0.913687 -1.533915 0.187533 22 | C -1.715834 -0.669322 -0.449382 23 | C -1.853525 0.768821 -0.177243 24 | C -0.976044 1.554465 0.462795 25 | C 2.754847 -0.444740 0.459840 26 | C 2.345263 0.340084 -0.535263 27 | H -2.354860 -1.053014 -1.245161 28 | H -0.277717 -1.232643 1.015071 29 | H -0.880241 -2.581163 -0.097543 30 | H 3.443477 -0.090070 1.222351 31 | H 2.424154 -1.477029 0.551672 32 | H 1.655283 -0.010849 -1.298391 33 | H 2.683273 1.368974 -0.625507 34 | H -1.186234 2.609335 0.618619 35 | H -0.023742 1.188339 0.836928 36 | H -2.766495 1.225042 -0.561349 37 | 16 38 | 1.478895 39 | C -0.862012 -1.563976 0.404896 40 | C -1.610225 -0.745232 -0.348753 41 | C -1.661555 0.722052 -0.286422 42 | C -0.858698 1.531667 0.419430 43 | C 2.515297 -0.510077 0.278021 44 | C 2.227209 0.531454 -0.501569 45 | H -2.252846 -1.195832 -1.105549 46 | H -0.213917 -1.202608 1.198279 47 | H -0.893079 -2.638497 0.255050 48 | H 2.963384 -0.376912 1.253475 49 | H 2.328472 -1.535975 -0.031444 50 | H 1.786165 0.413759 -1.487338 51 | H 2.436635 1.544652 -0.189634 52 | H -0.990181 2.610277 0.382011 53 | H -0.056579 1.160984 1.048611 54 | H -2.427716 1.182281 -0.910580 55 | 16 56 | 7.765404 57 | C -0.694458 -1.555304 0.566974 58 | C -1.409154 -0.788121 -0.276649 59 | C -1.408614 0.670334 -0.335108 60 | C -0.642153 1.491384 0.408335 61 | C 2.098259 -0.536763 0.095876 62 | C 1.918441 0.647731 -0.496784 63 | H -1.978206 -1.287542 -1.058070 64 | H -0.207836 -1.163088 1.453874 65 | H -0.690126 -2.635213 0.455803 66 | H 2.406360 -0.601510 1.137304 67 | H 2.050629 -1.475023 -0.447055 68 | H 1.673933 0.722975 -1.552021 69 | H 2.174325 1.579487 -0.001228 70 | H -0.663575 2.566203 0.244844 71 | H -0.129370 1.156221 1.302619 72 | H -2.016293 1.111057 -1.124126 73 | 16 74 | 21.280192 75 | C -0.420150 -1.451028 0.602280 76 | C -1.267940 -0.775051 -0.254681 77 | C -1.288366 0.627006 -0.367048 78 | C -0.402516 1.422120 0.345165 79 | C 1.704902 -0.591871 0.044956 80 | C 1.521726 0.701035 -0.418374 81 | H -1.793192 -1.349679 -1.016750 82 | H -0.131208 -1.042454 1.563221 83 | H -0.336585 -2.532324 0.524318 84 | H 2.140259 -0.749117 1.028793 85 | H 1.771581 -1.433531 -0.633717 86 | H 1.319710 0.855974 -1.473792 87 | H 1.998018 1.537045 0.085519 88 | H -0.380227 2.497200 0.180695 89 | H -0.083988 1.115028 1.335627 90 | H -1.844106 1.068089 -1.192926 91 | 16 92 | -19.377138 93 | C -0.124128 -1.362910 0.542966 94 | C -1.195103 -0.736543 -0.269685 95 | C -1.264899 0.603265 -0.366151 96 | C -0.175096 1.382278 0.265514 97 | C 1.374993 -0.676531 0.116026 98 | C 1.214711 0.747454 -0.389744 99 | H -1.805387 -1.375270 -0.910776 100 | H -0.093079 -1.082218 1.602865 101 | H -0.033271 -2.436084 0.391500 102 | H 1.930889 -0.731535 1.059052 103 | H 1.688393 -1.420128 -0.629494 104 | H 1.081894 0.864284 -1.463022 105 | H 1.914814 1.477007 0.037081 106 | H -0.156235 2.457680 0.081949 107 | H 0.020021 1.159262 1.326138 108 | H -1.927764 1.059928 -1.087913 109 | 16 110 | -40.167642 111 | C -0.043631 -1.423083 0.390027 112 | C -1.223129 -0.719727 -0.238834 113 | C -1.285440 0.614041 -0.305972 114 | C -0.110540 1.438090 0.163511 115 | C 1.318642 -0.663768 0.234854 116 | C 1.184563 0.760542 -0.336774 117 | H -2.032306 -1.333267 -0.630921 118 | H -0.241625 -1.544809 1.466733 119 | H 0.042182 -2.441174 -0.008400 120 | H 1.800563 -0.611322 1.218080 121 | H 1.981198 -1.254779 -0.407626 122 | H 1.146374 0.721416 -1.431358 123 | H 2.057487 1.364701 -0.059169 124 | H -0.174910 2.478099 -0.177659 125 | H -0.073662 1.464399 1.263033 126 | H -2.135959 1.108949 -0.769222 127 | 16 128 | -43.216128 129 | C -0.007642 -1.482522 0.230386 130 | C -1.237174 -0.698796 -0.159583 131 | C -1.283679 0.635141 -0.217067 132 | C -0.067734 1.480189 0.079068 133 | C 1.279494 -0.625940 0.387516 134 | C 1.200074 0.722413 -0.344946 135 | H -2.121765 -1.282024 -0.414727 136 | H -0.206083 -2.005829 1.177517 137 | H 0.151321 -2.282417 -0.507228 138 | H 1.466225 -0.438086 1.453022 139 | H 2.139116 -1.198938 0.019844 140 | H 1.161757 0.542476 -1.427966 141 | H 2.097421 1.320167 -0.141487 142 | H -0.136213 2.459801 -0.408798 143 | H -0.011175 1.675359 1.162303 144 | H -2.199839 1.133760 -0.529791 145 | 16 146 | -45.754017 147 | C 0.018565 -1.505102 0.071755 148 | C -1.254726 -0.702912 -0.048283 149 | C -1.285511 0.633242 -0.085278 150 | C -0.048111 1.496966 -0.044220 151 | C 1.216014 -0.631689 0.479480 152 | C 1.229452 0.684821 -0.310339 153 | H -2.187944 -1.262829 -0.104375 154 | H -0.121338 -2.316354 0.799873 155 | H 0.226636 -2.006431 -0.887349 156 | H 1.148348 -0.405323 1.552809 157 | H 2.153272 -1.182597 0.331990 158 | H 1.295645 0.458374 -1.383898 159 | H 2.115916 1.280139 -0.058569 160 | H -0.137620 2.309803 -0.778494 161 | H 0.019570 1.995007 0.936447 162 | H -2.244815 1.145933 -0.151545 163 | -------------------------------------------------------------------------------- /TEST/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | # TEST_DIR is passed as an argument to GFSTRINGQ_TEST function 2 | FUNCTION(GFSTRINGQ_TEST TEST_DIR TEST_NAME) 3 | 4 | #copy input files to the testing folder 5 | file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/${TEST_DIR}/ DESTINATION 6 | ${CMAKE_CURRENT_BINARY_DIR}/${TEST_NAME}) 7 | 8 | TRIBITS_ADD_ADVANCED_TEST( 9 | ${TEST_NAME} 10 | TEST_0 11 | MESSAGE "-- Working directory is 12 | ${CMAKE_CURRENT_SOURCE_DIR}/${TEST_NAME}" 13 | 14 | # the execution command 15 | EXEC gsm.${CALCULATOR} NOEXEPREFIX 16 | DIRECTORY ${PROJECT_BINARY_DIR}/${PROJECT_NAME} 17 | # the args for gstringq, 1 is the file name and 4 is the number of processors 18 | ARGS 1 4 19 | # where it executes 20 | WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${TEST_NAME} 21 | # don't clean it because we copied things there that it needs 22 | SKIP_CLEAN_WORKING_DIRECTORY 23 | OUTPUT_FILE 24 | ${CMAKE_CURRENT_BINARY_DIR}/${TEST_NAME}/scratch/test_output 25 | NO_ECHO_OUTPUT 26 | PASS_ANY 27 | COMM serial 28 | TIMEOUT 100000 29 | 30 | TEST_1 31 | MESSAGE "-- Comparing output in ${CMAKE_CURRENT_BINARY_DIR}/${TEST_NAME}" 32 | # the execution command 33 | CMND python 34 | # the args for CMND 35 | ARGS compare.py 36 | # where it executes 37 | WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${TEST_NAME} 38 | SKIP_CLEAN_WORKING_DIRECTORY 39 | # where the output should go 40 | OUTPUT_FILE 41 | ${CMAKE_CURRENT_BINARY_DIR}/${TEST_NAME}/scratch/compare_output 42 | #NO_ECHO_OUTPUT 43 | # don't clean it because we copied things there that it needs 44 | SKIP_CLEAN_WORKING_DIRECTORY 45 | FAIL_FAST 46 | NUM_TOTAL_CORES_USED 1 47 | CATEGORIES BASIC 48 | COMM serial 49 | 50 | ) 51 | ENDFUNCTION() 52 | 53 | #call the function 54 | if(GSM_ENABLE_QCHEM) 55 | MESSAGE(STATUS "QCHEM is enabled.") 56 | GFSTRINGQ_TEST(alanineDipeptideIsomerization/qchem/de-gsm alanine) 57 | GFSTRINGQ_TEST(ammoniaBorane/qchem/de-gsm ammonia) 58 | GFSTRINGQ_TEST(dielsAlder/qchem/de-gsm diels) 59 | GFSTRINGQ_TEST(dielsAlder/qchem/se-gsm se-diels) 60 | GFSTRINGQ_TEST(ethyleneRotation/qchem/de-gsm ethylene) 61 | GFSTRINGQ_TEST(methanolFormaldehydeHydTransfer/qchem/de-gsm methanol) 62 | 63 | elseif(GSM_ENABLE_GAUSSIAN) 64 | MESSAGE(STATUS "GAUSSIAN is enabled.") 65 | #GFSTRINGQ_TEST(alanineDipeptideIsomerization/gaussian/de-gsm alanine) 66 | #GFSTRINGQ_TEST(ammoniaBorane/gaussian/de-gsm ammonia) 67 | GFSTRINGQ_TEST(dielsAlder/gaussian/de-gsm diels) 68 | GFSTRINGQ_TEST(dielsAlder/gaussian/se-gsm se-diels) 69 | #GFSTRINGQ_TEST(ethyleneRotation/gaussian/de-gsm ethylene) 70 | #GFSTRINGQ_TEST(methanolFormaldehydeHydTransfer/gaussian/de-gsm methanol) 71 | 72 | elseif(GSM_ENABLE_ORCA) 73 | MESSAGE(STATUS "ORCA is enabled.") 74 | #GFSTRINGQ_TEST(alanineDipeptideIsomerization/orca/de-gsm alanine) 75 | #GFSTRINGQ_TEST(ammoniaBorane/orca/de-gsm ammonia) 76 | GFSTRINGQ_TEST(dielsAlder/orca/de-gsm diels) 77 | GFSTRINGQ_TEST(dielsAlder/orca/se-gsm se-diels) 78 | #GFSTRINGQ_TEST(ethyleneRotation/orca/de-gsm ethylene) 79 | #GFSTRINGQ_TEST(methanolFormaldehydeHydTransfer/orca/de-gsm methanol) 80 | elseif(GSM_ENABLE_ASE) 81 | MESSAGE(STATUS "ASE is enabled.") 82 | GFSTRINGQ_TEST(dielsAlder/ase/de-gsm diels) 83 | elseif(GSM_ENABLE_TURBOMOLE) 84 | MESSAGE(STATUS "TURBOMOLE is enabled.") 85 | GFSTRINGQ_TEST(dielsAlder/turbomole/de-gsm-wrapper diels-w-wrapper) 86 | GFSTRINGQ_TEST(dielsAlder/turbomole/de-gsm-nowrapper diels) 87 | else() 88 | MESSAGE(STATUS "MOPAC is enabled.") 89 | #GFSTRINGQ_TEST(alanineDipeptideIsomerization/mopac/de-gsm alanine) 90 | #GFSTRINGQ_TEST(ammoniaBorane/mopac/de-gsm ammonia) 91 | GFSTRINGQ_TEST(dielsAlder/mopac/de-gsm diels) 92 | GFSTRINGQ_TEST(ethyleneRotation/mopac/de-gsm ethylene) 93 | GFSTRINGQ_TEST(methanolFormaldehydeHydTransfer/mopac/de-gsm methanol) 94 | GFSTRINGQ_TEST(dielsAlder/mopac/se-gsm se-diels) 95 | endif() 96 | -------------------------------------------------------------------------------- /TEST/alanineDipeptideIsomerization/mopac/de-gsm/gscreate: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | file=molecule 4 | 5 | #nl $file > tmp.mole 6 | #nl link > tmp.link 7 | #join tmp.mole tmp.link > tmp.geom2 8 | #awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom 9 | 10 | #cat qstart tmp.geom qend > qcin 11 | #cat qstart molecule$1 qend > scratch/qcin$1 12 | cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 13 | 14 | #rm tmp.geom tmp.geom2 tmp.link tmp.mole 15 | 16 | 17 | -------------------------------------------------------------------------------- /TEST/alanineDipeptideIsomerization/mopac/de-gsm/inpfileq: -------------------------------------------------------------------------------- 1 | 2 | # FSM/GSM/SSM inpfileq 3 | 4 | ------------- QCHEM Scratch Info ------------------------ 5 | $QCSCRATCH/ # path for scratch dir. end with "/" 6 | GSM_go1q # name of run 7 | --------------------------------------------------------- 8 | 9 | ------------ String Info -------------------------------- 10 | SM_TYPE GSM # SSM, FSM or GSM 11 | RESTART 0 # read restart.xyz 12 | MAX_OPT_ITERS 80 # maximum iterations 13 | STEP_OPT_ITERS 30 # for FSM/SSM 14 | CONV_TOL 0.0005 # perp grad 15 | ADD_NODE_TOL 0.1 # for GSM 16 | SCALING 1.0 # for opt steps 17 | SSM_DQMAX 0.8 # add step size 18 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 19 | INT_THRESH 2.0 # intermediate detection 20 | MIN_SPACING 5.0 # node spacing SSM 21 | BOND_FRAGMENTS 1 # make IC's for fragments 22 | INITIAL_OPT 0 # opt steps first node 23 | FINAL_OPT 150 # opt steps last SSM node 24 | PRODUCT_LIMIT 100.0 # kcal/mol 25 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 26 | NNODES 9 # including endpoints 27 | --------------------------------------------------------- 28 | -------------------------------------------------------------------------------- /TEST/alanineDipeptideIsomerization/mopac/de-gsm/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 22 2 | 3 | C 3.229500143 -1.189208873 0.139884199 4 | C 2.146015609 -0.205277340 0.472350600 5 | N 1.118945963 -0.112570225 -0.476082396 6 | C -0.047243882 0.763674630 -0.244060076 7 | C -1.303372401 -0.141988306 -0.210244508 8 | N -2.291823409 0.245144133 0.683372021 9 | C -3.533352727 -0.542642118 0.823358708 10 | O 2.135600863 0.498914065 1.468642050 11 | C -0.213883265 1.775303506 -1.377215496 12 | O -1.430938786 -1.114644891 -0.937948112 13 | H 3.761964341 -0.925904727 -0.783924677 14 | H 2.849246312 -2.213259730 0.027908378 15 | H 3.977199149 -1.208576837 0.950327781 16 | H 1.044378979 -0.752094793 -1.266196463 17 | H 0.102202311 1.303404325 0.735056289 18 | H -2.174667309 1.020034576 1.323554728 19 | H -4.416281800 0.081571617 0.609553525 20 | H -3.620828522 -0.960320632 1.839472047 21 | H -3.535367434 -1.390382715 0.106911648 22 | H -1.058895373 2.448597515 -1.192128572 23 | H -0.391966619 1.284864578 -2.344308637 24 | H 0.688253393 2.392712099 -1.487113804 25 | 22 26 | 27 | C 2.631040800 -1.106006186 -1.087251446 28 | C 1.455433960 -0.247406296 -0.720351447 29 | N 1.111330581 -0.245040965 0.632617367 30 | C 0.013296964 0.566859303 1.209728990 31 | C -1.371253959 -0.047197126 0.856896402 32 | N -1.758278255 -0.027353669 -0.465545904 33 | C -3.048601731 -0.606776565 -0.886889731 34 | O 0.828411740 0.404243419 -1.546049991 35 | C 0.093495718 2.034730623 0.807075902 36 | O -2.076272130 -0.498913473 1.749500783 37 | H 2.309296004 -1.912838255 -1.766184327 38 | H 3.154692233 -1.571597680 -0.246396909 39 | H 3.367552489 -0.509479586 -1.650547015 40 | H 1.622930701 -0.819779117 1.296556514 41 | H 0.101544644 0.488022293 2.332977571 42 | H -1.131843859 0.311497590 -1.206453969 43 | H -2.896398772 -1.545093253 -1.446399685 44 | H -3.596199978 0.105940393 -1.525332072 45 | H -3.681066939 -0.836997366 -0.005680182 46 | H -0.743521789 2.607399517 1.225766714 47 | H 0.068112285 2.166270013 -0.287358711 48 | H 1.024023911 2.496248786 1.159830035 49 | -------------------------------------------------------------------------------- /TEST/alanineDipeptideIsomerization/qchem/.q002.product.inp.9354.qcin.1: -------------------------------------------------------------------------------- 1 | $rem 2 | JOBTYPE OPT 3 | EXCHANGE B3LYP 4 | ! CORRELATION PBE 5 | ! UNRESTRICTED TRUE 6 | SCF_ALGORITHM rca_diis 7 | SCF_MAX_CYCLES 150 8 | ! BASIS LANL2DZ 9 | ! ECP LANL2DZ 10 | BASIS 6-31G* 11 | WAVEFUNCTION_ANALYSIS FALSE 12 | GEOM_OPT_MAX_CYCLES 300 13 | 14 | scf_convergence 6 15 | 16 | SYM_IGNORE TRUE 17 | SYMMETRY FALSE 18 | 19 | molden_format true 20 | $end 21 | 22 | 23 | $molecule 24 | 0 1 25 | C 2.643785 -1.121028 -1.073991 26 | C 1.440890 -0.257653 -0.731562 27 | N 1.113549 -0.198238 0.587618 28 | C -0.002980 0.568839 1.173333 29 | C -1.390825 -0.048391 0.863046 30 | N -1.768439 -0.012358 -0.441195 31 | C -3.015698 -0.602464 -0.893016 32 | O 0.822529 0.344445 -1.613501 33 | C 0.081155 2.065992 0.847556 34 | O -2.082502 -0.492329 1.775255 35 | H 2.323771 -1.914876 -1.754602 36 | H 3.131647 -1.568635 -0.204417 37 | H 3.369802 -0.505402 -1.611088 38 | H 1.593996 -0.829628 1.210337 39 | H 0.094656 0.439609 2.253020 40 | H -1.059273 0.248575 -1.122879 41 | H -2.849726 -1.546821 -1.426538 42 | H -3.545070 0.084690 -1.560948 43 | H -3.631817 -0.800937 -0.015503 44 | H -0.734906 2.593966 1.349942 45 | H 0.013387 2.248453 -0.224778 46 | H 1.029499 2.473951 1.210080 47 | $end 48 | -------------------------------------------------------------------------------- /TEST/alanineDipeptideIsomerization/qchem/de-gsm/gscreate: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | file=molecule 4 | 5 | #nl $file > tmp.mole 6 | #nl link > tmp.link 7 | #join tmp.mole tmp.link > tmp.geom2 8 | #awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom 9 | 10 | #cat qstart tmp.geom qend > qcin 11 | #cat qstart molecule$1 qend > scratch/qcin$1 12 | cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 13 | 14 | #rm tmp.geom tmp.geom2 tmp.link tmp.mole 15 | -------------------------------------------------------------------------------- /TEST/alanineDipeptideIsomerization/qchem/de-gsm/inpfileq: -------------------------------------------------------------------------------- 1 | 2 | # FSM/GSM/SSM inpfileq 3 | 4 | ------------- QCHEM Scratch Info ------------------------ 5 | $QCSCRATCH/ # path for scratch dir. end with "/" 6 | GSM_go1q # name of run 7 | --------------------------------------------------------- 8 | 9 | ------------ String Info -------------------------------- 10 | SM_TYPE GSM # SSM, FSM or GSM 11 | RESTART 0 # read restart.xyz 12 | MAX_OPT_ITERS 80 # maximum iterations 13 | STEP_OPT_ITERS 30 # for FSM/SSM 14 | CONV_TOL 0.0005 # perp grad 15 | ADD_NODE_TOL 0.1 # for GSM 16 | SCALING 1.0 # for opt steps 17 | SSM_DQMAX 0.8 # add step size 18 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 19 | INT_THRESH 2.0 # intermediate detection 20 | MIN_SPACING 5.0 # node spacing SSM 21 | BOND_FRAGMENTS 1 # make IC's for fragments 22 | INITIAL_OPT 0 # opt steps first node 23 | FINAL_OPT 150 # opt steps last SSM node 24 | PRODUCT_LIMIT 100.0 # kcal/mol 25 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 26 | NNODES 9 # including endpoints 27 | --------------------------------------------------------- 28 | -------------------------------------------------------------------------------- /TEST/alanineDipeptideIsomerization/qchem/de-gsm/qend: -------------------------------------------------------------------------------- 1 | $end 2 | -------------------------------------------------------------------------------- /TEST/alanineDipeptideIsomerization/qchem/de-gsm/qstart: -------------------------------------------------------------------------------- 1 | $rem 2 | JOBTYPE FORCE 3 | EXCHANGE B3LYP 4 | ! CORRELATION PBE 5 | ! UNRESTRICTED TRUE 6 | SCF_ALGORITHM rca_diis 7 | SCF_MAX_CYCLES 150 8 | BASIS 6-31G* 9 | ! BASIS LANL2DZ 10 | ! ECP LANL2DZ 11 | WAVEFUNCTION_ANALYSIS FALSE 12 | GEOM_OPT_MAX_CYCLES 300 13 | 14 | scf_convergence 6 15 | 16 | SYM_IGNORE TRUE 17 | SYMMETRY FALSE 18 | 19 | molden_format true 20 | $end 21 | 22 | 23 | $molecule 24 | 0 1 25 | -------------------------------------------------------------------------------- /TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/gsmdone1: -------------------------------------------------------------------------------- 1 | done with paragsm0001 2 | -------------------------------------------------------------------------------- /TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 22 2 | Step 12 3 | C 3.31502854 -1.14428477 -0.07833863 4 | C 2.27368191 -0.08290184 0.24400427 5 | N 1.01775129 -0.33119131 -0.22147007 6 | C -0.09692549 0.54620720 0.07392889 7 | C -1.37806532 -0.29036768 -0.08159080 8 | N -2.49539554 0.26339992 0.46063556 9 | C -3.80842307 -0.35269813 0.36912712 10 | O 2.55113792 0.93207195 0.87781597 11 | C -0.12012907 1.78271184 -0.84626356 12 | O -1.37498666 -1.36563041 -0.67688002 13 | H 4.12904645 -0.68104364 -0.64462588 14 | H 2.91918708 -1.98892782 -0.65070653 15 | H 3.74116590 -1.51580717 0.85884633 16 | H 0.76711436 -1.20387519 -0.67179930 17 | H 0.00211259 0.88849993 1.11214377 18 | H -2.40559063 1.13949554 0.95541137 19 | H -4.51802867 0.30542439 -0.14557452 20 | H -4.20267956 -0.59135411 1.36362200 21 | H -3.69646626 -1.27532171 -0.20134847 22 | H -0.94802578 2.45554030 -0.59367880 23 | H -0.22744645 1.47893665 -1.89284377 24 | H 0.81910346 2.32835004 -0.72656094 25 | 22 26 | Step 17 27 | C 2.68428027 -1.08649423 -1.07658991 28 | C 1.43764723 -0.27868144 -0.75112617 29 | N 1.08519533 -0.23939519 0.56148774 30 | C -0.01031015 0.54587042 1.16150592 31 | C -1.43096499 -0.00151903 0.86895844 32 | N -1.75019004 -0.13876441 -0.44216906 33 | C -3.04815983 -0.61836881 -0.87853737 34 | O 0.80778926 0.29847342 -1.64193616 35 | C 0.09832240 2.04645209 0.84778740 36 | O -2.19309694 -0.23708699 1.80258638 37 | H 2.43759533 -1.81684693 -1.85267184 38 | H 3.11428148 -1.60798951 -0.21610339 39 | H 3.43919152 -0.41166148 -1.49301489 40 | H 1.62727464 -0.80165380 1.20111399 41 | H 0.09578035 0.40749321 2.23935300 42 | H -1.03119692 0.08231800 -1.12897404 43 | H -2.94961330 -1.53114107 -1.47879225 44 | H -3.56725345 0.13836900 -1.47944033 45 | H -3.64161887 -0.83639523 0.01057400 46 | H -0.71006138 2.58100721 1.35732517 47 | H 0.02781624 2.23620201 -0.22458996 48 | H 1.05472179 2.43957276 1.20942233 49 | -------------------------------------------------------------------------------- /TEST/alanineDipeptideIsomerization/qchem/de-gsm/scratch/tsq0001.xyz: -------------------------------------------------------------------------------- 1 | 22 2 | -495.840702 -495.852868 -495.850979 3 | C 2.982354 -1.210447 -0.786149 4 | C 1.975805 -0.078568 -0.597126 5 | N 1.095650 -0.279233 0.429745 6 | C 0.002267 0.579992 0.909097 7 | C -1.296511 -0.239344 0.710571 8 | N -2.163648 0.191919 -0.242855 9 | C -3.385570 -0.521792 -0.573235 10 | O 1.994318 0.908990 -1.322319 11 | C 0.001916 2.010931 0.368424 12 | O -1.467700 -1.254555 1.381053 13 | H 2.917802 -1.564322 -1.819506 14 | H 2.841423 -2.058964 -0.108966 15 | H 3.989987 -0.807218 -0.642628 16 | H 1.137417 -1.166073 0.914495 17 | H 0.112587 0.634778 1.998944 18 | H -1.932529 1.025002 -0.765127 19 | H -3.383041 -0.840598 -1.622243 20 | H -4.268644 0.103010 -0.395326 21 | H -3.433201 -1.401711 0.069285 22 | H -0.828055 2.556957 0.831447 23 | H -0.082280 2.057721 -0.718646 24 | H 0.933552 2.518284 0.628236 25 | 26 | -------------------------------------------------------------------------------- /TEST/ammoniaBorane/mopac/de-gsm/inpfileq: -------------------------------------------------------------------------------- 1 | # FSM/GSM/SSM inpfileq 2 | 3 | ------------- QCHEM Scratch Info ------------------------ 4 | $QCSCRATCH/ # path for scratch dir. end with "/" 5 | GSM_go1q # name of run 6 | --------------------------------------------------------- 7 | 8 | ------------ String Info -------------------------------- 9 | SM_TYPE GSM # SSM, FSM or GSM 10 | RESTART 0 # read restart.xyz 11 | MAX_OPT_ITERS 80 # maximum iterations 12 | STEP_OPT_ITERS 30 # for FSM/SSM 13 | CONV_TOL 0.0005 # perp grad 14 | ADD_NODE_TOL 0.1 # for GSM 15 | SCALING 1.0 # for opt steps 16 | SSM_DQMAX 0.8 # add step size 17 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 18 | INT_THRESH 2.0 # intermediate detection 19 | MIN_SPACING 5.0 # node spacing SSM 20 | BOND_FRAGMENTS 1 # make IC's for fragments 21 | INITIAL_OPT 0 # opt steps first node 22 | FINAL_OPT 150 # opt steps last SSM node 23 | PRODUCT_LIMIT 100.0 # kcal/mol 24 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 25 | NNODES 9 # including endpoints 26 | --------------------------------------------------------- 27 | -------------------------------------------------------------------------------- /TEST/ammoniaBorane/mopac/de-gsm/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 14 2 | 3 | N 1.383770091 -0.954052038 -0.151204418 4 | B 1.683770235 0.579434831 0.094123862 5 | B -1.913335463 -0.414385322 0.080253305 6 | N -1.573330405 0.917724710 -0.082088716 7 | H 0.362958858 -1.152502256 0.029547531 8 | H 1.952511500 -1.518899363 0.471861584 9 | H 1.603727220 -1.200723305 -1.111645175 10 | H 1.685884747 0.794108260 1.271411505 11 | H 2.747766790 0.856233208 -0.377519758 12 | H 0.828804768 1.233683197 -0.444071342 13 | H -1.033174789 -1.228986125 0.127204910 14 | H -3.042894590 -0.772202593 0.166197022 15 | H -2.251075338 1.648451353 -0.119053483 16 | H -0.592044246 1.235067187 -0.144664561 17 | 14 18 | 19 | N 0.776258143 -1.811801030 1.790990171 20 | B 0.716713960 1.226549327 -0.934956367 21 | B -1.014127649 0.539764998 -1.284401998 22 | N -0.301678868 0.653213154 0.099092833 23 | H 0.134910972 -2.386711679 2.314896494 24 | H 1.496448836 -1.504069465 2.425932533 25 | H 1.215582738 -2.403268982 1.101520813 26 | H 0.869063818 2.408771659 -0.895903859 27 | H 1.661925807 0.530875691 -1.147253283 28 | H -0.027246135 1.067121234 -2.073276994 29 | H -1.912840870 1.304309832 -1.458957446 30 | H -1.112481269 -0.571146366 -1.707139061 31 | H -0.046671886 -0.221234397 0.565424944 32 | H -0.692576571 1.307804790 0.761430894 33 | -------------------------------------------------------------------------------- /TEST/ammoniaBorane/mopac/de-gsm/stringfile.standard: -------------------------------------------------------------------------------- 1 | 14 2 | 0.000000 3 | N 1.383770 -0.954052 -0.151204 4 | B 1.683770 0.579435 0.094124 5 | B -1.913335 -0.414385 0.080253 6 | N -1.573330 0.917725 -0.082089 7 | H 0.362959 -1.152502 0.029548 8 | H 1.952511 -1.518899 0.471862 9 | H 1.603727 -1.200723 -1.111645 10 | H 1.685885 0.794108 1.271412 11 | H 2.747767 0.856233 -0.377520 12 | H 0.828805 1.233683 -0.444071 13 | H -1.033175 -1.228986 0.127205 14 | H -3.042895 -0.772203 0.166197 15 | H -2.251075 1.648451 -0.119053 16 | H -0.592044 1.235067 -0.144665 17 | 14 18 | 3.215260 19 | N 1.611639 -1.180262 0.062477 20 | B 1.771299 0.391804 -0.053884 21 | B -2.301420 0.027218 0.224064 22 | N -1.500284 1.060630 -0.237339 23 | H 0.697786 -1.429552 0.437188 24 | H 2.336197 -1.547210 0.675055 25 | H 1.715808 -1.599713 -0.858499 26 | H 1.783410 0.865336 1.045198 27 | H 2.798155 0.626495 -0.621569 28 | H 0.842616 0.805598 -0.693006 29 | H -1.821243 -0.800644 0.931150 30 | H -3.454598 -0.019265 -0.061770 31 | H -1.832386 1.777772 -0.845227 32 | H -0.495459 1.092739 -0.041914 33 | 14 34 | 18.208530 35 | N 1.822987 -1.227330 0.248078 36 | B 1.834923 0.471821 0.128015 37 | B -2.604282 0.268874 0.025559 38 | N -1.522893 0.987839 -0.483776 39 | H 1.031844 -1.716630 0.643202 40 | H 2.635783 -1.409901 0.840574 41 | H 2.028787 -1.590892 -0.676815 42 | H 1.913462 1.056711 1.159602 43 | H 2.835893 0.458892 -0.530853 44 | H 0.737084 0.512262 -0.350175 45 | H -2.497568 -0.165859 1.134972 46 | H -3.635624 0.211709 -0.564024 47 | H -1.525954 1.381233 -1.394456 48 | H -0.577390 0.783993 -0.137069 49 | 14 50 | 53.824930 51 | N 1.347470 -1.857039 0.345380 52 | B 2.035774 1.481577 0.242721 53 | B -2.420825 0.211511 -0.164943 54 | N -1.290338 0.610686 -0.867826 55 | H 0.552711 -2.286926 0.789346 56 | H 2.089240 -1.809456 1.022382 57 | H 1.650994 -2.465350 -0.396204 58 | H 2.221782 2.633115 0.415066 59 | H 2.944116 0.745754 0.414420 60 | H 1.010419 0.994359 -0.092466 61 | H -2.516101 0.469656 0.990963 62 | H -3.300378 -0.355250 -0.731476 63 | H -1.136559 0.331839 -1.813208 64 | H -0.456430 0.984914 -0.421514 65 | 14 66 | 51.280610 67 | N 1.235240 -1.335808 0.957553 68 | B 1.746627 1.713540 -0.028384 69 | B -2.406543 0.029159 -0.505538 70 | N -1.151432 -0.058781 -1.093132 71 | H 0.407998 -1.584049 1.476607 72 | H 1.953820 -1.099987 1.621721 73 | H 1.539613 -2.155974 0.460766 74 | H 1.702286 2.093474 1.087501 75 | H 2.788842 1.492998 -0.535497 76 | H 0.741541 1.567834 -0.638608 77 | H -2.514866 0.559659 0.555195 78 | H -3.358853 -0.415789 -1.062080 79 | H -1.003369 -0.493376 -1.976914 80 | H -0.310077 0.304941 -0.660795 81 | 14 82 | 53.138610 83 | N 1.035862 -1.462016 1.445476 84 | B 1.150064 1.927339 -0.474332 85 | B -1.885288 0.092936 -0.746053 86 | N -0.585397 -0.321500 -1.010257 87 | H 0.151507 -1.565504 1.918727 88 | H 1.701792 -1.117706 2.118711 89 | H 1.336896 -2.380999 1.163992 90 | H 1.019167 1.822922 0.693606 91 | H 2.167518 1.620891 -0.988983 92 | H 0.265252 2.347131 -1.134657 93 | H -2.103597 0.726939 0.237618 94 | H -2.755423 -0.171603 -1.511047 95 | H -0.339746 -0.887891 -1.791043 96 | H 0.154938 -0.205899 -0.339674 97 | 14 98 | 17.441480 99 | N 0.790413 -1.500913 1.892034 100 | B 0.571107 1.412403 -0.912726 101 | B -1.302949 0.395094 -0.983220 102 | N 0.065859 -0.158854 -0.776959 103 | H -0.150836 -1.585372 2.246941 104 | H 1.337740 -1.083538 2.630228 105 | H 1.147004 -2.429521 1.736014 106 | H 0.500352 1.874379 0.186873 107 | H 1.652616 1.367275 -1.416890 108 | H -0.210179 1.909473 -1.686593 109 | H -1.785828 1.003380 -0.086903 110 | H -1.870795 0.147897 -1.994083 111 | H 0.474818 -0.797000 -1.447067 112 | H 0.466756 -0.336392 0.159625 113 | 14 114 | -0.641950 115 | N 0.685498 -1.651150 2.060968 116 | B 0.695640 1.337923 -1.108185 117 | B -1.018213 0.538755 -1.236736 118 | N 0.125376 0.161777 -0.251958 119 | H -0.246963 -1.875871 2.374924 120 | H 1.189791 -1.291717 2.857193 121 | H 1.125665 -2.517929 1.792375 122 | H 0.722602 2.384545 -0.533552 123 | H 1.623380 1.057356 -1.802428 124 | H -0.314108 1.478389 -1.989857 125 | H -1.898273 1.198401 -0.773424 126 | H -1.254897 -0.259908 -2.088973 127 | H 0.558535 -0.748900 -0.367464 128 | H 0.012809 0.355732 0.736825 129 | 14 130 | -0.920680 131 | N 0.776258 -1.811801 1.790990 132 | B 0.716714 1.226549 -0.934956 133 | B -1.014128 0.539765 -1.284402 134 | N -0.301679 0.653213 0.099093 135 | H 0.134911 -2.386712 2.314896 136 | H 1.496449 -1.504069 2.425933 137 | H 1.215583 -2.403269 1.101521 138 | H 0.869064 2.408772 -0.895904 139 | H 1.661926 0.530876 -1.147253 140 | H -0.027246 1.067121 -2.073277 141 | H -1.912841 1.304310 -1.458957 142 | H -1.112481 -0.571146 -1.707139 143 | H -0.046672 -0.221234 0.565425 144 | H -0.692577 1.307805 0.761431 145 | -------------------------------------------------------------------------------- /TEST/ammoniaBorane/mopac/de-gsm/stringfile.standard.fr: -------------------------------------------------------------------------------- 1 | 14 2 | 3 | N 1.354486 -1.869638 0.342672 4 | B 2.029562 1.483705 0.244537 5 | B -2.416934 0.210520 -0.162772 6 | N -1.293976 0.630855 -0.866415 7 | H 0.558388 -2.300738 0.782941 8 | H 2.092499 -1.821713 1.023929 9 | H 1.661525 -2.475192 -0.399250 10 | H 2.228974 2.640783 0.350040 11 | H 2.921519 0.738304 0.460781 12 | H 1.004294 0.984006 -0.074390 13 | H -2.521967 0.466556 0.993272 14 | H -3.287546 -0.369691 -0.730017 15 | H -1.134353 0.355903 -1.811770 16 | H -0.464599 1.015729 -0.420917 17 | 14 18 | 19 | N 1.347470 -1.857039 0.345380 20 | B 2.035774 1.481577 0.242721 21 | B -2.420825 0.211511 -0.164943 22 | N -1.290338 0.610686 -0.867826 23 | H 0.552711 -2.286926 0.789346 24 | H 2.089240 -1.809456 1.022382 25 | H 1.650994 -2.465350 -0.396204 26 | H 2.221782 2.633115 0.415066 27 | H 2.944116 0.745754 0.414420 28 | H 1.010419 0.994359 -0.092466 29 | H -2.516101 0.469656 0.990963 30 | H -3.300378 -0.355250 -0.731476 31 | H -1.136559 0.331839 -1.813208 32 | H -0.456430 0.984914 -0.421514 33 | 14 34 | 35 | N 1.339765 -1.842487 0.348688 36 | B 2.042652 1.479057 0.240619 37 | B -2.425581 0.211841 -0.167239 38 | N -1.285618 0.588814 -0.870544 39 | H 0.546820 -2.271047 0.796827 40 | H 2.085698 -1.795413 1.020934 41 | H 1.638999 -2.453789 -0.392708 42 | H 2.215793 2.619956 0.487296 43 | H 2.967796 0.755243 0.362022 44 | H 1.015635 1.007365 -0.111024 45 | H -2.509976 0.472288 0.989466 46 | H -3.314677 -0.340307 -0.732803 47 | H -1.138461 0.305978 -1.815322 48 | H -0.446971 0.951888 -0.423571 49 | 14 50 | 51 | N 1.339045 -1.862137 0.343494 52 | B 2.035998 1.484587 0.248975 53 | B -2.415273 0.212834 -0.163278 54 | N -1.288664 0.609350 -0.870898 55 | H 0.545149 -2.290052 0.788811 56 | H 2.083501 -1.820258 1.018528 57 | H 1.640532 -2.469458 -0.400276 58 | H 2.226737 2.638059 0.419780 59 | H 2.954624 0.760751 0.417906 60 | H 1.016371 0.995882 -0.084124 61 | H -2.515770 0.475014 0.990037 62 | H -3.288398 -0.379384 -0.718103 63 | H -1.140894 0.321918 -1.814941 64 | H -0.461083 1.012282 -0.443269 65 | 14 66 | 67 | N 1.347470 -1.857039 0.345380 68 | B 2.035774 1.481577 0.242721 69 | B -2.420825 0.211511 -0.164943 70 | N -1.290338 0.610686 -0.867826 71 | H 0.552711 -2.286926 0.789346 72 | H 2.089240 -1.809456 1.022382 73 | H 1.650994 -2.465350 -0.396204 74 | H 2.221782 2.633115 0.415066 75 | H 2.944116 0.745754 0.414420 76 | H 1.010419 0.994359 -0.092466 77 | H -2.516101 0.469656 0.990963 78 | H -3.300378 -0.355250 -0.731476 79 | H -1.136559 0.331839 -1.813208 80 | H -0.456430 0.984914 -0.421514 81 | 14 82 | 83 | N 1.356002 -1.851866 0.347182 84 | B 2.035306 1.478344 0.236910 85 | B -2.426305 0.210185 -0.166412 86 | N -1.291931 0.612047 -0.865115 87 | H 0.560413 -2.283510 0.789981 88 | H 2.095195 -1.798472 1.025963 89 | H 1.661353 -2.461386 -0.392110 90 | H 2.216455 2.627912 0.411051 91 | H 2.933204 0.730649 0.411325 92 | H 1.004221 0.992575 -0.100591 93 | H -2.516112 0.464485 0.992118 94 | H -3.312047 -0.331010 -0.743807 95 | H -1.132614 0.341672 -1.811681 96 | H -0.451266 0.957763 -0.402173 97 | 14 98 | 99 | N 1.366252 -1.868753 0.344036 100 | B 2.036837 1.479322 0.240894 101 | B -2.432779 0.222666 -0.164501 102 | N -1.288270 0.586679 -0.859740 103 | H 0.567207 -2.296526 0.782033 104 | H 2.102448 -1.822301 1.027236 105 | H 1.675454 -2.480928 -0.391852 106 | H 2.208789 2.636516 0.392288 107 | H 2.943239 0.746572 0.429996 108 | H 1.000792 1.006461 -0.085778 109 | H -2.528050 0.480352 0.990876 110 | H -3.320521 -0.322215 -0.740072 111 | H -1.140158 0.344619 -1.816120 112 | H -0.459365 0.976924 -0.416654 113 | 14 114 | 115 | N 1.347470 -1.857039 0.345380 116 | B 2.035774 1.481577 0.242721 117 | B -2.420825 0.211511 -0.164943 118 | N -1.290338 0.610686 -0.867826 119 | H 0.552711 -2.286926 0.789346 120 | H 2.089240 -1.809456 1.022382 121 | H 1.650994 -2.465350 -0.396204 122 | H 2.221782 2.633115 0.415066 123 | H 2.944116 0.745754 0.414420 124 | H 1.010419 0.994359 -0.092466 125 | H -2.516101 0.469656 0.990963 126 | H -3.300378 -0.355250 -0.731476 127 | H -1.136559 0.331839 -1.813208 128 | H -0.456430 0.984914 -0.421514 129 | 14 130 | 131 | N 1.329162 -1.845404 0.346779 132 | B 2.033538 1.483542 0.244392 133 | B -2.408379 0.200747 -0.165888 134 | N -1.293498 0.635127 -0.875000 135 | H 0.538629 -2.277340 0.796359 136 | H 2.076297 -1.796392 1.017692 137 | H 1.627548 -2.449832 -0.400197 138 | H 2.235148 2.628593 0.437643 139 | H 2.943741 0.745011 0.398906 140 | H 1.020360 0.980959 -0.100437 141 | H -2.503832 0.459103 0.989730 142 | H -3.279173 -0.387796 -0.723280 143 | H -1.133420 0.318994 -1.808514 144 | H -0.454246 0.994076 -0.425543 145 | -------------------------------------------------------------------------------- /TEST/ammoniaBorane/qchem/de-gsm/gscreate: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | file=molecule 4 | 5 | #nl $file > tmp.mole 6 | #nl link > tmp.link 7 | #join tmp.mole tmp.link > tmp.geom2 8 | #awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom 9 | 10 | #cat qstart tmp.geom qend > qcin 11 | #cat qstart molecule$1 qend > scratch/qcin$1 12 | cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 13 | 14 | #rm tmp.geom tmp.geom2 tmp.link tmp.mole 15 | -------------------------------------------------------------------------------- /TEST/ammoniaBorane/qchem/de-gsm/inpfileq: -------------------------------------------------------------------------------- 1 | 2 | # FSM/GSM/SSM inpfileq 3 | 4 | ------------- QCHEM Scratch Info ------------------------ 5 | $QCSCRATCH/ # path for scratch dir. end with "/" 6 | GSM_go1q # name of run 7 | --------------------------------------------------------- 8 | 9 | ------------ String Info -------------------------------- 10 | SM_TYPE GSM # SSM, FSM or GSM 11 | RESTART 0 # read restart.xyz 12 | MAX_OPT_ITERS 80 # maximum iterations 13 | STEP_OPT_ITERS 30 # for FSM/SSM 14 | CONV_TOL 0.0005 # perp grad 15 | ADD_NODE_TOL 0.1 # for GSM 16 | SCALING 1.0 # for opt steps 17 | SSM_DQMAX 0.8 # add step size 18 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 19 | INT_THRESH 2.0 # intermediate detection 20 | MIN_SPACING 5.0 # node spacing SSM 21 | BOND_FRAGMENTS 1 # make IC's for fragments 22 | INITIAL_OPT 0 # opt steps first node 23 | FINAL_OPT 150 # opt steps last SSM node 24 | PRODUCT_LIMIT 100.0 # kcal/mol 25 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 26 | NNODES 9 # including endpoints 27 | --------------------------------------------------------- 28 | -------------------------------------------------------------------------------- /TEST/ammoniaBorane/qchem/de-gsm/qend: -------------------------------------------------------------------------------- 1 | $end 2 | -------------------------------------------------------------------------------- /TEST/ammoniaBorane/qchem/de-gsm/qstart: -------------------------------------------------------------------------------- 1 | $rem 2 | JOBTYPE FORCE 3 | EXCHANGE B3LYP 4 | ! CORRELATION PBE 5 | ! UNRESTRICTED TRUE 6 | SCF_ALGORITHM rca_diis 7 | SCF_MAX_CYCLES 150 8 | BASIS 6-31G* 9 | ! BASIS LANL2DZ 10 | ! ECP LANL2DZ 11 | WAVEFUNCTION_ANALYSIS FALSE 12 | GEOM_OPT_MAX_CYCLES 300 13 | 14 | scf_convergence 6 15 | 16 | SYM_IGNORE TRUE 17 | SYMMETRY FALSE 18 | 19 | molden_format true 20 | $end 21 | 22 | 23 | $molecule 24 | 0 1 25 | -------------------------------------------------------------------------------- /TEST/ammoniaBorane/qchem/de-gsm/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 14 2 | Step 4 3 | N 1.42404391 -0.81362238 0.16432836 4 | B 1.91120439 0.72094317 -0.22413883 5 | B -2.35330285 -0.36214677 -0.26327912 6 | N -1.42908691 0.56361934 0.22417517 7 | H 0.42248853 -0.81199165 0.38582555 8 | H 1.93282356 -1.17333424 0.97200968 9 | H 1.57373286 -1.46150641 -0.60975022 10 | H 1.69255432 1.37924732 0.77052984 11 | H 3.08350510 0.63770092 -0.50771637 12 | H 1.21661838 1.03584692 -1.17276368 13 | H -2.23026857 -0.76469220 -1.38406550 14 | H -3.22416240 -0.75303043 0.45855394 15 | H -1.50321926 0.98359541 1.14279875 16 | H -0.69850405 0.99200398 -0.33889060 17 | 14 18 | Step 18 19 | N 0.67997031 -1.68795249 1.58958866 20 | B 0.75189698 1.24383924 -0.89412778 21 | B -0.94827614 0.38622710 -1.13772599 22 | N -0.23816136 0.74860471 0.19709107 23 | H -0.04839454 -2.25921752 2.01513996 24 | H 1.44294111 -1.63283109 2.26235003 25 | H 1.03293400 -2.21598277 0.79266125 26 | H 0.82297709 2.43387009 -1.00501563 27 | H 1.74137707 0.57557798 -0.99743196 28 | H 0.00591577 0.87195915 -1.95520338 29 | H -1.90677014 1.05629824 -1.39466826 30 | H -0.95908370 -0.78743159 -1.38072218 31 | H 0.07355444 -0.04777152 0.77821649 32 | H -0.68183590 1.47227448 0.75078672 33 | -------------------------------------------------------------------------------- /TEST/ammoniaBorane/qchem/de-gsm/stringfile.standard: -------------------------------------------------------------------------------- 1 | 14 2 | 0.000000 3 | N 1.424044 -0.813622 0.164328 4 | B 1.911204 0.720943 -0.224139 5 | B -2.353303 -0.362147 -0.263279 6 | N -1.429087 0.563619 0.224175 7 | H 0.422489 -0.811992 0.385826 8 | H 1.932824 -1.173334 0.972010 9 | H 1.573733 -1.461506 -0.609750 10 | H 1.692554 1.379247 0.770530 11 | H 3.083505 0.637701 -0.507716 12 | H 1.216618 1.035847 -1.172764 13 | H -2.230269 -0.764692 -1.384065 14 | H -3.224162 -0.753030 0.458554 15 | H -1.503219 0.983595 1.142799 16 | H -0.698504 0.992004 -0.338891 17 | 14 18 | 1.030116 19 | N 1.387924 -0.796895 0.316176 20 | B 1.900219 0.649500 -0.312526 21 | B -2.247689 -0.274713 -0.368981 22 | N -1.376442 0.606436 0.271641 23 | H 0.387382 -0.746233 0.527017 24 | H 1.900003 -1.036682 1.165562 25 | H 1.532730 -1.548926 -0.357671 26 | H 1.707083 1.468758 0.562764 27 | H 3.071781 0.486945 -0.566966 28 | H 1.201164 0.813170 -1.291393 29 | H -2.228353 -0.346838 -1.561889 30 | H -2.970588 -0.958205 0.297676 31 | H -1.384296 0.760263 1.271384 32 | H -0.743349 1.232306 -0.216516 33 | 14 34 | 6.561957 35 | N 1.329973 -0.839574 0.452457 36 | B 1.827775 0.568864 -0.376863 37 | B -2.065768 -0.185139 -0.459225 38 | N -1.414596 0.779467 0.305341 39 | H 0.345757 -0.914697 0.706672 40 | H 1.934709 -0.947617 1.264451 41 | H 1.553126 -1.577291 -0.214061 42 | H 1.723914 1.485459 0.409892 43 | H 2.978203 0.242325 -0.584935 44 | H 1.111624 0.643690 -1.345890 45 | H -2.237388 0.011022 -1.624666 46 | H -2.431284 -1.193299 0.078351 47 | H -1.224196 0.696404 1.294278 48 | H -1.041718 1.638126 -0.072321 49 | 14 50 | 26.578206 51 | N 1.188402 -0.981890 0.732609 52 | B 1.861115 0.770441 -0.522700 53 | B -1.977323 -0.116173 -0.553410 54 | N -1.365177 0.843507 0.248327 55 | H 0.322379 -1.398120 1.075304 56 | H 1.932691 -1.080457 1.417375 57 | H 1.467195 -1.530761 -0.077810 58 | H 1.882690 1.633731 0.307720 59 | H 2.828468 0.067221 -0.629069 60 | H 1.088060 0.863429 -1.435742 61 | H -2.422317 0.207110 -1.615680 62 | H -2.059038 -1.244581 -0.148263 63 | H -0.896327 0.647736 1.119901 64 | H -1.239457 1.808832 -0.020344 65 | 14 66 | 31.410545 67 | N 1.088765 -1.208783 1.139950 68 | B 1.859222 1.118609 -0.800762 69 | B -2.008890 -0.051930 -0.624440 70 | N -1.156273 0.720389 0.157579 71 | H 0.320760 -1.782136 1.489532 72 | H 1.848006 -1.305476 1.811843 73 | H 1.404304 -1.654438 0.280879 74 | H 1.851823 1.842236 0.149010 75 | H 2.638139 0.213640 -0.847674 76 | H 1.164942 1.354239 -1.741550 77 | H -2.767815 0.479310 -1.383714 78 | H -1.966814 -1.245977 -0.514334 79 | H -0.446047 0.308269 0.759537 80 | H -1.098321 1.726286 0.075693 81 | 14 82 | 30.194854 83 | N 0.996811 -1.490662 1.271656 84 | B 1.312799 1.234283 -0.968175 85 | B -1.659851 -0.024051 -0.708877 86 | N -0.922106 0.797614 0.154008 87 | H 0.149978 -1.969502 1.578786 88 | H 1.713181 -1.746020 1.950478 89 | H 1.256302 -1.928232 0.389626 90 | H 1.433632 2.031658 -0.084129 91 | H 1.945888 0.224478 -0.926998 92 | H 0.735744 1.549372 -1.964265 93 | H -2.294785 0.473156 -1.591218 94 | H -1.638227 -1.208029 -0.532079 95 | H -0.393896 0.420581 0.938114 96 | H -0.927236 1.806965 0.080137 97 | 14 98 | 22.832646 99 | N 0.936775 -1.525646 1.369134 100 | B 0.913751 1.141270 -0.941646 101 | B -1.340542 0.097476 -0.833864 102 | N -0.636066 0.821793 0.173890 103 | H 0.079674 -2.005145 1.647418 104 | H 1.621108 -1.774971 2.081730 105 | H 1.232316 -1.962424 0.498393 106 | H 1.266873 2.109692 -0.320224 107 | H 1.581683 0.153378 -0.865162 108 | H 0.380517 1.396648 -1.991496 109 | H -2.044846 0.679051 -1.596690 110 | H -1.220824 -1.089684 -0.844173 111 | H -0.200342 0.341272 0.965238 112 | H -0.781036 1.816352 0.291288 113 | 14 114 | 7.919647 115 | N 0.879581 -1.550891 1.509633 116 | B 0.753192 1.068553 -0.861120 117 | B -1.073316 0.305224 -1.055694 118 | N -0.442868 0.790678 0.217581 119 | H 0.038997 -2.077506 1.746967 120 | H 1.536169 -1.736741 2.266123 121 | H 1.254920 -1.980643 0.666393 122 | H 1.128895 2.195199 -0.676722 123 | H 1.549764 0.176344 -0.878413 124 | H 0.046345 1.085661 -1.916469 125 | H -1.949025 0.959387 -1.539185 126 | H -0.947139 -0.858748 -1.284865 127 | H -0.076619 0.182137 0.960196 128 | H -0.700324 1.715430 0.539413 129 | 14 130 | -2.432273 131 | N 0.679970 -1.687952 1.589589 132 | B 0.751897 1.243839 -0.894128 133 | B -0.948276 0.386227 -1.137726 134 | N -0.238161 0.748605 0.197091 135 | H -0.048395 -2.259218 2.015140 136 | H 1.442941 -1.632831 2.262350 137 | H 1.032934 -2.215983 0.792661 138 | H 0.822977 2.433870 -1.005016 139 | H 1.741377 0.575578 -0.997432 140 | H 0.005916 0.871959 -1.955203 141 | H -1.906770 1.056298 -1.394668 142 | H -0.959084 -0.787432 -1.380722 143 | H 0.073554 -0.047772 0.778216 144 | H -0.681836 1.472274 0.750787 145 | -------------------------------------------------------------------------------- /TEST/compare.py: -------------------------------------------------------------------------------- 1 | # Use this script to compare generated test stringfiles (stringfile.xyz000*) 2 | # with standard stringfiles (stringfile.standard) 3 | 4 | # for reading csv format files 5 | import csv 6 | 7 | # function to convert strings to float and skip conversion if the value is not a float 8 | def convertToFloat(inList): 9 | for element in inList: 10 | try: 11 | yield float(element) 12 | except ValueError: 13 | yield element 14 | 15 | # subtract two floats and for strings check their equality 16 | def subtractFloat(number1, number2): 17 | try: 18 | return (number1 - number2) 19 | except TypeError: 20 | if isinstance(number1, str) and isinstance(number2, str): 21 | if number1 == number2: 22 | return 0 23 | else: 24 | return 1 25 | else: 26 | return 1 27 | 28 | def main(): 29 | threshold = 0.2 30 | try: 31 | # read standard and output files 32 | standard = csv.reader(open('stringfile.standard', 'r'), delimiter=' ') 33 | currentOutput = csv.reader(open('stringfile.xyz0001', 'r'), delimiter=' ') 34 | # error if file does not exist 35 | except IOError: 36 | print("Error: File cannot be found!") 37 | exit(1) 38 | # loop over elements of two files simultaneously 39 | for rowStd, rowOut in zip(standard, currentOutput): 40 | rowStd = filter(None, rowStd) 41 | rowOut = filter(None, rowOut) 42 | for valStd, valOut in zip(list(convertToFloat(rowStd)), list(convertToFloat(rowOut))): 43 | # error if difference larger than threshold 44 | if ((subtractFloat(valStd, valOut)) > threshold): 45 | print ((subtractFloat(valStd, valOut))) 46 | exit(2) 47 | return 0 48 | 49 | if __name__ == "__main__": 50 | main() 51 | -------------------------------------------------------------------------------- /TEST/dielsAlder/gaussian/de-gsm/ggrad: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # The path to Gaussian should be added to PATH 3 | # If using another version of Gaussian, change g09 to your version 4 | 5 | if [ -z $2 ] 6 | then 7 | echo " need two arguments! " 8 | exit 9 | fi 10 | 11 | #echo " in ggrad: $1 $2 " 12 | 13 | # Remove check files if starting a new calculation 14 | chkfile=scratch/gfs$1.chk 15 | fchkfile=scratch/gfs$1.fchk 16 | gfile=scratch/gin$1.gjf 17 | molfile=scratch/structure$1 18 | ncpu=$2 19 | 20 | chkexists=0 21 | if [ -e $chkfile ] 22 | then 23 | chkexists=1 24 | fi 25 | 26 | #echo " chkfile: $chkfile gfile: $gfile molfile: $molfile ncpu: $ncpu" 27 | 28 | echo "%nprocshared=$ncpu " > $gfile 29 | echo "%chk=$chkfile " >> $gfile 30 | if [ $chkexists -eq 1 ] 31 | then 32 | echo "# guess=(read)" >> $gfile 33 | fi 34 | cat gstart >> $gfile 35 | cat $molfile >> $gfile 36 | echo " " >> $gfile 37 | echo " " >> $gfile 38 | echo " " >> $gfile 39 | echo " " >> $gfile 40 | echo " " >> $gfile 41 | echo " " >> $gfile 42 | 43 | #echo "running: g09 < $gfile >& $gfile.log" 44 | g09 < $gfile >& $gfile.log 45 | 46 | #check for SCF failure here 47 | gfail=`grep -c "Convergence failure" $gfile.log` 48 | if [ $gfail -ge 1 ] 49 | then 50 | echo " SCF failure in Gaussian " 51 | #present fix: use previous gradient 52 | else 53 | #echo "running: formchk $chkfile $fchkfile" 54 | formchk $chkfile $fchkfile > scratch/fchkout 55 | fi 56 | -------------------------------------------------------------------------------- /TEST/dielsAlder/gaussian/de-gsm/gscreate: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | file=molecule 4 | 5 | #nl $file > tmp.mole 6 | #nl link > tmp.link 7 | #join tmp.mole tmp.link > tmp.geom2 8 | #awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom 9 | 10 | #cat qstart tmp.geom qend > qcin 11 | #cat qstart molecule$1 qend > scratch/qcin$1 12 | cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 13 | 14 | #rm tmp.geom tmp.geom2 tmp.link tmp.mole 15 | -------------------------------------------------------------------------------- /TEST/dielsAlder/gaussian/de-gsm/gstart: -------------------------------------------------------------------------------- 1 | # B3LYP/6-31G** nosymm Force test 2 | 3 | Title Card Required 4 | 5 | 0 1 6 | -------------------------------------------------------------------------------- /TEST/dielsAlder/gaussian/de-gsm/inpfileq: -------------------------------------------------------------------------------- 1 | 2 | # FSM/GSM/SSM inpfileq 3 | 4 | ------------- QCHEM Scratch Info ------------------------ 5 | $QCSCRATCH/ # path for scratch dir. end with "/" 6 | GSM_go1q # name of run 7 | --------------------------------------------------------- 8 | 9 | ------------ String Info -------------------------------- 10 | SM_TYPE GSM # SSM, FSM or GSM 11 | RESTART 0 # read restart.xyz 12 | MAX_OPT_ITERS 80 # maximum iterations 13 | STEP_OPT_ITERS 30 # for FSM/SSM 14 | CONV_TOL 0.0005 # perp grad 15 | ADD_NODE_TOL 0.1 # for GSM 16 | SCALING 1.0 # for opt steps 17 | SSM_DQMAX 0.8 # add step size 18 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 19 | INT_THRESH 2.0 # intermediate detection 20 | MIN_SPACING 5.0 # node spacing SSM 21 | BOND_FRAGMENTS 1 # make IC's for fragments 22 | INITIAL_OPT 0 # opt steps first node 23 | FINAL_OPT 150 # opt steps last SSM node 24 | PRODUCT_LIMIT 100.0 # kcal/mol 25 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 26 | NNODES 9 # including endpoints 27 | --------------------------------------------------------- 28 | -------------------------------------------------------------------------------- /TEST/dielsAlder/gaussian/de-gsm/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | Step 35 3 | C -1.06001665 -1.51714564 0.05288674 4 | C -1.82955412 -0.59408623 -0.53968755 5 | C -2.01260392 0.79370866 -0.08977969 6 | C -1.09740592 1.54095108 0.54110413 7 | C 3.01841440 -0.33274049 0.53420511 8 | C 2.48267950 0.16990394 -0.57660955 9 | H -2.40063347 -0.88235561 -1.42321617 10 | H -0.51365172 -1.30383154 0.96828855 11 | H -0.96688964 -2.52122005 -0.35117707 12 | H 3.89171154 0.11254122 1.00536203 13 | H 2.60849064 -1.21591676 1.01902222 14 | H 1.60806045 -0.27640639 -1.04373753 15 | H 2.89526366 1.05096138 -1.06301386 16 | H -1.32088987 2.55628492 0.85667305 17 | H -0.09454533 1.17390089 0.74481476 18 | H -2.98142355 1.23828062 -0.32070817 19 | 16 20 | Step 22 21 | C 0.01856467 -1.50510245 0.07175535 22 | C -1.25472580 -0.70291222 -0.04828280 23 | C -1.28551058 0.63324180 -0.08527776 24 | C -0.04811068 1.49696591 -0.04422009 25 | C 1.21601433 -0.63168912 0.47947978 26 | C 1.22945185 0.68482088 -0.31033881 27 | H -2.18794361 -1.26282927 -0.10437525 28 | H -0.12133841 -2.31635373 0.79987325 29 | H 0.22663560 -2.00643122 -0.88734886 30 | H 1.14834814 -0.40532251 1.55280900 31 | H 2.15327210 -1.18259709 0.33198960 32 | H 1.29564501 0.45837391 -1.38389788 33 | H 2.11591575 1.28013898 -0.05856919 34 | H -0.13761965 2.30980257 -0.77849415 35 | H 0.01956981 1.99500653 0.93644690 36 | H -2.24481452 1.14593304 -0.15154508 37 | -------------------------------------------------------------------------------- /TEST/dielsAlder/gaussian/de-gsm/stringfile.intel: -------------------------------------------------------------------------------- 1 | 16 2 | 0.000000 3 | C -1.060017 -1.517146 0.052887 4 | C -1.829554 -0.594086 -0.539688 5 | C -2.012604 0.793709 -0.089780 6 | C -1.097406 1.540951 0.541104 7 | C 3.018414 -0.332740 0.534205 8 | C 2.482680 0.169904 -0.576610 9 | H -2.400633 -0.882356 -1.423216 10 | H -0.513652 -1.303832 0.968289 11 | H -0.966890 -2.521220 -0.351177 12 | H 3.891712 0.112541 1.005362 13 | H 2.608491 -1.215917 1.019022 14 | H 1.608060 -0.276406 -1.043738 15 | H 2.895264 1.050961 -1.063014 16 | H -1.320890 2.556285 0.856673 17 | H -0.094545 1.173901 0.744815 18 | H -2.981424 1.238281 -0.320708 19 | 16 20 | 0.503265 21 | C -0.913693 -1.533920 0.187535 22 | C -1.715834 -0.669323 -0.449377 23 | C -1.853523 0.768826 -0.177249 24 | C -0.976031 1.554471 0.462792 25 | C 2.754827 -0.444767 0.459848 26 | C 2.345252 0.340066 -0.535259 27 | H -2.354806 -1.052981 -1.245076 28 | H -0.277729 -1.232657 1.015056 29 | H -0.880256 -2.581236 -0.097556 30 | H 3.443429 -0.090113 1.222349 31 | H 2.424180 -1.476912 0.551659 32 | H 1.655274 -0.010861 -1.298403 33 | H 2.683290 1.369028 -0.625497 34 | H -1.186199 2.609281 0.618596 35 | H -0.023721 1.188334 0.836940 36 | H -2.766542 1.225080 -0.561386 37 | 16 38 | 1.478707 39 | C -0.861998 -1.563986 0.404869 40 | C -1.610255 -0.745223 -0.348725 41 | C -1.661553 0.722049 -0.286403 42 | C -0.858636 1.531658 0.419396 43 | C 2.515212 -0.510098 0.277975 44 | C 2.227147 0.531403 -0.501631 45 | H -2.252920 -1.195812 -1.105492 46 | H -0.213910 -1.202666 1.198192 47 | H -0.893088 -2.638580 0.254991 48 | H 2.963445 -0.376851 1.253791 49 | H 2.328411 -1.536024 -0.031480 50 | H 1.786129 0.413693 -1.487416 51 | H 2.436669 1.544962 -0.189599 52 | H -0.990094 2.610242 0.381946 53 | H -0.056499 1.160977 1.048591 54 | H -2.427707 1.182272 -0.910522 55 | 16 56 | 7.768310 57 | C -0.694401 -1.555219 0.566954 58 | C -1.409037 -0.788118 -0.276692 59 | C -1.408503 0.670289 -0.335146 60 | C -0.642082 1.491333 0.408355 61 | C 2.098115 -0.536818 0.095852 62 | C 1.918351 0.647724 -0.496836 63 | H -1.978090 -1.287588 -1.058147 64 | H -0.207856 -1.162951 1.453926 65 | H -0.690055 -2.635066 0.455849 66 | H 2.406164 -0.601592 1.137283 67 | H 2.050511 -1.474848 -0.446970 68 | H 1.673959 0.722971 -1.552107 69 | H 2.174154 1.579420 -0.001249 70 | H -0.663551 2.566127 0.244935 71 | H -0.129262 1.156140 1.302634 72 | H -2.016253 1.111022 -1.124052 73 | 16 74 | 21.282304 75 | C -0.420065 -1.450991 0.602170 76 | C -1.267918 -0.774980 -0.254761 77 | C -1.288378 0.627059 -0.367026 78 | C -0.402531 1.422148 0.345203 79 | C 1.704845 -0.591876 0.045104 80 | C 1.521729 0.700931 -0.418476 81 | H -1.793080 -1.349532 -1.016777 82 | H -0.131266 -1.042542 1.563179 83 | H -0.336445 -2.532254 0.524129 84 | H 2.140135 -0.748948 1.029048 85 | H 1.771672 -1.433677 -0.633436 86 | H 1.319589 0.855739 -1.473978 87 | H 1.997953 1.536999 0.085260 88 | H -0.380427 2.497249 0.180912 89 | H -0.083677 1.114926 1.335463 90 | H -1.844219 1.068190 -1.192727 91 | 16 92 | -19.514758 93 | C -0.121710 -1.360030 0.547036 94 | C -1.198293 -0.734401 -0.263898 95 | C -1.262951 0.601912 -0.369661 96 | C -0.178504 1.380599 0.264363 97 | C 1.373395 -0.677212 0.112676 98 | C 1.215082 0.748115 -0.386622 99 | H -1.809277 -1.374450 -0.903481 100 | H -0.087476 -1.079289 1.609899 101 | H -0.030985 -2.433651 0.396546 102 | H 1.935963 -0.739667 1.047057 103 | H 1.677654 -1.416494 -0.638508 104 | H 1.088938 0.870928 -1.460039 105 | H 1.914519 1.474572 0.046754 106 | H -0.162039 2.457696 0.083924 107 | H 0.013002 1.155692 1.322696 108 | H -1.916561 1.055618 -1.102434 109 | 16 110 | -40.165897 111 | C -0.043623 -1.423077 0.390002 112 | C -1.223127 -0.719757 -0.238884 113 | C -1.285293 0.613962 -0.306375 114 | C -0.110586 1.437987 0.163482 115 | C 1.318646 -0.663727 0.234651 116 | C 1.184632 0.760641 -0.336631 117 | H -2.032975 -1.333259 -0.629732 118 | H -0.241272 -1.544574 1.466719 119 | H 0.042156 -2.441162 -0.008256 120 | H 1.800834 -0.611532 1.217946 121 | H 1.980913 -1.254794 -0.408071 122 | H 1.146721 0.721784 -1.431312 123 | H 2.057204 1.364794 -0.058570 124 | H -0.174954 2.478161 -0.177460 125 | H -0.073788 1.463947 1.263079 126 | H -2.135680 1.108914 -0.770283 127 | 16 128 | -43.214570 129 | C -0.007661 -1.482510 0.230453 130 | C -1.237173 -0.698801 -0.159634 131 | C -1.283676 0.635135 -0.217117 132 | C -0.067752 1.480176 0.079108 133 | C 1.279518 -0.625953 0.387462 134 | C 1.200066 0.722435 -0.344938 135 | H -2.121743 -1.282044 -0.414854 136 | H -0.206122 -2.005653 1.177658 137 | H 0.151274 -2.282523 -0.507028 138 | H 1.466382 -0.438148 1.452951 139 | H 2.139088 -1.198964 0.019662 140 | H 1.161754 0.542552 -1.427965 141 | H 2.097406 1.320196 -0.141447 142 | H -0.136224 2.459830 -0.408696 143 | H -0.011210 1.675265 1.162354 144 | H -2.199823 1.133758 -0.529905 145 | 16 146 | -45.754017 147 | C 0.018565 -1.505102 0.071755 148 | C -1.254726 -0.702912 -0.048283 149 | C -1.285511 0.633242 -0.085278 150 | C -0.048111 1.496966 -0.044220 151 | C 1.216014 -0.631689 0.479480 152 | C 1.229452 0.684821 -0.310339 153 | H -2.187944 -1.262829 -0.104375 154 | H -0.121338 -2.316354 0.799873 155 | H 0.226636 -2.006431 -0.887349 156 | H 1.148348 -0.405323 1.552809 157 | H 2.153272 -1.182597 0.331990 158 | H 1.295645 0.458374 -1.383898 159 | H 2.115916 1.280139 -0.058569 160 | H -0.137620 2.309803 -0.778494 161 | H 0.019570 1.995007 0.936447 162 | H -2.244815 1.145933 -0.151545 163 | -------------------------------------------------------------------------------- /TEST/dielsAlder/gaussian/ggrad: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # The path to Gaussian should be added to PATH 3 | # If using another version of Gaussian, change g09 to your version 4 | 5 | if [ -z $2 ] 6 | then 7 | echo " need two arguments! " 8 | exit 9 | fi 10 | 11 | #echo " in ggrad: $1 $2 " 12 | 13 | # Remove check files if starting a new calculation 14 | chkfile=scratch/gfs$1.chk 15 | fchkfile=scratch/gfs$1.fchk 16 | gfile=scratch/gin$1.gjf 17 | molfile=scratch/structure$1 18 | ncpu=$2 19 | 20 | chkexists=0 21 | if [ -e $chkfile ] 22 | then 23 | chkexists=1 24 | fi 25 | 26 | #echo " chkfile: $chkfile gfile: $gfile molfile: $molfile ncpu: $ncpu" 27 | 28 | echo "%nprocshared=$ncpu " > $gfile 29 | echo "%chk=$chkfile " >> $gfile 30 | if [ $chkexists -eq 1 ] 31 | then 32 | echo "# guess=(read)" >> $gfile 33 | fi 34 | cat gstart >> $gfile 35 | cat $molfile >> $gfile 36 | echo " " >> $gfile 37 | echo " " >> $gfile 38 | echo " " >> $gfile 39 | echo " " >> $gfile 40 | echo " " >> $gfile 41 | echo " " >> $gfile 42 | 43 | #echo "running: g09 < $gfile >& $gfile.log" 44 | g09 < $gfile >& $gfile.log 45 | 46 | #check for SCF failure here 47 | gfail=`grep -c "Convergence failure" $gfile.log` 48 | if [ $gfail -ge 1 ] 49 | then 50 | echo " SCF failure in Gaussian " 51 | #present fix: use previous gradient 52 | else 53 | #echo "running: formchk $chkfile $fchkfile" 54 | formchk $chkfile $fchkfile > scratch/fchkout 55 | fi 56 | -------------------------------------------------------------------------------- /TEST/dielsAlder/gaussian/gstart: -------------------------------------------------------------------------------- 1 | # B3LYP/6-31G** nosymm Force test 2 | 3 | Title Card Required 4 | 5 | 0 1 6 | -------------------------------------------------------------------------------- /TEST/dielsAlder/gaussian/se-gsm/ISOMERS0001: -------------------------------------------------------------------------------- 1 | NEW 2 | ADD 6 4 3 | ADD 5 1 4 | -------------------------------------------------------------------------------- /TEST/dielsAlder/gaussian/se-gsm/ggrad: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # The path to Gaussian should be added to PATH 3 | # If using another version of Gaussian, change g09 to your version 4 | 5 | if [ -z $2 ] 6 | then 7 | echo " need two arguments! " 8 | exit 9 | fi 10 | 11 | #echo " in ggrad: $1 $2 " 12 | 13 | # Remove check files if starting a new calculation 14 | chkfile=scratch/gfs$1.chk 15 | fchkfile=scratch/gfs$1.fchk 16 | gfile=scratch/gin$1.gjf 17 | molfile=scratch/structure$1 18 | ncpu=$2 19 | 20 | chkexists=0 21 | if [ -e $chkfile ] 22 | then 23 | chkexists=1 24 | fi 25 | 26 | #echo " chkfile: $chkfile gfile: $gfile molfile: $molfile ncpu: $ncpu" 27 | 28 | echo "%nprocshared=$ncpu " > $gfile 29 | echo "%chk=$chkfile " >> $gfile 30 | if [ $chkexists -eq 1 ] 31 | then 32 | echo "# guess=(read)" >> $gfile 33 | fi 34 | cat gstart >> $gfile 35 | cat $molfile >> $gfile 36 | echo " " >> $gfile 37 | echo " " >> $gfile 38 | echo " " >> $gfile 39 | echo " " >> $gfile 40 | echo " " >> $gfile 41 | echo " " >> $gfile 42 | 43 | #echo "running: g09 < $gfile >& $gfile.log" 44 | g09 < $gfile >& $gfile.log 45 | 46 | #check for SCF failure here 47 | gfail=`grep -c "Convergence failure" $gfile.log` 48 | if [ $gfail -ge 1 ] 49 | then 50 | echo " SCF failure in Gaussian " 51 | #present fix: use previous gradient 52 | else 53 | #echo "running: formchk $chkfile $fchkfile" 54 | formchk $chkfile $fchkfile > scratch/fchkout 55 | fi 56 | -------------------------------------------------------------------------------- /TEST/dielsAlder/gaussian/se-gsm/gscreate: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | file=molecule 4 | 5 | #nl $file > tmp.mole 6 | #nl link > tmp.link 7 | #join tmp.mole tmp.link > tmp.geom2 8 | #awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom 9 | 10 | #cat qstart tmp.geom qend > qcin 11 | #cat qstart molecule$1 qend > scratch/qcin$1 12 | cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 13 | 14 | #rm tmp.geom tmp.geom2 tmp.link tmp.mole 15 | -------------------------------------------------------------------------------- /TEST/dielsAlder/gaussian/se-gsm/gstart: -------------------------------------------------------------------------------- 1 | # B3LYP/6-31G** nosymm Force test 2 | 3 | Title Card Required 4 | 5 | 0 1 6 | -------------------------------------------------------------------------------- /TEST/dielsAlder/gaussian/se-gsm/inpfileq: -------------------------------------------------------------------------------- 1 | 2 | # FSM/GSM/SSM inpfileq 3 | 4 | ------------- QCHEM Scratch Info ------------------------ 5 | $QCSCRATCH/ # path for scratch dir. end with "/" 6 | GSM_go1q # name of run 7 | --------------------------------------------------------- 8 | 9 | ------------ String Info -------------------------------- 10 | SM_TYPE SSM # SSM, FSM or GSM 11 | RESTART 0 # read restart.xyz 12 | MAX_OPT_ITERS 80 # maximum iterations 13 | STEP_OPT_ITERS 30 # for FSM/SSM 14 | CONV_TOL 0.0005 # perp grad 15 | ADD_NODE_TOL 0.1 # for GSM 16 | SCALING 1.0 # for opt steps 17 | SSM_DQMAX 0.8 # add step size 18 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 19 | INT_THRESH 2.0 # intermediate detection 20 | MIN_SPACING 5.0 # node spacing SSM 21 | BOND_FRAGMENTS 1 # make IC's for fragments 22 | INITIAL_OPT 0 # opt steps first node 23 | FINAL_OPT 150 # opt steps last SSM node 24 | PRODUCT_LIMIT 100.0 # kcal/mol 25 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 26 | NNODES 20 # including endpoints 27 | --------------------------------------------------------- 28 | -------------------------------------------------------------------------------- /TEST/dielsAlder/gaussian/se-gsm/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | Step 35 3 | C -1.06001665 -1.51714564 0.05288674 4 | C -1.82955412 -0.59408623 -0.53968755 5 | C -2.01260392 0.79370866 -0.08977969 6 | C -1.09740592 1.54095108 0.54110413 7 | C 3.01841440 -0.33274049 0.53420511 8 | C 2.48267950 0.16990394 -0.57660955 9 | H -2.40063347 -0.88235561 -1.42321617 10 | H -0.51365172 -1.30383154 0.96828855 11 | H -0.96688964 -2.52122005 -0.35117707 12 | H 3.89171154 0.11254122 1.00536203 13 | H 2.60849064 -1.21591676 1.01902222 14 | H 1.60806045 -0.27640639 -1.04373753 15 | H 2.89526366 1.05096138 -1.06301386 16 | H -1.32088987 2.55628492 0.85667305 17 | H -0.09454533 1.17390089 0.74481476 18 | H -2.98142355 1.23828062 -0.32070817 19 | 16 20 | Step 22 21 | C 0.01856467 -1.50510245 0.07175535 22 | C -1.25472580 -0.70291222 -0.04828280 23 | C -1.28551058 0.63324180 -0.08527776 24 | C -0.04811068 1.49696591 -0.04422009 25 | C 1.21601433 -0.63168912 0.47947978 26 | C 1.22945185 0.68482088 -0.31033881 27 | H -2.18794361 -1.26282927 -0.10437525 28 | H -0.12133841 -2.31635373 0.79987325 29 | H 0.22663560 -2.00643122 -0.88734886 30 | H 1.14834814 -0.40532251 1.55280900 31 | H 2.15327210 -1.18259709 0.33198960 32 | H 1.29564501 0.45837391 -1.38389788 33 | H 2.11591575 1.28013898 -0.05856919 34 | H -0.13761965 2.30980257 -0.77849415 35 | H 0.01956981 1.99500653 0.93644690 36 | H -2.24481452 1.14593304 -0.15154508 37 | -------------------------------------------------------------------------------- /TEST/dielsAlder/mopac/de-gsm/inpfileq: -------------------------------------------------------------------------------- 1 | # FSM/GSM/SSM inpfileq 2 | 3 | ------------- QCHEM Scratch Info ------------------------ 4 | $QCSCRATCH/ # path for scratch dir. end with "/" 5 | GSM_go1q # name of run 6 | --------------------------------------------------------- 7 | 8 | ------------ String Info -------------------------------- 9 | SM_TYPE GSM # SSM, FSM or GSM 10 | RESTART 0 # read restart.xyz 11 | MAX_OPT_ITERS 80 # maximum iterations 12 | STEP_OPT_ITERS 30 # for FSM/SSM 13 | CONV_TOL 0.0005 # perp grad 14 | ADD_NODE_TOL 0.1 # for GSM 15 | SCALING 1.0 # for opt steps 16 | SSM_DQMAX 0.8 # add step size 17 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 18 | INT_THRESH 2.0 # intermediate detection 19 | MIN_SPACING 5.0 # node spacing SSM 20 | BOND_FRAGMENTS 1 # make IC's for fragments 21 | INITIAL_OPT 0 # opt steps first node 22 | FINAL_OPT 150 # opt steps last SSM node 23 | PRODUCT_LIMIT 100.0 # kcal/mol 24 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 25 | NNODES 9 # including endpoints 26 | --------------------------------------------------------- 27 | -------------------------------------------------------------------------------- /TEST/dielsAlder/mopac/de-gsm/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C -1.037225935 -1.575057079 0.267707912 4 | C -1.708337045 -0.692852836 -0.473272941 5 | C -1.940300404 0.707404075 -0.088479364 6 | C -1.009041948 1.497621701 0.446255054 7 | C 2.732868692 -0.399002174 0.382328885 8 | C 2.511914031 0.465946545 -0.599791985 9 | H -2.143698307 -0.972175001 -1.437026627 10 | H -0.604491208 -1.340650761 1.230189495 11 | H -0.877954350 -2.600126276 -0.033220247 12 | H 3.637983428 -0.412060550 0.974372413 13 | H 2.025495997 -1.165771090 0.670414088 14 | H 1.605947473 0.476343117 -1.192479427 15 | H 3.218026083 1.231192741 -0.891866332 16 | H -1.184626031 2.531163345 0.706314557 17 | H 0.000968997 1.169351717 0.656481639 18 | H -2.951061069 1.071129245 -0.293712793 19 | 16 20 | 21 | C 0.020341526 -1.496218373 0.058645511 22 | C -1.252780557 -0.711946442 -0.072432699 23 | C -1.293528451 0.622754843 -0.135300138 24 | C -0.070828081 1.489109844 -0.053029021 25 | C 1.214362608 -0.621210736 0.473790004 26 | C 1.222148922 0.698487297 -0.309128963 27 | H -2.158648998 -1.313484501 -0.128547977 28 | H -0.114950764 -2.316203080 0.791886225 29 | H 0.235607739 -1.989611408 -0.913009420 30 | H 1.160153427 -0.406733507 1.558378455 31 | H 2.159983399 -1.169252234 0.309815327 32 | H 1.318154252 0.486249766 -1.391273973 33 | H 2.102026514 1.305572159 -0.030670432 34 | H -0.148426579 2.325855087 -0.774547169 35 | H -0.035454506 1.955341019 0.954403786 36 | H -2.233314668 1.162539924 -0.235848986 37 | -------------------------------------------------------------------------------- /TEST/dielsAlder/mopac/de-gsm/stringfile.standard: -------------------------------------------------------------------------------- 1 | 16 2 | 0.000000 3 | C -1.037226 -1.575057 0.267708 4 | C -1.708337 -0.692853 -0.473273 5 | C -1.940300 0.707404 -0.088479 6 | C -1.009042 1.497622 0.446255 7 | C 2.732869 -0.399002 0.382329 8 | C 2.511914 0.465947 -0.599792 9 | H -2.143698 -0.972175 -1.437027 10 | H -0.604491 -1.340651 1.230189 11 | H -0.877954 -2.600126 -0.033220 12 | H 3.637983 -0.412061 0.974372 13 | H 2.025496 -1.165771 0.670414 14 | H 1.605947 0.476343 -1.192479 15 | H 3.218026 1.231193 -0.891866 16 | H -1.184626 2.531163 0.706315 17 | H 0.000969 1.169352 0.656482 18 | H -2.951061 1.071129 -0.293713 19 | 16 20 | 0.065310 21 | C -0.881227 -1.557393 0.272088 22 | C -1.610064 -0.713467 -0.460324 23 | C -1.801024 0.711054 -0.152196 24 | C -0.890612 1.487041 0.437951 25 | C 2.516894 -0.421962 0.383741 26 | C 2.332001 0.487098 -0.565349 27 | H -2.131418 -1.053644 -1.358624 28 | H -0.360952 -1.269568 1.174926 29 | H -0.761400 -2.601536 0.023569 30 | H 3.282981 -0.341264 1.145961 31 | H 1.919776 -1.320261 0.475426 32 | H 1.563600 0.411668 -1.325032 33 | H 2.931619 1.380162 -0.657183 34 | H -1.050398 2.537562 0.636875 35 | H 0.082037 1.136030 0.758548 36 | H -2.766779 1.113634 -0.463469 37 | 16 38 | 0.506110 39 | C -0.796213 -1.546366 0.316857 40 | C -1.581470 -0.741371 -0.402069 41 | C -1.689394 0.712253 -0.231819 42 | C -0.804860 1.477922 0.409772 43 | C 2.400950 -0.465178 0.325678 44 | C 2.196365 0.542582 -0.513453 45 | H -2.215361 -1.148859 -1.197479 46 | H -0.163997 -1.207652 1.125446 47 | H -0.738437 -2.611869 0.147557 48 | H 2.978108 -0.369047 1.235955 49 | H 2.015322 -1.464875 0.172962 50 | H 1.613410 0.461604 -1.420321 51 | H 2.595213 1.535082 -0.355424 52 | H -0.906494 2.551454 0.489679 53 | H 0.083333 1.097796 0.898836 54 | H -2.571812 1.156786 -0.702092 55 | 16 56 | 0.880430 57 | C -0.773656 -1.546591 0.472532 58 | C -1.491325 -0.778970 -0.351364 59 | C -1.516592 0.689471 -0.330509 60 | C -0.734188 1.456596 0.432272 61 | C 2.272667 -0.488455 0.166942 62 | C 2.053222 0.632231 -0.510071 63 | H -2.118514 -1.231139 -1.125406 64 | H -0.146620 -1.158463 1.263531 65 | H -0.766659 -2.625765 0.414225 66 | H 2.685318 -0.509616 1.165315 67 | H 2.054867 -1.473402 -0.223612 68 | H 1.633976 0.653653 -1.508679 69 | H 2.286377 1.616590 -0.127518 70 | H -0.766468 2.535261 0.411078 71 | H -0.011460 1.064033 1.135358 72 | H -2.234327 1.140548 -1.022353 73 | 16 74 | 4.734660 75 | C -0.878653 -1.655783 0.622469 76 | C -1.425230 -0.866669 -0.308849 77 | C -1.251858 0.587183 -0.380542 78 | C -0.488954 1.298446 0.454910 79 | C 2.132875 -0.307538 0.035760 80 | C 1.822029 0.839205 -0.565831 81 | H -2.036980 -1.298229 -1.109032 82 | H -0.268635 -1.292091 1.440143 83 | H -1.007304 -2.729808 0.625769 84 | H 2.531295 -0.358842 1.038453 85 | H 1.963165 -1.279964 -0.411926 86 | H 1.453384 0.882774 -1.581722 87 | H 2.114963 1.803252 -0.172116 88 | H -0.410434 2.376656 0.387283 89 | H -0.075423 0.897178 1.369427 90 | H -1.751796 1.073410 -1.226178 91 | 16 92 | 19.862190 93 | C -0.936904 -1.758158 0.666023 94 | C -1.403170 -0.931289 -0.304680 95 | C -1.096471 0.459894 -0.432923 96 | C -0.208516 1.170519 0.387715 97 | C 2.083203 -0.140715 0.019883 98 | C 1.544146 1.014178 -0.514757 99 | H -2.076998 -1.336546 -1.068278 100 | H -0.282889 -1.436396 1.459186 101 | H -1.194052 -2.804456 0.699992 102 | H 2.648762 -0.143011 0.934258 103 | H 1.912961 -1.111272 -0.410950 104 | H 1.176104 1.022702 -1.538194 105 | H 1.911065 1.985654 -0.189011 106 | H -0.229192 2.256279 0.365238 107 | H 0.074000 0.770541 1.357724 108 | H -1.556636 0.985251 -1.269557 109 | 16 110 | 9.543110 111 | C -0.259513 -1.416306 0.561108 112 | C -1.184493 -0.746664 -0.327551 113 | C -1.215408 0.595876 -0.463874 114 | C -0.190163 1.308990 0.299073 115 | C 1.483214 -0.546741 0.097788 116 | C 1.188923 0.810311 -0.426922 117 | H -1.789512 -1.378472 -0.983300 118 | H 0.066218 -1.074205 1.538478 119 | H -0.219200 -2.489995 0.457589 120 | H 2.005453 -0.582724 1.041541 121 | H 1.528331 -1.429858 -0.521695 122 | H 1.021584 0.864326 -1.508456 123 | H 1.854981 1.618954 -0.091635 124 | H -0.190559 2.404694 0.293960 125 | H -0.050903 0.958019 1.337631 126 | H -1.855245 1.110842 -1.164070 127 | 16 128 | -45.764830 129 | C -0.032995 -1.430824 0.318130 130 | C -1.213111 -0.716288 -0.273258 131 | C -1.279329 0.617461 -0.345462 132 | C -0.122122 1.445331 0.132950 133 | C 1.299930 -0.642627 0.279896 134 | C 1.179943 0.762785 -0.326191 135 | H -2.011589 -1.358452 -0.639483 136 | H -0.268867 -1.662777 1.379502 137 | H 0.104625 -2.407920 -0.185292 138 | H 1.698181 -0.567336 1.307960 139 | H 2.037251 -1.226545 -0.298564 140 | H 1.174664 0.683124 -1.431925 141 | H 2.053647 1.379201 -0.054076 142 | H -0.174029 2.486566 -0.226458 143 | H -0.141820 1.489050 1.241376 144 | H -2.124519 1.146835 -0.773733 145 | 16 146 | -48.332610 147 | C 0.020342 -1.496218 0.058646 148 | C -1.252781 -0.711946 -0.072433 149 | C -1.293528 0.622755 -0.135300 150 | C -0.070828 1.489110 -0.053029 151 | C 1.214363 -0.621211 0.473790 152 | C 1.222149 0.698487 -0.309129 153 | H -2.158649 -1.313485 -0.128548 154 | H -0.114951 -2.316203 0.791886 155 | H 0.235608 -1.989611 -0.913009 156 | H 1.160153 -0.406734 1.558378 157 | H 2.159983 -1.169252 0.309815 158 | H 1.318154 0.486250 -1.391274 159 | H 2.102027 1.305572 -0.030670 160 | H -0.148427 2.325855 -0.774547 161 | H -0.035455 1.955341 0.954404 162 | H -2.233315 1.162540 -0.235849 163 | -------------------------------------------------------------------------------- /TEST/dielsAlder/mopac/se-gsm/ISOMERS0001: -------------------------------------------------------------------------------- 1 | NEW 2 | ADD 6 4 3 | ADD 5 1 4 | -------------------------------------------------------------------------------- /TEST/dielsAlder/mopac/se-gsm/inpfileq: -------------------------------------------------------------------------------- 1 | 2 | # FSM/GSM/SSM inpfileq 3 | 4 | ------------- QCHEM Scratch Info ------------------------ 5 | $QCSCRATCH/ # path for scratch dir. end with "/" 6 | GSM_go1q # name of run 7 | --------------------------------------------------------- 8 | 9 | ------------ String Info -------------------------------- 10 | SM_TYPE SSM # SSM, FSM or GSM 11 | RESTART 0 # read restart.xyz 12 | MAX_OPT_ITERS 80 # maximum iterations 13 | STEP_OPT_ITERS 30 # for FSM/SSM 14 | CONV_TOL 0.0005 # perp grad 15 | ADD_NODE_TOL 0.1 # for GSM 16 | SCALING 1.0 # for opt steps 17 | SSM_DQMAX 0.8 # add step size 18 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 19 | INT_THRESH 2.0 # intermediate detection 20 | MIN_SPACING 5.0 # node spacing SSM 21 | BOND_FRAGMENTS 1 # make IC's for fragments 22 | INITIAL_OPT 0 # opt steps first node 23 | FINAL_OPT 150 # opt steps last SSM node 24 | PRODUCT_LIMIT 100.0 # kcal/mol 25 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 26 | NNODES 20 # including endpoints 27 | --------------------------------------------------------- 28 | -------------------------------------------------------------------------------- /TEST/dielsAlder/mopac/se-gsm/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C -1.037225935 -1.575057079 0.267707912 4 | C -1.708337045 -0.692852836 -0.473272941 5 | C -1.940300404 0.707404075 -0.088479364 6 | C -1.009041948 1.497621701 0.446255054 7 | C 2.732868692 -0.399002174 0.382328885 8 | C 2.511914031 0.465946545 -0.599791985 9 | H -2.143698307 -0.972175001 -1.437026627 10 | H -0.604491208 -1.340650761 1.230189495 11 | H -0.877954350 -2.600126276 -0.033220247 12 | H 3.637983428 -0.412060550 0.974372413 13 | H 2.025495997 -1.165771090 0.670414088 14 | H 1.605947473 0.476343117 -1.192479427 15 | H 3.218026083 1.231192741 -0.891866332 16 | H -1.184626031 2.531163345 0.706314557 17 | H 0.000968997 1.169351717 0.656481639 18 | H -2.951061069 1.071129245 -0.293712793 19 | 16 20 | 21 | C 0.020341526 -1.496218373 0.058645511 22 | C -1.252780557 -0.711946442 -0.072432699 23 | C -1.293528451 0.622754843 -0.135300138 24 | C -0.070828081 1.489109844 -0.053029021 25 | C 1.214362608 -0.621210736 0.473790004 26 | C 1.222148922 0.698487297 -0.309128963 27 | H -2.158648998 -1.313484501 -0.128547977 28 | H -0.114950764 -2.316203080 0.791886225 29 | H 0.235607739 -1.989611408 -0.913009420 30 | H 1.160153427 -0.406733507 1.558378455 31 | H 2.159983399 -1.169252234 0.309815327 32 | H 1.318154252 0.486249766 -1.391273973 33 | H 2.102026514 1.305572159 -0.030670432 34 | H -0.148426579 2.325855087 -0.774547169 35 | H -0.035454506 1.955341019 0.954403786 36 | H -2.233314668 1.162539924 -0.235848986 37 | -------------------------------------------------------------------------------- /TEST/dielsAlder/mopac/se-gsm/stringfile.standard: -------------------------------------------------------------------------------- 1 | 16 2 | 0.000000 3 | C -1.037226 -1.575057 0.267708 4 | C -1.708337 -0.692853 -0.473273 5 | C -1.940300 0.707404 -0.088479 6 | C -1.009042 1.497622 0.446255 7 | C 2.732869 -0.399002 0.382329 8 | C 2.511914 0.465947 -0.599792 9 | H -2.143698 -0.972175 -1.437027 10 | H -0.604491 -1.340651 1.230189 11 | H -0.877954 -2.600126 -0.033220 12 | H 3.637983 -0.412061 0.974372 13 | H 2.025496 -1.165771 0.670414 14 | H 1.605947 0.476343 -1.192479 15 | H 3.218026 1.231193 -0.891866 16 | H -1.184626 2.531163 0.706315 17 | H 0.000969 1.169352 0.656482 18 | H -2.951061 1.071129 -0.293713 19 | 16 20 | 0.065310 21 | C -0.881227 -1.557393 0.272088 22 | C -1.610064 -0.713467 -0.460324 23 | C -1.801024 0.711054 -0.152196 24 | C -0.890612 1.487041 0.437951 25 | C 2.516894 -0.421962 0.383741 26 | C 2.332001 0.487098 -0.565349 27 | H -2.131418 -1.053644 -1.358624 28 | H -0.360952 -1.269568 1.174926 29 | H -0.761400 -2.601536 0.023569 30 | H 3.282981 -0.341264 1.145961 31 | H 1.919776 -1.320261 0.475426 32 | H 1.563600 0.411668 -1.325032 33 | H 2.931619 1.380162 -0.657183 34 | H -1.050398 2.537562 0.636875 35 | H 0.082037 1.136030 0.758548 36 | H -2.766779 1.113634 -0.463469 37 | 16 38 | 0.506110 39 | C -0.796213 -1.546366 0.316857 40 | C -1.581470 -0.741371 -0.402069 41 | C -1.689394 0.712253 -0.231819 42 | C -0.804860 1.477922 0.409772 43 | C 2.400950 -0.465178 0.325678 44 | C 2.196365 0.542582 -0.513453 45 | H -2.215361 -1.148859 -1.197479 46 | H -0.163997 -1.207652 1.125446 47 | H -0.738437 -2.611869 0.147557 48 | H 2.978108 -0.369047 1.235955 49 | H 2.015322 -1.464875 0.172962 50 | H 1.613410 0.461604 -1.420321 51 | H 2.595213 1.535082 -0.355424 52 | H -0.906494 2.551454 0.489679 53 | H 0.083333 1.097796 0.898836 54 | H -2.571812 1.156786 -0.702092 55 | 16 56 | 0.880430 57 | C -0.773656 -1.546591 0.472532 58 | C -1.491325 -0.778970 -0.351364 59 | C -1.516592 0.689471 -0.330509 60 | C -0.734188 1.456596 0.432272 61 | C 2.272667 -0.488455 0.166942 62 | C 2.053222 0.632231 -0.510071 63 | H -2.118514 -1.231139 -1.125406 64 | H -0.146620 -1.158463 1.263531 65 | H -0.766659 -2.625765 0.414225 66 | H 2.685318 -0.509616 1.165315 67 | H 2.054867 -1.473402 -0.223612 68 | H 1.633976 0.653653 -1.508679 69 | H 2.286377 1.616590 -0.127518 70 | H -0.766468 2.535261 0.411078 71 | H -0.011460 1.064033 1.135358 72 | H -2.234327 1.140548 -1.022353 73 | 16 74 | 4.734660 75 | C -0.878653 -1.655783 0.622469 76 | C -1.425230 -0.866669 -0.308849 77 | C -1.251858 0.587183 -0.380542 78 | C -0.488954 1.298446 0.454910 79 | C 2.132875 -0.307538 0.035760 80 | C 1.822029 0.839205 -0.565831 81 | H -2.036980 -1.298229 -1.109032 82 | H -0.268635 -1.292091 1.440143 83 | H -1.007304 -2.729808 0.625769 84 | H 2.531295 -0.358842 1.038453 85 | H 1.963165 -1.279964 -0.411926 86 | H 1.453384 0.882774 -1.581722 87 | H 2.114963 1.803252 -0.172116 88 | H -0.410434 2.376656 0.387283 89 | H -0.075423 0.897178 1.369427 90 | H -1.751796 1.073410 -1.226178 91 | 16 92 | 19.862190 93 | C -0.936904 -1.758158 0.666023 94 | C -1.403170 -0.931289 -0.304680 95 | C -1.096471 0.459894 -0.432923 96 | C -0.208516 1.170519 0.387715 97 | C 2.083203 -0.140715 0.019883 98 | C 1.544146 1.014178 -0.514757 99 | H -2.076998 -1.336546 -1.068278 100 | H -0.282889 -1.436396 1.459186 101 | H -1.194052 -2.804456 0.699992 102 | H 2.648762 -0.143011 0.934258 103 | H 1.912961 -1.111272 -0.410950 104 | H 1.176104 1.022702 -1.538194 105 | H 1.911065 1.985654 -0.189011 106 | H -0.229192 2.256279 0.365238 107 | H 0.074000 0.770541 1.357724 108 | H -1.556636 0.985251 -1.269557 109 | 16 110 | 9.543110 111 | C -0.259513 -1.416306 0.561108 112 | C -1.184493 -0.746664 -0.327551 113 | C -1.215408 0.595876 -0.463874 114 | C -0.190163 1.308990 0.299073 115 | C 1.483214 -0.546741 0.097788 116 | C 1.188923 0.810311 -0.426922 117 | H -1.789512 -1.378472 -0.983300 118 | H 0.066218 -1.074205 1.538478 119 | H -0.219200 -2.489995 0.457589 120 | H 2.005453 -0.582724 1.041541 121 | H 1.528331 -1.429858 -0.521695 122 | H 1.021584 0.864326 -1.508456 123 | H 1.854981 1.618954 -0.091635 124 | H -0.190559 2.404694 0.293960 125 | H -0.050903 0.958019 1.337631 126 | H -1.855245 1.110842 -1.164070 127 | 16 128 | -45.764830 129 | C -0.032995 -1.430824 0.318130 130 | C -1.213111 -0.716288 -0.273258 131 | C -1.279329 0.617461 -0.345462 132 | C -0.122122 1.445331 0.132950 133 | C 1.299930 -0.642627 0.279896 134 | C 1.179943 0.762785 -0.326191 135 | H -2.011589 -1.358452 -0.639483 136 | H -0.268867 -1.662777 1.379502 137 | H 0.104625 -2.407920 -0.185292 138 | H 1.698181 -0.567336 1.307960 139 | H 2.037251 -1.226545 -0.298564 140 | H 1.174664 0.683124 -1.431925 141 | H 2.053647 1.379201 -0.054076 142 | H -0.174029 2.486566 -0.226458 143 | H -0.141820 1.489050 1.241376 144 | H -2.124519 1.146835 -0.773733 145 | 16 146 | -48.332610 147 | C 0.020342 -1.496218 0.058646 148 | C -1.252781 -0.711946 -0.072433 149 | C -1.293528 0.622755 -0.135300 150 | C -0.070828 1.489110 -0.053029 151 | C 1.214363 -0.621211 0.473790 152 | C 1.222149 0.698487 -0.309129 153 | H -2.158649 -1.313485 -0.128548 154 | H -0.114951 -2.316203 0.791886 155 | H 0.235608 -1.989611 -0.913009 156 | H 1.160153 -0.406734 1.558378 157 | H 2.159983 -1.169252 0.309815 158 | H 1.318154 0.486250 -1.391274 159 | H 2.102027 1.305572 -0.030670 160 | H -0.148427 2.325855 -0.774547 161 | H -0.035455 1.955341 0.954404 162 | H -2.233315 1.162540 -0.235849 163 | -------------------------------------------------------------------------------- /TEST/dielsAlder/orca/de-gsm/inpfileq: -------------------------------------------------------------------------------- 1 | # FSM/GSM/SSM inpfileq 2 | 3 | ------------- QCHEM Scratch Info ------------------------ 4 | $QCSCRATCH/ # path for scratch dir. end with "/" 5 | GSM_go1q # name of run 6 | --------------------------------------------------------- 7 | 8 | ------------ String Info -------------------------------- 9 | SM_TYPE GSM # SSM, FSM or GSM 10 | RESTART 0 # read restart.xyz 11 | MAX_OPT_ITERS 80 # maximum iterations 12 | STEP_OPT_ITERS 30 # for FSM/SSM 13 | CONV_TOL 0.0005 # perp grad 14 | ADD_NODE_TOL 0.1 # for GSM 15 | SCALING 1.0 # for opt steps 16 | SSM_DQMAX 0.8 # add step size 17 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 18 | INT_THRESH 2.0 # intermediate detection 19 | MIN_SPACING 5.0 # node spacing SSM 20 | BOND_FRAGMENTS 1 # make IC's for fragments 21 | INITIAL_OPT 0 # opt steps first node 22 | FINAL_OPT 150 # opt steps last SSM node 23 | PRODUCT_LIMIT 100.0 # kcal/mol 24 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 25 | NNODES 9 # including endpoints 26 | --------------------------------------------------------- 27 | -------------------------------------------------------------------------------- /TEST/dielsAlder/orca/de-gsm/ograd: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # The path to ORCA should be added to .bashrc or exported in command line 3 | 4 | 5 | if [ -z $2 ] 6 | then 7 | echo " need two arguments! " 8 | exit 9 | fi 10 | 11 | #echo " in ograd: $1 $2 " 12 | 13 | ofile=$SLURM_LOCAL_SCRATCH/orcain$1.in 14 | ofileout=scratch/orcain$1.out 15 | molfile=scratch/structure$1 16 | ncpu=$2 17 | 18 | #echo " ofile: $ofile ofileout: $ofileout molfile: $molfile ncpu: $ncpu" 19 | 20 | ########## DFT settings: ################# 21 | #echo '! DFT BP86 ECP{LANL2} ENGRAD' > $ofile 22 | echo '! DFT B3LYP ENGRAD 6-31G*' > $ofile 23 | #echo '! veryslowconv SCFCONV6' >> $ofile 24 | echo '! nomoprint' >> $ofile 25 | echo '%scf' >> $ofile 26 | echo ' maxiter 350' >> $ofile 27 | echo 'end' >> $ofile 28 | # charge and spin multiplicity 29 | echo '* xyz 0 1' >> $ofile 30 | cat $molfile >> $ofile 31 | echo '*' >> $ofile 32 | 33 | #echo "running: orca $ofile > $ofileout" 34 | orca $ofile > $ofileout 35 | -------------------------------------------------------------------------------- /TEST/dielsAlder/orca/de-gsm/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | Step 35 3 | C -1.06001665 -1.51714564 0.05288674 4 | C -1.82955412 -0.59408623 -0.53968755 5 | C -2.01260392 0.79370866 -0.08977969 6 | C -1.09740592 1.54095108 0.54110413 7 | C 3.01841440 -0.33274049 0.53420511 8 | C 2.48267950 0.16990394 -0.57660955 9 | H -2.40063347 -0.88235561 -1.42321617 10 | H -0.51365172 -1.30383154 0.96828855 11 | H -0.96688964 -2.52122005 -0.35117707 12 | H 3.89171154 0.11254122 1.00536203 13 | H 2.60849064 -1.21591676 1.01902222 14 | H 1.60806045 -0.27640639 -1.04373753 15 | H 2.89526366 1.05096138 -1.06301386 16 | H -1.32088987 2.55628492 0.85667305 17 | H -0.09454533 1.17390089 0.74481476 18 | H -2.98142355 1.23828062 -0.32070817 19 | 16 20 | Step 22 21 | C 0.01856467 -1.50510245 0.07175535 22 | C -1.25472580 -0.70291222 -0.04828280 23 | C -1.28551058 0.63324180 -0.08527776 24 | C -0.04811068 1.49696591 -0.04422009 25 | C 1.21601433 -0.63168912 0.47947978 26 | C 1.22945185 0.68482088 -0.31033881 27 | H -2.18794361 -1.26282927 -0.10437525 28 | H -0.12133841 -2.31635373 0.79987325 29 | H 0.22663560 -2.00643122 -0.88734886 30 | H 1.14834814 -0.40532251 1.55280900 31 | H 2.15327210 -1.18259709 0.33198960 32 | H 1.29564501 0.45837391 -1.38389788 33 | H 2.11591575 1.28013898 -0.05856919 34 | H -0.13761965 2.30980257 -0.77849415 35 | H 0.01956981 1.99500653 0.93644690 36 | H -2.24481452 1.14593304 -0.15154508 37 | -------------------------------------------------------------------------------- /TEST/dielsAlder/orca/de-gsm/scratch/stringfile.xyz0001g1: -------------------------------------------------------------------------------- 1 | 16 2 | 0.000000 3 | C -1.060017 -1.517146 0.052887 4 | C -1.829554 -0.594086 -0.539688 5 | C -2.012604 0.793709 -0.089780 6 | C -1.097406 1.540951 0.541104 7 | C 3.018414 -0.332740 0.534205 8 | C 2.482680 0.169904 -0.576610 9 | H -2.400633 -0.882356 -1.423216 10 | H -0.513652 -1.303832 0.968289 11 | H -0.966890 -2.521220 -0.351177 12 | H 3.891712 0.112541 1.005362 13 | H 2.608491 -1.215917 1.019022 14 | H 1.608060 -0.276406 -1.043738 15 | H 2.895264 1.050961 -1.063014 16 | H -1.320890 2.556285 0.856673 17 | H -0.094545 1.173901 0.744815 18 | H -2.981424 1.238281 -0.320708 19 | 16 20 | 111.111000 21 | C -0.869040 -1.558366 0.031753 22 | C -1.728043 -0.615395 -0.483475 23 | C -1.896322 0.774924 -0.099527 24 | C -0.961500 1.600920 0.439408 25 | C 2.784391 -0.359223 0.584383 26 | C 2.300469 0.236710 -0.520097 27 | H -2.395608 -0.947986 -1.279295 28 | H -0.433601 -1.478665 1.026633 29 | H -0.738281 -2.502725 -0.493724 30 | H 3.577968 0.106880 1.167034 31 | H 2.523374 -1.360466 0.924315 32 | H 1.504334 -0.196709 -1.111968 33 | H 2.784596 1.119848 -0.934476 34 | H -1.186504 2.654460 0.593767 35 | H -0.025802 1.293225 0.820644 36 | H -2.882515 1.194883 -0.300405 37 | 16 38 | 111.111000 39 | C -0.114240 -1.565650 0.061302 40 | C -1.340350 -0.732612 -0.147912 41 | C -1.384295 0.641566 -0.122683 42 | C -0.192917 1.538958 0.002315 43 | C 1.449320 -0.548711 0.543102 44 | C 1.410361 0.629607 -0.327679 45 | H -2.264950 -1.273352 -0.349564 46 | H -0.181317 -2.243842 0.921436 47 | H 0.093675 -2.149328 -0.847374 48 | H 1.511969 -0.230955 1.591657 49 | H 2.220521 -1.311532 0.387108 50 | H 1.354375 0.422820 -1.373281 51 | H 2.235200 1.332270 -0.164448 52 | H -0.291415 2.452418 -0.597616 53 | H 0.072778 1.864208 0.998265 54 | H -2.354612 1.128886 -0.216564 55 | 16 56 | 6421394.882137 57 | C 0.018565 -1.505102 0.071755 58 | C -1.254726 -0.702912 -0.048283 59 | C -1.285511 0.633242 -0.085278 60 | C -0.048111 1.496966 -0.044220 61 | C 1.216014 -0.631689 0.479480 62 | C 1.229452 0.684821 -0.310339 63 | H -2.187944 -1.262829 -0.104375 64 | H -0.121338 -2.316354 0.799873 65 | H 0.226636 -2.006431 -0.887349 66 | H 1.148348 -0.405323 1.552809 67 | H 2.153272 -1.182597 0.331990 68 | H 1.295645 0.458374 -1.383898 69 | H 2.115916 1.280139 -0.058569 70 | H -0.137620 2.309803 -0.778494 71 | H 0.019570 1.995007 0.936447 72 | H -2.244815 1.145933 -0.151545 73 | -------------------------------------------------------------------------------- /TEST/dielsAlder/orca/de-gsm/scratch/tsq0001.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | -234.494298 -234.527461 -234.592352 3 | C -0.379248 -1.407261 0.663075 4 | C -1.254539 -0.799703 -0.227493 5 | C -1.300292 0.597018 -0.401987 6 | C -0.453292 1.451289 0.293329 7 | C 1.658855 -0.651341 -0.053845 8 | C 1.565003 0.710674 -0.326124 9 | H -1.775048 -1.422776 -0.953449 10 | H -0.095895 -0.920463 1.589077 11 | H -0.278530 -2.489188 0.672032 12 | H 2.141635 -0.987735 0.859235 13 | H 1.639036 -1.377023 -0.858248 14 | H 1.428368 1.050683 -1.345928 15 | H 2.038774 1.431035 0.335522 16 | H -0.431602 2.511342 0.054480 17 | H -0.140120 1.214882 1.304459 18 | H -1.856866 0.988877 -1.250718 19 | 20 | -------------------------------------------------------------------------------- /TEST/dielsAlder/orca/de-gsm/slurm_orca_gsm.sbatch: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | #SBATCH --array=1 3 | #SBATCH --job-name=orcagsm 4 | #SBATCH --time=3-00:00:00 5 | #SBATCH --nodes=1 --ntasks=4 6 | #SBATCH -o orca.output -e orac.error -p guest 7 | ##SBATCH --mail-type=END --mail-user= 8 | 9 | time 10 | 11 | . /etc/profile.d/slurm.sh 12 | 13 | item=$SLURM_ARRAY_TASK_ID 14 | ID=`printf "%0*d\n" 4 ${item}` 15 | module unload Openmpi 16 | shtcut="/export/applications" 17 | 18 | export LD_LIBRARY_PATH=/export/apps/Intel/composer_xe_2013.4.183/compiler/lib/intel64:/export/zimmerman/khyungju/OpenMPI/2.0.2/lib:$LD_LIBRARY_PATH 19 | export PATH=//export/zimmerman/khyungju/OpenMPI/2.0.2/bin:$PATH 20 | export OMP_NUM_THREADS=1 21 | ./gsm.orca.exe ${item} 4 > scratch/paragsm$ID 22 | 23 | 24 | wait 25 | 26 | 27 | 28 | 29 | 30 | 31 | -------------------------------------------------------------------------------- /TEST/dielsAlder/orca/de-gsm/stringfile.xyz0001fr: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C -0.313183 -1.382053 0.648594 4 | C -1.225476 -0.788285 -0.245080 5 | C -1.275990 0.587002 -0.416007 6 | C -0.396109 1.436079 0.284923 7 | C 1.569631 -0.670055 -0.033038 8 | C 1.479822 0.720116 -0.305523 9 | H -1.745040 -1.421687 -0.961066 10 | H -0.067398 -0.899295 1.588763 11 | H -0.204492 -2.463906 0.658962 12 | H 2.078855 -0.996754 0.868505 13 | H 1.576240 -1.384735 -0.846687 14 | H 1.363395 1.051552 -1.332309 15 | H 1.987217 1.427333 0.345304 16 | H -0.368460 2.495620 0.045541 17 | H -0.115210 1.200940 1.308806 18 | H -1.837565 0.988439 -1.256272 19 | 16 20 | 21 | C -0.379248 -1.407261 0.663075 22 | C -1.254539 -0.799703 -0.227493 23 | C -1.300292 0.597018 -0.401987 24 | C -0.453292 1.451289 0.293329 25 | C 1.658855 -0.651341 -0.053845 26 | C 1.565003 0.710674 -0.326124 27 | H -1.775048 -1.422776 -0.953449 28 | H -0.095895 -0.920463 1.589077 29 | H -0.278530 -2.489188 0.672032 30 | H 2.141635 -0.987735 0.859235 31 | H 1.639036 -1.377023 -0.858248 32 | H 1.428368 1.050683 -1.345928 33 | H 2.038774 1.431035 0.335522 34 | H -0.431602 2.511342 0.054480 35 | H -0.140120 1.214882 1.304459 36 | H -1.856866 0.988877 -1.250718 37 | 16 38 | 39 | C -0.445604 -1.431171 0.676803 40 | C -1.284740 -0.811274 -0.209424 41 | C -1.325455 0.606752 -0.387457 42 | C -0.510234 1.464894 0.301371 43 | C 1.748633 -0.632303 -0.073918 44 | C 1.651027 0.701756 -0.345919 45 | H -1.806240 -1.424054 -0.945014 46 | H -0.124708 -0.941939 1.587740 47 | H -0.352765 -2.513107 0.684080 48 | H 2.205332 -0.977792 0.849750 49 | H 1.701995 -1.367884 -0.868944 50 | H 1.493985 1.049225 -1.358433 51 | H 2.091260 1.434119 0.325639 52 | H -0.494135 2.525332 0.062658 53 | H -0.165028 1.228562 1.298814 54 | H -1.877084 0.989193 -1.244329 55 | 16 56 | 57 | C -0.390821 -1.421363 0.650743 58 | C -1.255109 -0.793532 -0.236566 59 | C -1.299233 0.604864 -0.392070 60 | C -0.437489 1.446812 0.302269 61 | C 1.668869 -0.640273 -0.030964 62 | C 1.550961 0.710187 -0.346860 63 | H -1.776364 -1.407224 -0.970096 64 | H -0.104833 -0.956650 1.586624 65 | H -0.292634 -2.502897 0.634391 66 | H 2.134195 -0.934541 0.905590 67 | H 1.674888 -1.396908 -0.806258 68 | H 1.393214 1.015130 -1.374095 69 | H 2.035324 1.457013 0.277319 70 | H -0.421788 2.510459 0.077803 71 | H -0.112886 1.202729 1.308803 72 | H -1.860054 1.006504 -1.233217 73 | 16 74 | 75 | C -0.379248 -1.407261 0.663075 76 | C -1.254539 -0.799703 -0.227493 77 | C -1.300292 0.597018 -0.401987 78 | C -0.453292 1.451289 0.293329 79 | C 1.658855 -0.651341 -0.053845 80 | C 1.565003 0.710674 -0.326124 81 | H -1.775048 -1.422776 -0.953449 82 | H -0.095895 -0.920463 1.589077 83 | H -0.278530 -2.489188 0.672032 84 | H 2.141635 -0.987735 0.859235 85 | H 1.639036 -1.377023 -0.858248 86 | H 1.428368 1.050683 -1.345928 87 | H 2.038774 1.431035 0.335522 88 | H -0.431602 2.511342 0.054480 89 | H -0.140120 1.214882 1.304459 90 | H -1.856866 0.988877 -1.250718 91 | 16 92 | 93 | C -0.367083 -1.393257 0.675349 94 | C -1.253671 -0.805963 -0.218205 95 | C -1.301009 0.589255 -0.411940 96 | C -0.468643 1.455790 0.284095 97 | C 1.648020 -0.661473 -0.076691 98 | C 1.578416 0.709929 -0.304831 99 | H -1.773346 -1.438371 -0.936496 100 | H -0.086414 -0.884669 1.591020 101 | H -0.263325 -2.474951 0.709431 102 | H 2.147001 -1.039582 0.810909 103 | H 1.602623 -1.354433 -0.908796 104 | H 1.463373 1.084889 -1.315910 105 | H 2.040692 1.402665 0.392938 106 | H -0.440249 2.512026 0.030994 107 | H -0.167059 1.227336 1.299866 108 | H -1.853088 0.971117 -1.268316 109 | 16 110 | 111 | C -0.411645 -1.431969 0.672763 112 | C -1.266849 -0.809169 -0.221567 113 | C -1.291381 0.588139 -0.397597 114 | C -0.424121 1.434860 0.289811 115 | C 1.681355 -0.629261 -0.060068 116 | C 1.537962 0.730051 -0.317607 117 | H -1.797754 -1.424859 -0.946505 118 | H -0.080813 -0.935623 1.579776 119 | H -0.315252 -2.514126 0.682580 120 | H 2.168891 -0.970132 0.849432 121 | H 1.614773 -1.358105 -0.858816 122 | H 1.425732 1.069297 -1.343000 123 | H 2.033654 1.451129 0.329499 124 | H -0.403177 2.493699 0.042457 125 | H -0.156331 1.224422 1.321853 126 | H -1.808805 0.981956 -1.269592 127 | 16 128 | 129 | C -0.379248 -1.407261 0.663075 130 | C -1.254539 -0.799703 -0.227493 131 | C -1.300292 0.597018 -0.401987 132 | C -0.453292 1.451289 0.293329 133 | C 1.658855 -0.651341 -0.053845 134 | C 1.565003 0.710674 -0.326124 135 | H -1.775048 -1.422776 -0.953449 136 | H -0.095895 -0.920463 1.589077 137 | H -0.278530 -2.489188 0.672032 138 | H 2.141635 -0.987735 0.859235 139 | H 1.639036 -1.377023 -0.858248 140 | H 1.428368 1.050683 -1.345928 141 | H 2.038774 1.431035 0.335522 142 | H -0.431602 2.511342 0.054480 143 | H -0.140120 1.214882 1.304459 144 | H -1.856866 0.988877 -1.250718 145 | 16 146 | 147 | C -0.346676 -1.381953 0.653048 148 | C -1.242130 -0.790161 -0.233327 149 | C -1.309150 0.606183 -0.406259 150 | C -0.482011 1.467656 0.297461 151 | C 1.635693 -0.672460 -0.047891 152 | C 1.591985 0.690382 -0.334262 153 | H -1.752449 -1.420493 -0.960046 154 | H -0.111465 -0.905752 1.595941 155 | H -0.241922 -2.463660 0.661192 156 | H 2.114464 -1.004023 0.868449 157 | H 1.662983 -1.394677 -0.855520 158 | H 1.431280 1.031105 -1.348827 159 | H 2.044491 1.409583 0.340960 160 | H -0.460266 2.528928 0.067388 161 | H -0.124398 1.205407 1.285741 162 | H -1.904191 0.994243 -1.230630 163 | -------------------------------------------------------------------------------- /TEST/dielsAlder/orca/se-gsm/ISOMERS0001: -------------------------------------------------------------------------------- 1 | NEW 2 | ADD 6 4 3 | ADD 5 1 4 | -------------------------------------------------------------------------------- /TEST/dielsAlder/orca/se-gsm/inpfileq: -------------------------------------------------------------------------------- 1 | 2 | # FSM/GSM/SSM inpfileq 3 | 4 | ------------- QCHEM Scratch Info ------------------------ 5 | $QCSCRATCH/ # path for scratch dir. end with "/" 6 | GSM_go1q # name of run 7 | --------------------------------------------------------- 8 | 9 | ------------ String Info -------------------------------- 10 | SM_TYPE SSM # SSM, FSM or GSM 11 | RESTART 0 # read restart.xyz 12 | MAX_OPT_ITERS 80 # maximum iterations 13 | STEP_OPT_ITERS 30 # for FSM/SSM 14 | CONV_TOL 0.0005 # perp grad 15 | ADD_NODE_TOL 0.1 # for GSM 16 | SCALING 1.0 # for opt steps 17 | SSM_DQMAX 0.8 # add step size 18 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 19 | INT_THRESH 2.0 # intermediate detection 20 | MIN_SPACING 5.0 # node spacing SSM 21 | BOND_FRAGMENTS 1 # make IC's for fragments 22 | INITIAL_OPT 0 # opt steps first node 23 | FINAL_OPT 150 # opt steps last SSM node 24 | PRODUCT_LIMIT 100.0 # kcal/mol 25 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 26 | NNODES 20 # including endpoints 27 | --------------------------------------------------------- 28 | -------------------------------------------------------------------------------- /TEST/dielsAlder/orca/se-gsm/ograd: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # The path to ORCA should be added to .bashrc or exported in command line 3 | 4 | 5 | if [ -z $2 ] 6 | then 7 | echo " need two arguments! " 8 | exit 9 | fi 10 | 11 | #echo " in ograd: $1 $2 " 12 | 13 | ofile=scratch/orcain$1.in 14 | ofileout=scratch/orcain$1.out 15 | molfile=scratch/structure$1 16 | ncpu=$2 17 | 18 | #echo " ofile: $ofile ofileout: $ofileout molfile: $molfile ncpu: $ncpu" 19 | 20 | ########## DFT settings: ################# 21 | #echo '! DFT BP86 ECP{LANL2} ENGRAD' > $ofile 22 | echo '! DFT B3LYP ENGRAD' > $ofile 23 | #echo '! veryslowconv SCFCONV6' >> $ofile 24 | echo '! nomoprint' >> $ofile 25 | echo '%scf' >> $ofile 26 | echo ' maxiter 350' >> $ofile 27 | echo 'end' >> $ofile 28 | # charge and spin multiplicity 29 | echo '* xyz 0 1' >> $ofile 30 | cat $molfile >> $ofile 31 | echo '*' >> $ofile 32 | 33 | #echo "running: orca $ofile > $ofileout" 34 | orca $ofile > $ofileout 35 | -------------------------------------------------------------------------------- /TEST/dielsAlder/orca/se-gsm/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | Step 35 3 | C -1.06001665 -1.51714564 0.05288674 4 | C -1.82955412 -0.59408623 -0.53968755 5 | C -2.01260392 0.79370866 -0.08977969 6 | C -1.09740592 1.54095108 0.54110413 7 | C 3.01841440 -0.33274049 0.53420511 8 | C 2.48267950 0.16990394 -0.57660955 9 | H -2.40063347 -0.88235561 -1.42321617 10 | H -0.51365172 -1.30383154 0.96828855 11 | H -0.96688964 -2.52122005 -0.35117707 12 | H 3.89171154 0.11254122 1.00536203 13 | H 2.60849064 -1.21591676 1.01902222 14 | H 1.60806045 -0.27640639 -1.04373753 15 | H 2.89526366 1.05096138 -1.06301386 16 | H -1.32088987 2.55628492 0.85667305 17 | H -0.09454533 1.17390089 0.74481476 18 | H -2.98142355 1.23828062 -0.32070817 19 | 16 20 | Step 22 21 | C 0.01856467 -1.50510245 0.07175535 22 | C -1.25472580 -0.70291222 -0.04828280 23 | C -1.28551058 0.63324180 -0.08527776 24 | C -0.04811068 1.49696591 -0.04422009 25 | C 1.21601433 -0.63168912 0.47947978 26 | C 1.22945185 0.68482088 -0.31033881 27 | H -2.18794361 -1.26282927 -0.10437525 28 | H -0.12133841 -2.31635373 0.79987325 29 | H 0.22663560 -2.00643122 -0.88734886 30 | H 1.14834814 -0.40532251 1.55280900 31 | H 2.15327210 -1.18259709 0.33198960 32 | H 1.29564501 0.45837391 -1.38389788 33 | H 2.11591575 1.28013898 -0.05856919 34 | H -0.13761965 2.30980257 -0.77849415 35 | H 0.01956981 1.99500653 0.93644690 36 | H -2.24481452 1.14593304 -0.15154508 37 | -------------------------------------------------------------------------------- /TEST/dielsAlder/orca/se-gsm/scratch/tsq0001.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | -234.494298 -234.527461 -234.592352 3 | C -0.379248 -1.407261 0.663075 4 | C -1.254539 -0.799703 -0.227493 5 | C -1.300292 0.597018 -0.401987 6 | C -0.453292 1.451289 0.293329 7 | C 1.658855 -0.651341 -0.053845 8 | C 1.565003 0.710674 -0.326124 9 | H -1.775048 -1.422776 -0.953449 10 | H -0.095895 -0.920463 1.589077 11 | H -0.278530 -2.489188 0.672032 12 | H 2.141635 -0.987735 0.859235 13 | H 1.639036 -1.377023 -0.858248 14 | H 1.428368 1.050683 -1.345928 15 | H 2.038774 1.431035 0.335522 16 | H -0.431602 2.511342 0.054480 17 | H -0.140120 1.214882 1.304459 18 | H -1.856866 0.988877 -1.250718 19 | 20 | -------------------------------------------------------------------------------- /TEST/dielsAlder/qchem/de-gsm/gscreate: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | file=molecule 4 | 5 | #nl $file > tmp.mole 6 | #nl link > tmp.link 7 | #join tmp.mole tmp.link > tmp.geom2 8 | #awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom 9 | 10 | #cat qstart tmp.geom qend > qcin 11 | #cat qstart molecule$1 qend > scratch/qcin$1 12 | cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 13 | 14 | #rm tmp.geom tmp.geom2 tmp.link tmp.mole 15 | -------------------------------------------------------------------------------- /TEST/dielsAlder/qchem/de-gsm/inpfileq: -------------------------------------------------------------------------------- 1 | 2 | # FSM/GSM/SSM inpfileq 3 | 4 | ------------- QCHEM Scratch Info ------------------------ 5 | $QCSCRATCH/ # path for scratch dir. end with "/" 6 | GSM_go1q # name of run 7 | --------------------------------------------------------- 8 | 9 | ------------ String Info -------------------------------- 10 | SM_TYPE GSM # SSM, FSM or GSM 11 | RESTART 0 # read restart.xyz 12 | MAX_OPT_ITERS 80 # maximum iterations 13 | STEP_OPT_ITERS 30 # for FSM/SSM 14 | CONV_TOL 0.0005 # perp grad 15 | ADD_NODE_TOL 0.1 # for GSM 16 | SCALING 1.0 # for opt steps 17 | SSM_DQMAX 0.8 # add step size 18 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 19 | INT_THRESH 2.0 # intermediate detection 20 | MIN_SPACING 5.0 # node spacing SSM 21 | BOND_FRAGMENTS 1 # make IC's for fragments 22 | INITIAL_OPT 0 # opt steps first node 23 | FINAL_OPT 150 # opt steps last SSM node 24 | PRODUCT_LIMIT 100.0 # kcal/mol 25 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 26 | NNODES 9 # including endpoints 27 | --------------------------------------------------------- 28 | -------------------------------------------------------------------------------- /TEST/dielsAlder/qchem/de-gsm/qend: -------------------------------------------------------------------------------- 1 | $end 2 | -------------------------------------------------------------------------------- /TEST/dielsAlder/qchem/de-gsm/qstart: -------------------------------------------------------------------------------- 1 | $rem 2 | JOBTYPE FORCE 3 | EXCHANGE B3LYP 4 | ! CORRELATION PBE 5 | ! UNRESTRICTED TRUE 6 | SCF_ALGORITHM rca_diis 7 | SCF_MAX_CYCLES 150 8 | BASIS 6-31G* 9 | ! BASIS LANL2DZ 10 | ! ECP LANL2DZ 11 | WAVEFUNCTION_ANALYSIS FALSE 12 | GEOM_OPT_MAX_CYCLES 300 13 | 14 | scf_convergence 6 15 | 16 | SYM_IGNORE TRUE 17 | SYMMETRY FALSE 18 | 19 | molden_format true 20 | $end 21 | 22 | 23 | $molecule 24 | 0 1 25 | -------------------------------------------------------------------------------- /TEST/dielsAlder/qchem/de-gsm/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | Step 35 3 | C -1.06001665 -1.51714564 0.05288674 4 | C -1.82955412 -0.59408623 -0.53968755 5 | C -2.01260392 0.79370866 -0.08977969 6 | C -1.09740592 1.54095108 0.54110413 7 | C 3.01841440 -0.33274049 0.53420511 8 | C 2.48267950 0.16990394 -0.57660955 9 | H -2.40063347 -0.88235561 -1.42321617 10 | H -0.51365172 -1.30383154 0.96828855 11 | H -0.96688964 -2.52122005 -0.35117707 12 | H 3.89171154 0.11254122 1.00536203 13 | H 2.60849064 -1.21591676 1.01902222 14 | H 1.60806045 -0.27640639 -1.04373753 15 | H 2.89526366 1.05096138 -1.06301386 16 | H -1.32088987 2.55628492 0.85667305 17 | H -0.09454533 1.17390089 0.74481476 18 | H -2.98142355 1.23828062 -0.32070817 19 | 16 20 | Step 22 21 | C 0.01856467 -1.50510245 0.07175535 22 | C -1.25472580 -0.70291222 -0.04828280 23 | C -1.28551058 0.63324180 -0.08527776 24 | C -0.04811068 1.49696591 -0.04422009 25 | C 1.21601433 -0.63168912 0.47947978 26 | C 1.22945185 0.68482088 -0.31033881 27 | H -2.18794361 -1.26282927 -0.10437525 28 | H -0.12133841 -2.31635373 0.79987325 29 | H 0.22663560 -2.00643122 -0.88734886 30 | H 1.14834814 -0.40532251 1.55280900 31 | H 2.15327210 -1.18259709 0.33198960 32 | H 1.29564501 0.45837391 -1.38389788 33 | H 2.11591575 1.28013898 -0.05856919 34 | H -0.13761965 2.30980257 -0.77849415 35 | H 0.01956981 1.99500653 0.93644690 36 | H -2.24481452 1.14593304 -0.15154508 37 | -------------------------------------------------------------------------------- /TEST/dielsAlder/qchem/se-gsm/ISOMERS0001: -------------------------------------------------------------------------------- 1 | NEW 2 | ADD 6 4 3 | ADD 5 1 4 | -------------------------------------------------------------------------------- /TEST/dielsAlder/qchem/se-gsm/gscreate: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | file=molecule 4 | 5 | #nl $file > tmp.mole 6 | #nl link > tmp.link 7 | #join tmp.mole tmp.link > tmp.geom2 8 | #awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom 9 | 10 | #cat qstart tmp.geom qend > qcin 11 | #cat qstart molecule$1 qend > scratch/qcin$1 12 | cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 13 | 14 | #rm tmp.geom tmp.geom2 tmp.link tmp.mole 15 | -------------------------------------------------------------------------------- /TEST/dielsAlder/qchem/se-gsm/inpfileq: -------------------------------------------------------------------------------- 1 | 2 | # FSM/GSM/SSM inpfileq 3 | 4 | ------------- QCHEM Scratch Info ------------------------ 5 | $QCSCRATCH/ # path for scratch dir. end with "/" 6 | GSM_go1q # name of run 7 | --------------------------------------------------------- 8 | 9 | ------------ String Info -------------------------------- 10 | SM_TYPE SSM # SSM, FSM or GSM 11 | RESTART 0 # read restart.xyz 12 | MAX_OPT_ITERS 80 # maximum iterations 13 | STEP_OPT_ITERS 30 # for FSM/SSM 14 | CONV_TOL 0.0005 # perp grad 15 | ADD_NODE_TOL 0.1 # for GSM 16 | SCALING 1.0 # for opt steps 17 | SSM_DQMAX 0.8 # add step size 18 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 19 | INT_THRESH 2.0 # intermediate detection 20 | MIN_SPACING 5.0 # node spacing SSM 21 | BOND_FRAGMENTS 1 # make IC's for fragments 22 | INITIAL_OPT 0 # opt steps first node 23 | FINAL_OPT 150 # opt steps last SSM node 24 | PRODUCT_LIMIT 100.0 # kcal/mol 25 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 26 | NNODES 20 # including endpoints 27 | --------------------------------------------------------- 28 | -------------------------------------------------------------------------------- /TEST/dielsAlder/qchem/se-gsm/qend: -------------------------------------------------------------------------------- 1 | $end 2 | -------------------------------------------------------------------------------- /TEST/dielsAlder/qchem/se-gsm/qstart: -------------------------------------------------------------------------------- 1 | $rem 2 | JOBTYPE FORCE 3 | EXCHANGE B3LYP 4 | ! CORRELATION PBE 5 | ! UNRESTRICTED TRUE 6 | SCF_ALGORITHM rca_diis 7 | SCF_MAX_CYCLES 150 8 | BASIS 6-31G* 9 | ! BASIS LANL2DZ 10 | ! ECP LANL2DZ 11 | WAVEFUNCTION_ANALYSIS FALSE 12 | GEOM_OPT_MAX_CYCLES 300 13 | 14 | scf_convergence 6 15 | 16 | SYM_IGNORE TRUE 17 | SYMMETRY FALSE 18 | 19 | molden_format true 20 | $end 21 | 22 | 23 | $molecule 24 | 0 1 25 | -------------------------------------------------------------------------------- /TEST/dielsAlder/qchem/se-gsm/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | Step 35 3 | C -1.06001665 -1.51714564 0.05288674 4 | C -1.82955412 -0.59408623 -0.53968755 5 | C -2.01260392 0.79370866 -0.08977969 6 | C -1.09740592 1.54095108 0.54110413 7 | C 3.01841440 -0.33274049 0.53420511 8 | C 2.48267950 0.16990394 -0.57660955 9 | H -2.40063347 -0.88235561 -1.42321617 10 | H -0.51365172 -1.30383154 0.96828855 11 | H -0.96688964 -2.52122005 -0.35117707 12 | H 3.89171154 0.11254122 1.00536203 13 | H 2.60849064 -1.21591676 1.01902222 14 | H 1.60806045 -0.27640639 -1.04373753 15 | H 2.89526366 1.05096138 -1.06301386 16 | H -1.32088987 2.55628492 0.85667305 17 | H -0.09454533 1.17390089 0.74481476 18 | H -2.98142355 1.23828062 -0.32070817 19 | 16 20 | Step 22 21 | C 0.01856467 -1.50510245 0.07175535 22 | C -1.25472580 -0.70291222 -0.04828280 23 | C -1.28551058 0.63324180 -0.08527776 24 | C -0.04811068 1.49696591 -0.04422009 25 | C 1.21601433 -0.63168912 0.47947978 26 | C 1.22945185 0.68482088 -0.31033881 27 | H -2.18794361 -1.26282927 -0.10437525 28 | H -0.12133841 -2.31635373 0.79987325 29 | H 0.22663560 -2.00643122 -0.88734886 30 | H 1.14834814 -0.40532251 1.55280900 31 | H 2.15327210 -1.18259709 0.33198960 32 | H 1.29564501 0.45837391 -1.38389788 33 | H 2.11591575 1.28013898 -0.05856919 34 | H -0.13761965 2.30980257 -0.77849415 35 | H 0.01956981 1.99500653 0.93644690 36 | H -2.24481452 1.14593304 -0.15154508 37 | -------------------------------------------------------------------------------- /TEST/dielsAlder/turbomole/de-gsm-nowrapper/TM/auxbasis: -------------------------------------------------------------------------------- 1 | $jbas 2 | * 3 | c def2-SVP 4 | # c (12s5p4d2f1g) / [6s4p3d1f1g] {711111/2111/211/2/1} 5 | * 6 | 7 s 7 | 1861.0916331 0.74417100000E-01 8 | 642.99397640 0.16539570000 9 | 235.11057250 0.55764840000 10 | 90.702889400 1.3108298000 11 | 36.779455200 2.1694681000 12 | 15.604627300 1.7668846000 13 | 6.8907294000 0.29307690000 14 | 1 s 15 | 3.1478850000 -0.17087020000 16 | 1 s 17 | 1.4777287000 0.16415530000 18 | 1 s 19 | 0.70764660000 0.41499410000 20 | 1 s 21 | 0.34301220000 0.16243660000 22 | 1 s 23 | 0.16694530000 0.20767500000E-01 24 | 2 p 25 | 13.547289200 -0.20647700000E-01 26 | 5.4669419000 -0.11528200000E-01 27 | 1 p 28 | 2.1751721000 0.45591400000E-01 29 | 1 p 30 | 0.85821940000 0.28360000000E-02 31 | 1 p 32 | 0.33767200000 0.18187500000E-01 33 | 2 d 34 | 5.9287253000 -0.22594800000E-01 35 | 1.9809209000 -0.47682700000E-01 36 | 1 d 37 | 0.80554170000 -0.36537200000E-01 38 | 1 d 39 | 0.35312440000 -0.14541700000E-01 40 | 2 f 41 | 1.6755626000 0.88798000000E-02 42 | 0.59975360000 0.69903000000E-02 43 | 1 g 44 | 1.0024600000 -0.22192000000E-02 45 | * 46 | h def2-SVP 47 | # h (5s2p1d) / [3s1p1d] {311/2/1} 48 | * 49 | 3 s 50 | 15.675292700 0.18688600000E-01 51 | 3.6063578000 0.63167000000E-01 52 | 1.2080016000 0.12046090000 53 | 1 s 54 | 0.47267940000 0.59248500000E-01 55 | 1 s 56 | 0.20181000000 0.51272000000E-02 57 | 2 p 58 | 2.0281365000 1.0000000000 59 | 0.53587300000 1.0000000000 60 | 1 d 61 | 2.2165124000 0.33116000000E-02 62 | * 63 | $end 64 | -------------------------------------------------------------------------------- /TEST/dielsAlder/turbomole/de-gsm-nowrapper/TM/basis: -------------------------------------------------------------------------------- 1 | $basis 2 | * 3 | c def2-SVP 4 | # c (7s4p1d) / [3s2p1d] {511/31/1} 5 | * 6 | 5 s 7 | 1238.4016938 0.54568832082E-02 8 | 186.29004992 0.40638409211E-01 9 | 42.251176346 0.18025593888 10 | 11.676557932 0.46315121755 11 | 3.5930506482 0.44087173314 12 | 1 s 13 | 0.40245147363 1.0000000000 14 | 1 s 15 | 0.13090182668 1.0000000000 16 | 3 p 17 | 9.4680970621 0.38387871728E-01 18 | 2.0103545142 0.21117025112 19 | 0.54771004707 0.51328172114 20 | 1 p 21 | 0.15268613795 1.0000000000 22 | 1 d 23 | 0.80000000000 1.0000000000 24 | * 25 | h def2-SVP 26 | # h (4s1p) / [2s1p] {31/1} 27 | * 28 | 3 s 29 | 13.010701000 0.19682158000E-01 30 | 1.9622572000 0.13796524000 31 | 0.44453796000 0.47831935000 32 | 1 s 33 | 0.12194962000 1.0000000000 34 | 1 p 35 | 0.80000000000 1.0000000000 36 | * 37 | $end 38 | -------------------------------------------------------------------------------- /TEST/dielsAlder/turbomole/de-gsm-nowrapper/TM/control: -------------------------------------------------------------------------------- 1 | $cosmo 2 | epsilon= 80.000 3 | rsolv= 1.30 4 | $cosmo_atoms 5 | # radii in Angstrom units 6 | c 1-6 \ 7 | radius= 2.0000 8 | h 7-16 \ 9 | radius= 1.3000 10 | $cosmo_out file=out.ccf 11 | $title 12 | $operating system unix 13 | $symmetry c1 14 | $coord file=coord 15 | $user-defined bonds file=coord 16 | $atoms 17 | c 1-6 \ 18 | basis =c def2-SVP \ 19 | jbas =c def2-SVP 20 | h 7-16 \ 21 | basis =h def2-SVP \ 22 | jbas =h def2-SVP 23 | $basis file=basis 24 | $rundimensions 25 | dim(fock,dens)=10026 26 | natoms=16 27 | nshell=66 28 | nbf(CAO)=140 29 | nbf(AO)=134 30 | dim(trafo[SAO<-->AO/CAO])=152 31 | rhfshells=1 32 | $scfmo file=mos 33 | $closed shells 34 | a 1-23 ( 2 ) 35 | $scfiterlimit 1200 36 | $thize 0.10000000E-04 37 | $thime 5 38 | $scfdump 39 | $scfintunit 40 | unit=30 size=0 file=twoint 41 | $scfdiis 42 | $maxcor 500 43 | $scforbitalshift automatic=.1 44 | $drvopt 45 | cartesian on 46 | basis off 47 | global off 48 | hessian on 49 | dipole on 50 | nuclear polarizability 51 | $interconversion off 52 | qconv=1.d-7 53 | maxiter=25 54 | $optimize 55 | internal off 56 | cartesian on 57 | global off 58 | basis off logarithm 59 | $coordinateupdate 60 | dqmax=0.3 61 | interpolate on 62 | statistics 5 63 | $forceupdate 64 | ahlrichs numgeo=0 mingeo=3 maxgeo=4 modus= dynamic fail=0.3 65 | threig=0.005 reseig=0.005 thrbig=3.0 scale=1.00 damping=0.0 66 | $forceinit on 67 | diag=default 68 | $energy file=energy 69 | $grad file=gradient 70 | $forceapprox file=forceapprox 71 | $lock off 72 | $dft 73 | functional b-p 74 | gridsize m3 75 | $scfconv 6 76 | $scfdamp start=0.700 step=0.050 min=0.050 77 | $ricore 500 78 | $rij 79 | $jbas file=auxbasis 80 | $last step define 81 | $end 82 | -------------------------------------------------------------------------------- /TEST/dielsAlder/turbomole/de-gsm-nowrapper/TM/coord: -------------------------------------------------------------------------------- 1 | $coord 2 | -1.95562844204390 -2.98850172367360 0.52104284826376 c 3 | -3.25528947966213 -1.31900427431445 -0.86679092098878 c 4 | -3.62369347899432 1.36888926477037 -0.27001918767576 c 5 | -2.01735634617461 2.84141300039431 1.01513253269417 c 6 | 5.21575373088008 -0.74749817939811 0.69237486810184 c 7 | 4.82372437543456 0.85208696194880 -1.20750665302193 c 8 | -4.18407286644023 -1.98419543199473 -2.58082732557392 h 9 | -1.07896181228465 -2.46314274092233 2.30171099629444 h 10 | -1.75230713822833 -4.94142974707361 -0.07218564855010 h 11 | 6.91374069141862 -0.67296927044324 1.84509836053142 h 12 | 3.84322674330391 -2.19950893784959 1.16529395066553 h 13 | 3.11792150761041 0.76708897021774 -2.34648805701317 h 14 | 6.18587676654119 2.30891841176527 -1.69778098039005 h 15 | -2.45973745443087 4.80657322105249 1.40354117286909 h 16 | -0.20337232642115 2.15133225981780 1.68385558851682 h 17 | -5.36139303421545 2.20639887933009 -0.99227062593852 h 18 | $user-defined bonds 19 | $end 20 | -------------------------------------------------------------------------------- /TEST/dielsAlder/turbomole/de-gsm-nowrapper/TM/coord.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C -1.034874 -1.581447 0.275724 4 | C -1.722625 -0.697987 -0.458686 5 | C -1.917576 0.724385 -0.142888 6 | C -1.067539 1.503611 0.537185 7 | C 2.760058 -0.395559 0.366389 8 | C 2.552605 0.450905 -0.638985 9 | H -2.214116 -1.049991 -1.365715 10 | H -0.570962 -1.303439 1.218013 11 | H -0.927281 -2.614892 -0.038199 12 | H 3.658594 -0.356120 0.976384 13 | H 2.033748 -1.163930 0.616647 14 | H 1.649933 0.405926 -1.241708 15 | H 3.273425 1.221827 -0.898427 16 | H -1.301637 2.543529 0.742722 17 | H -0.107620 1.138436 0.891058 18 | H -2.837127 1.167576 -0.525087 19 | -------------------------------------------------------------------------------- /TEST/dielsAlder/turbomole/de-gsm-nowrapper/gscreate: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | if [ ! -d $TMSCRATCH/COORD_$1 ]; then 4 | mkdir $TMSCRATCH/COORD_$1 5 | fi 6 | 7 | cat $TMSCRATCH/COORD_$1/coord >> $TMSCRATCH/COORD_$1/coord_PREV 8 | number=$(echo $1 | sed 's/^0*//') 9 | #echo "MOLECULE NUMBER:" $number 10 | 11 | if [ $number = 1 ]; then 12 | if [ ! -f $TMSCRATCH/COORD_$1/control ]; 13 | then 14 | cp TM/* $TMSCRATCH/COORD_$1 15 | fi 16 | x2t $TMSCRATCH/molecule$1 > $TMSCRATCH/COORD_$1/coord 17 | else 18 | # cp TM/* $TMSCRATCH/COORD_$1 19 | if [ ! -f $TMSCRATCH/COORD_$1/control ]; 20 | then 21 | previous=$(printf "%07d" $(($number-1))) 22 | cp $TMSCRATCH/COORD_"$previous"/* $TMSCRATCH/COORD_$1 23 | fi 24 | x2t $TMSCRATCH/molecule$1 > $TMSCRATCH/COORD_$1/coord 25 | fi 26 | 27 | -------------------------------------------------------------------------------- /TEST/dielsAlder/turbomole/de-gsm-nowrapper/inpfileq: -------------------------------------------------------------------------------- 1 | # FSM/GSM/SSM inpfileq 2 | 3 | ------------- TURBOMOLE Scratch Info ------------------------ 4 | $TMSCRATCH/ # path for scratch dir. end with "/ 5 | GSM_go1q # name of run 6 | RI 1 # if RI should be used 7 | COSMO 1 8 | turboDIR /programs/turbomole/current/bin/em64t-unknown-linux-gnu 9 | --------------------------------------------------------- 10 | 11 | ------------ String Info -------------------------------- 12 | SM_TYPE SSM # SSM, FSM or GSM 13 | RESTART 0 # read restart.xyz 14 | MAX_OPT_ITERS 100 # maximum iterations 15 | STEP_OPT_ITERS 30 # for FSM/SSM 16 | CONV_TOL 0.0005 # perp grad 17 | ADD_NODE_TOL 0.1 # for GSM 18 | SCALING 1.0 # for opt steps 19 | SSM_DQMAX 0.8 # add step size 20 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 21 | INT_THRESH 2.0 # intermediate detection 22 | MIN_SPACING 5.0 # node spacing SSM 23 | BOND_FRAGMENTS 1 # make IC's for fragments 24 | INITIAL_OPT 150 # opt steps first node 25 | FINAL_OPT 150 # opt steps last SSM node 26 | PRODUCT_LIMIT 100.0 # kcal/mol 27 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 28 | NNODES 30 # including endpoints 29 | --------------------------------------------------------- 30 | -------------------------------------------------------------------------------- /TEST/dielsAlder/turbomole/de-gsm-nowrapper/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | Step 35 3 | C -1.06001665 -1.51714564 0.05288674 4 | C -1.82955412 -0.59408623 -0.53968755 5 | C -2.01260392 0.79370866 -0.08977969 6 | C -1.09740592 1.54095108 0.54110413 7 | C 3.01841440 -0.33274049 0.53420511 8 | C 2.48267950 0.16990394 -0.57660955 9 | H -2.40063347 -0.88235561 -1.42321617 10 | H -0.51365172 -1.30383154 0.96828855 11 | H -0.96688964 -2.52122005 -0.35117707 12 | H 3.89171154 0.11254122 1.00536203 13 | H 2.60849064 -1.21591676 1.01902222 14 | H 1.60806045 -0.27640639 -1.04373753 15 | H 2.89526366 1.05096138 -1.06301386 16 | H -1.32088987 2.55628492 0.85667305 17 | H -0.09454533 1.17390089 0.74481476 18 | H -2.98142355 1.23828062 -0.32070817 19 | 16 20 | Step 22 21 | C 0.01856467 -1.50510245 0.07175535 22 | C -1.25472580 -0.70291222 -0.04828280 23 | C -1.28551058 0.63324180 -0.08527776 24 | C -0.04811068 1.49696591 -0.04422009 25 | C 1.21601433 -0.63168912 0.47947978 26 | C 1.22945185 0.68482088 -0.31033881 27 | H -2.18794361 -1.26282927 -0.10437525 28 | H -0.12133841 -2.31635373 0.79987325 29 | H 0.22663560 -2.00643122 -0.88734886 30 | H 1.14834814 -0.40532251 1.55280900 31 | H 2.15327210 -1.18259709 0.33198960 32 | H 1.29564501 0.45837391 -1.38389788 33 | H 2.11591575 1.28013898 -0.05856919 34 | H -0.13761965 2.30980257 -0.77849415 35 | H 0.01956981 1.99500653 0.93644690 36 | H -2.24481452 1.14593304 -0.15154508 37 | -------------------------------------------------------------------------------- /TEST/dielsAlder/turbomole/de-gsm-wrapper/gscreate: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | if [ ! -d $TMSCRATCH/COORD_$1 ]; then 4 | mkdir $TMSCRATCH/COORD_$1 5 | fi 6 | 7 | cat $TMSCRATCH/COORD_$1/coord >> $TMSCRATCH/COORD_$1/coord_PREV 8 | number=$(echo $1 | sed 's/^0*//') 9 | #echo "MOLECULE NUMBER:" $number 10 | 11 | if [ $number = 1 ]; then 12 | if [ ! -f $TMSCRATCH/COORD_$1/control ]; 13 | then 14 | cp tm_define cosmo_inp $TMSCRATCH/COORD_$1 15 | x2t $TMSCRATCH/molecule$1 > $TMSCRATCH/COORD_$1/coord 16 | cd $TMSCRATCH/COORD_$1/ 17 | define < tm_define > define_$1.log 18 | cd - 19 | else 20 | x2t $TMSCRATCH/molecule$1 > $TMSCRATCH/COORD_$1/coord 21 | fi 22 | else 23 | # cp TM/* $TMSCRATCH/COORD_$1 24 | if [ ! -f $TMSCRATCH/COORD_$1/control ]; 25 | then 26 | previous=$(printf "%07d" $(($number-1))) 27 | cp $TMSCRATCH/COORD_"$previous"/* $TMSCRATCH/COORD_$1 28 | fi 29 | x2t $TMSCRATCH/molecule$1 > $TMSCRATCH/COORD_$1/coord 30 | fi 31 | 32 | -------------------------------------------------------------------------------- /TEST/dielsAlder/turbomole/de-gsm-wrapper/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | Step 35 3 | C -1.06001665 -1.51714564 0.05288674 4 | C -1.82955412 -0.59408623 -0.53968755 5 | C -2.01260392 0.79370866 -0.08977969 6 | C -1.09740592 1.54095108 0.54110413 7 | C 3.01841440 -0.33274049 0.53420511 8 | C 2.48267950 0.16990394 -0.57660955 9 | H -2.40063347 -0.88235561 -1.42321617 10 | H -0.51365172 -1.30383154 0.96828855 11 | H -0.96688964 -2.52122005 -0.35117707 12 | H 3.89171154 0.11254122 1.00536203 13 | H 2.60849064 -1.21591676 1.01902222 14 | H 1.60806045 -0.27640639 -1.04373753 15 | H 2.89526366 1.05096138 -1.06301386 16 | H -1.32088987 2.55628492 0.85667305 17 | H -0.09454533 1.17390089 0.74481476 18 | H -2.98142355 1.23828062 -0.32070817 19 | 16 20 | Step 22 21 | C 0.01856467 -1.50510245 0.07175535 22 | C -1.25472580 -0.70291222 -0.04828280 23 | C -1.28551058 0.63324180 -0.08527776 24 | C -0.04811068 1.49696591 -0.04422009 25 | C 1.21601433 -0.63168912 0.47947978 26 | C 1.22945185 0.68482088 -0.31033881 27 | H -2.18794361 -1.26282927 -0.10437525 28 | H -0.12133841 -2.31635373 0.79987325 29 | H 0.22663560 -2.00643122 -0.88734886 30 | H 1.14834814 -0.40532251 1.55280900 31 | H 2.15327210 -1.18259709 0.33198960 32 | H 1.29564501 0.45837391 -1.38389788 33 | H 2.11591575 1.28013898 -0.05856919 34 | H -0.13761965 2.30980257 -0.77849415 35 | H 0.01956981 1.99500653 0.93644690 36 | H -2.24481452 1.14593304 -0.15154508 37 | -------------------------------------------------------------------------------- /TEST/ethyleneRotation/mopac/de-gsm/gscreate: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | file=molecule 4 | 5 | #nl $file > tmp.mole 6 | #nl link > tmp.link 7 | #join tmp.mole tmp.link > tmp.geom2 8 | #awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom 9 | 10 | #cat qstart tmp.geom qend > qcin 11 | #cat qstart molecule$1 qend > scratch/qcin$1 12 | cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 13 | 14 | #rm tmp.geom tmp.geom2 tmp.link tmp.mole 15 | 16 | 17 | -------------------------------------------------------------------------------- /TEST/ethyleneRotation/mopac/de-gsm/inpfileq: -------------------------------------------------------------------------------- 1 | # FSM/GSM/SSM inpfileq 2 | 3 | ------------- QCHEM Scratch Info ------------------------ 4 | $QCSCRATCH/ # path for scratch dir. end with "/" 5 | GSM_go1q # name of run 6 | --------------------------------------------------------- 7 | 8 | ------------ String Info -------------------------------- 9 | SM_TYPE GSM # SSM, FSM or GSM 10 | RESTART 0 # read restart.xyz 11 | MAX_OPT_ITERS 80 # maximum iterations 12 | STEP_OPT_ITERS 30 # for FSM/SSM 13 | CONV_TOL 0.0005 # perp grad 14 | ADD_NODE_TOL 0.1 # for GSM 15 | SCALING 1.0 # for opt steps 16 | SSM_DQMAX 0.8 # add step size 17 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 18 | INT_THRESH 2.0 # intermediate detection 19 | MIN_SPACING 5.0 # node spacing SSM 20 | BOND_FRAGMENTS 1 # make IC's for fragments 21 | INITIAL_OPT 0 # opt steps first node 22 | FINAL_OPT 150 # opt steps last SSM node 23 | PRODUCT_LIMIT 100.0 # kcal/mol 24 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 25 | NNODES 9 # including endpoints 26 | --------------------------------------------------------- 27 | -------------------------------------------------------------------------------- /TEST/ethyleneRotation/mopac/de-gsm/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | Step 2 3 | C 0.66560204 0.00000000 0.00000000 4 | C -0.66555970 0.00000000 0.00000000 5 | H -1.23967945 0.92228617 -0.05058564 6 | H 1.23965778 -0.92231833 0.05060017 7 | H 1.23965778 0.92231833 -0.05060017 8 | H -1.23967945 -0.92228617 0.05058564 9 | 6 10 | Step 3 11 | C 0.66543421 0.00807607 0.00254083 12 | C -0.66543186 -0.00709879 -0.00260160 13 | H -1.23542454 -0.06339719 -0.92708417 14 | H 1.24370124 -0.03492594 -0.91749945 15 | H 1.23541877 0.06474270 0.92700959 16 | H -1.24367682 0.03648516 0.91742380 17 | -------------------------------------------------------------------------------- /TEST/ethyleneRotation/mopac/de-gsm/stringfile.standard: -------------------------------------------------------------------------------- 1 | 6 2 | 0.000000 3 | C 0.665602 0.000000 0.000000 4 | C -0.665560 0.000000 0.000000 5 | H -1.239679 0.922286 -0.050586 6 | H 1.239658 -0.922318 0.050600 7 | H 1.239658 0.922318 -0.050600 8 | H -1.239679 -0.922286 0.050586 9 | 6 10 | 32.850548 11 | C 0.633732 0.000764 -0.000879 12 | C -0.695465 0.068320 -0.270271 13 | H -0.973380 -0.851843 0.341405 14 | H 1.278116 0.884774 0.077546 15 | H 1.186358 -0.936884 -0.112246 16 | H -1.429377 0.835391 -0.035587 17 | 6 18 | 110.921453 19 | C 0.480807 -0.087997 -0.020865 20 | C -0.819717 0.213910 -0.399085 21 | H -0.176616 -0.664485 0.741674 22 | H 1.255475 0.641274 0.287004 23 | H 0.972561 -0.997719 -0.426777 24 | H -1.711014 0.779445 -0.175673 25 | 6 26 | 113.680151 27 | C 0.439444 -0.185193 0.018729 28 | C -0.851332 0.330331 -0.269523 29 | H 0.140888 -0.822609 0.890009 30 | H 1.226628 0.491921 0.417973 31 | H 0.907501 -0.889049 -0.700492 32 | H -1.857235 0.683894 -0.335441 33 | 6 34 | 112.519457 35 | C 0.453427 -0.244936 0.014679 36 | C -0.844803 0.276209 -0.275144 37 | H 0.186310 -0.781462 0.951727 38 | H 1.245996 0.468540 0.314079 39 | H 0.897335 -1.023635 -0.640281 40 | H -1.920736 0.288635 -0.309631 41 | 6 42 | 82.477842 43 | C 0.366601 0.143813 -0.148378 44 | C -0.830211 -0.725317 -0.021263 45 | H -0.058040 1.080792 -0.571852 46 | H 1.098887 -0.211364 -0.879912 47 | H 0.875493 0.454637 0.778977 48 | H -1.458681 -0.330292 0.820009 49 | 6 50 | 89.261181 51 | C 0.449466 -0.024345 -0.081148 52 | C -0.901536 -0.500768 -0.053375 53 | H -0.289241 0.732602 -0.644215 54 | H 1.100404 -0.341416 -0.898686 55 | H 0.970037 0.513942 0.718387 56 | H -1.330436 -0.265647 0.952824 57 | 6 58 | 27.533917 59 | C 0.640136 -0.019431 -0.008104 60 | C -0.704888 -0.257028 -0.016075 61 | H -1.139216 0.322412 -0.870137 62 | H 1.249235 -0.265455 -0.877733 63 | H 1.202382 0.341793 0.852610 64 | H -1.247345 -0.129988 0.919858 65 | 6 66 | 0.001010 67 | C 0.665434 0.008076 0.002541 68 | C -0.665432 -0.007099 -0.002602 69 | H -1.235425 -0.063397 -0.927084 70 | H 1.243701 -0.034926 -0.917499 71 | H 1.235419 0.064743 0.927010 72 | H -1.243677 0.036485 0.917424 73 | -------------------------------------------------------------------------------- /TEST/ethyleneRotation/qchem/de-gsm/gscreate: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | file=molecule 4 | 5 | #nl $file > tmp.mole 6 | #nl link > tmp.link 7 | #join tmp.mole tmp.link > tmp.geom2 8 | #awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom 9 | 10 | #cat qstart tmp.geom qend > qcin 11 | #cat qstart molecule$1 qend > scratch/qcin$1 12 | cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 13 | 14 | #rm tmp.geom tmp.geom2 tmp.link tmp.mole 15 | -------------------------------------------------------------------------------- /TEST/ethyleneRotation/qchem/de-gsm/inpfileq: -------------------------------------------------------------------------------- 1 | 2 | # FSM/GSM/SSM inpfileq 3 | 4 | ------------- QCHEM Scratch Info ------------------------ 5 | $QCSCRATCH/ # path for scratch dir. end with "/" 6 | GSM_go1q # name of run 7 | --------------------------------------------------------- 8 | 9 | ------------ String Info -------------------------------- 10 | SM_TYPE GSM # SSM, FSM or GSM 11 | RESTART 0 # read restart.xyz 12 | MAX_OPT_ITERS 80 # maximum iterations 13 | STEP_OPT_ITERS 30 # for FSM/SSM 14 | CONV_TOL 0.0005 # perp grad 15 | ADD_NODE_TOL 0.1 # for GSM 16 | SCALING 1.0 # for opt steps 17 | SSM_DQMAX 0.8 # add step size 18 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 19 | INT_THRESH 2.0 # intermediate detection 20 | MIN_SPACING 5.0 # node spacing SSM 21 | BOND_FRAGMENTS 1 # make IC's for fragments 22 | INITIAL_OPT 0 # opt steps first node 23 | FINAL_OPT 150 # opt steps last SSM node 24 | PRODUCT_LIMIT 100.0 # kcal/mol 25 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 26 | NNODES 9 # including endpoints 27 | --------------------------------------------------------- 28 | -------------------------------------------------------------------------------- /TEST/ethyleneRotation/qchem/de-gsm/qend: -------------------------------------------------------------------------------- 1 | $end 2 | -------------------------------------------------------------------------------- /TEST/ethyleneRotation/qchem/de-gsm/qstart: -------------------------------------------------------------------------------- 1 | $rem 2 | JOBTYPE FORCE 3 | EXCHANGE B3LYP 4 | ! CORRELATION PBE 5 | ! UNRESTRICTED TRUE 6 | SCF_ALGORITHM rca_diis 7 | SCF_MAX_CYCLES 150 8 | BASIS 6-31G* 9 | ! BASIS LANL2DZ 10 | ! ECP LANL2DZ 11 | WAVEFUNCTION_ANALYSIS FALSE 12 | GEOM_OPT_MAX_CYCLES 300 13 | 14 | scf_convergence 6 15 | 16 | SYM_IGNORE TRUE 17 | SYMMETRY FALSE 18 | 19 | molden_format true 20 | $end 21 | 22 | 23 | $molecule 24 | 0 1 25 | -------------------------------------------------------------------------------- /TEST/ethyleneRotation/qchem/de-gsm/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | Step 2 3 | C 0.66560204 0.00000000 0.00000000 4 | C -0.66555970 0.00000000 0.00000000 5 | H -1.23967945 0.92228617 -0.05058564 6 | H 1.23965778 -0.92231833 0.05060017 7 | H 1.23965778 0.92231833 -0.05060017 8 | H -1.23967945 -0.92228617 0.05058564 9 | 6 10 | Step 3 11 | C 0.66543421 0.00807607 0.00254083 12 | C -0.66543186 -0.00709879 -0.00260160 13 | H -1.23542454 -0.06339719 -0.92708417 14 | H 1.24370124 -0.03492594 -0.91749945 15 | H 1.23541877 0.06474270 0.92700959 16 | H -1.24367682 0.03648516 0.91742380 17 | -------------------------------------------------------------------------------- /TEST/ethyleneRotation/qchem/de-gsm/stringfile.standard: -------------------------------------------------------------------------------- 1 | 6 2 | 0.000000 3 | C 0.665602 0.000000 0.000000 4 | C -0.665560 0.000000 0.000000 5 | H -1.239679 0.922286 -0.050586 6 | H 1.239658 -0.922318 0.050600 7 | H 1.239658 0.922318 -0.050600 8 | H -1.239679 -0.922286 0.050586 9 | 6 10 | 13.780310 11 | C 0.653646 -0.003726 -0.026008 12 | C -0.677326 -0.060936 -0.158262 13 | H -1.225900 -0.874680 0.326709 14 | H 1.187267 0.935453 0.124372 15 | H 1.297798 -0.874092 -0.158918 16 | H -1.235501 0.878503 -0.107925 17 | 6 18 | 64.957763 19 | C 0.583732 -0.053826 -0.094747 20 | C -0.781241 -0.124982 -0.335798 21 | H -0.933431 -0.698520 0.639033 22 | H 1.150912 0.780481 0.350624 23 | H 1.228801 -0.868007 -0.429623 24 | H -1.247272 0.848457 -0.123169 25 | 6 26 | 82.231267 27 | C 0.443431 -0.128702 -0.153993 28 | C -0.937997 -0.085856 -0.461192 29 | H -0.216097 -0.643583 0.700610 30 | H 1.014154 0.555981 0.505279 31 | H 1.075829 -0.882850 -0.635303 32 | H -1.373418 0.792924 0.065924 33 | 6 34 | 101.332948 35 | C 0.525735 -0.259179 -0.208048 36 | C -0.851632 -0.309189 -0.305006 37 | H -0.415808 -0.310477 0.851697 38 | H 1.172016 0.360793 0.448167 39 | H 1.131256 -0.971982 -0.790717 40 | H -1.543790 0.459858 0.060083 41 | 6 42 | 62.641735 43 | C 0.665761 0.012589 0.010824 44 | C -0.634425 -0.078096 0.353322 45 | H -0.860351 0.463252 -0.636515 46 | H 1.044639 0.156556 -0.996924 47 | H 1.475231 -0.054488 0.753464 48 | H -1.696816 -0.086079 0.493335 49 | 6 50 | 51.876494 51 | C 0.687754 -0.004173 0.036113 52 | C -0.615077 -0.106980 0.334189 53 | H -0.939810 0.195644 -0.759277 54 | H 1.069172 0.041357 -0.971006 55 | H 1.471730 0.024343 0.808301 56 | H -1.675079 -0.034992 0.545425 57 | 6 58 | 21.666469 59 | C 0.673307 0.006328 0.033670 60 | C -0.646032 -0.190651 0.155559 61 | H -1.091926 -0.122435 -0.855914 62 | H 1.129602 0.125531 -0.945619 63 | H 1.374508 -0.057105 0.867102 64 | H -1.480625 0.219747 0.720185 65 | 6 66 | -0.000139 67 | C 0.665434 0.008076 0.002541 68 | C -0.665432 -0.007099 -0.002602 69 | H -1.235425 -0.063397 -0.927084 70 | H 1.243701 -0.034926 -0.917499 71 | H 1.235419 0.064743 0.927010 72 | H -1.243677 0.036485 0.917424 73 | -------------------------------------------------------------------------------- /TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/inpfileq: -------------------------------------------------------------------------------- 1 | # FSM/GSM/SSM inpfileq 2 | 3 | ------------- QCHEM Scratch Info ------------------------ 4 | $QCSCRATCH/ # path for scratch dir. end with "/" 5 | GSM_go1q # name of run 6 | --------------------------------------------------------- 7 | 8 | ------------ String Info -------------------------------- 9 | SM_TYPE GSM # SSM, FSM or GSM 10 | RESTART 0 # read restart.xyz 11 | MAX_OPT_ITERS 120 # maximum iterations 12 | STEP_OPT_ITERS 30 # for FSM/SSM 13 | CONV_TOL 0.0005 # perp grad 14 | ADD_NODE_TOL 0.1 # for GSM 15 | SCALING 1.0 # for opt steps 16 | SSM_DQMAX 0.8 # add step size 17 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 18 | INT_THRESH 2.0 # intermediate detection 19 | MIN_SPACING 5.0 # node spacing SSM 20 | BOND_FRAGMENTS 1 # make IC's for fragments 21 | INITIAL_OPT 0 # opt steps first node 22 | FINAL_OPT 150 # opt steps last SSM node 23 | PRODUCT_LIMIT 100.0 # kcal/mol 24 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 25 | NNODES 9 # including endpoints 26 | --------------------------------------------------------- 27 | -------------------------------------------------------------------------------- /TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 11 2 | Step 5 3 | H 0.41797324 0.94736684 -0.39562105 4 | C 0.23463898 1.11282329 0.66131673 5 | C 0.64075280 0.23925801 1.58339559 6 | H -0.28695375 2.01445005 0.96002081 7 | H 0.46045309 0.40790985 2.64613421 8 | O 1.30089798 -0.91413688 1.27688069 9 | H 1.50257557 -1.39412410 2.10286864 10 | O 1.19203118 -2.73369610 3.40309101 11 | C 0.37322499 -3.45250540 2.86892341 12 | H -0.00656927 -4.36236697 3.36949173 13 | H -0.02689882 -3.23019659 1.86359922 14 | 11 15 | Step 20 16 | H -0.19936743 0.59407144 0.74388584 17 | C -0.40617656 -0.33905946 1.27660171 18 | C 0.86105725 -0.80690813 1.99099738 19 | H -1.21318809 -0.17115368 1.99621611 20 | H 1.15156591 -0.07305690 2.75681870 21 | O 1.87101317 -0.96523074 0.99795803 22 | H 2.71471571 -1.12994105 1.44729950 23 | O 0.30236175 -2.25148677 3.85738347 24 | C 0.59626418 -2.13750850 2.68899351 25 | H -0.73244687 -1.08584907 0.54426337 26 | H 0.68810598 -3.02017613 2.01425240 27 | -------------------------------------------------------------------------------- /TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/stringfile.standard: -------------------------------------------------------------------------------- 1 | 11 2 | 0.000000 3 | H 0.417973 0.947367 -0.395621 4 | C 0.234639 1.112823 0.661317 5 | C 0.640753 0.239258 1.583396 6 | H -0.286954 2.014450 0.960021 7 | H 0.460453 0.407910 2.646134 8 | O 1.300898 -0.914137 1.276881 9 | H 1.502576 -1.394124 2.102869 10 | O 1.192031 -2.733696 3.403091 11 | C 0.373225 -3.452505 2.868923 12 | H -0.006569 -4.362367 3.369492 13 | H -0.026899 -3.230197 1.863599 14 | 11 15 | -1.778260 16 | H 0.111327 0.636785 -0.190579 17 | C 0.040974 0.864117 0.862500 18 | C 0.711478 0.187246 1.794395 19 | H -0.607428 1.692746 1.088688 20 | H 0.698338 0.361907 2.864529 21 | O 1.516854 -0.853081 1.381077 22 | H 1.920053 -1.330146 2.167792 23 | O 1.125364 -2.659719 3.294191 24 | C 0.296988 -3.281424 2.657377 25 | H -0.365118 -4.009914 3.139672 26 | H 0.176767 -3.136448 1.574426 27 | 11 28 | -1.033450 29 | H -0.087848 0.446552 -0.033640 30 | C -0.085076 0.673037 1.022161 31 | C 0.753936 0.099332 1.883262 32 | H -0.809266 1.415397 1.311346 33 | H 0.826053 0.278284 2.950393 34 | O 1.640486 -0.839237 1.387051 35 | H 2.156558 -1.263501 2.126035 36 | O 1.027471 -2.641282 3.359284 37 | C 0.267116 -3.133161 2.549138 38 | H -0.689411 -3.575580 2.851542 39 | H 0.502343 -3.148496 1.475645 40 | 11 41 | -0.105310 42 | H -0.183695 0.360736 0.096163 43 | C -0.150842 0.530181 1.162503 44 | C 0.799268 0.025981 1.948054 45 | H -0.946239 1.157276 1.529410 46 | H 0.912011 0.159819 3.018312 47 | O 1.761517 -0.773773 1.351662 48 | H 2.383306 -1.140180 2.028229 49 | O 0.817701 -2.721676 3.475931 50 | C 0.205940 -3.027421 2.473289 51 | H -0.879122 -3.186939 2.484047 52 | H 0.708478 -3.148633 1.504071 53 | 11 54 | 0.434300 55 | H -0.189371 0.292847 0.113754 56 | C -0.144788 0.392189 1.188589 57 | C 0.888491 -0.032360 1.913642 58 | H -1.004014 0.879399 1.619297 59 | H 1.028303 0.064716 2.984550 60 | O 1.917867 -0.669075 1.236863 61 | H 2.627344 -0.956958 1.857129 62 | O 0.492148 -2.763683 3.504097 63 | C 0.094876 -2.881702 2.363649 64 | H -0.968464 -2.795551 2.109056 65 | H 0.780225 -3.071293 1.526792 66 | 11 67 | 1.949710 68 | H -0.236350 0.148334 0.163122 69 | C -0.137979 0.198566 1.238711 70 | C 0.975261 -0.154804 1.881689 71 | H -1.014395 0.578441 1.739369 72 | H 1.204047 -0.006497 2.931349 73 | O 2.021731 -0.629063 1.106947 74 | H 2.788385 -0.904088 1.659032 75 | O 0.177998 -2.682883 3.572604 76 | C 0.002824 -2.652281 2.373684 77 | H -0.945199 -2.313548 1.933323 78 | H 0.758329 -2.984207 1.649625 79 | 11 80 | 25.024590 81 | H -0.253306 0.071175 0.277171 82 | C -0.182918 0.032639 1.353095 83 | C 0.945358 -0.350696 1.981416 84 | H -1.022394 0.459258 1.881466 85 | H 1.224664 -0.000779 2.973857 86 | O 2.039316 -0.516626 1.121297 87 | H 2.811834 -0.885420 1.604189 88 | O -0.104373 -2.672826 3.470226 89 | C 0.120313 -2.447801 2.299781 90 | H -0.735920 -2.040600 1.690392 91 | H 0.771739 -3.009796 1.626475 92 | 11 93 | 47.522970 94 | H -0.329227 -0.092794 0.355220 95 | C -0.308691 -0.167614 1.428260 96 | C 0.926484 -0.662446 2.094527 97 | H -1.047840 0.372421 1.987658 98 | H 1.242637 -0.158530 3.022751 99 | O 1.979764 -0.666423 1.130689 100 | H 2.819279 -0.952095 1.548376 101 | O -0.060373 -2.450741 3.441762 102 | C 0.345547 -2.097429 2.284369 103 | H -0.798281 -1.796464 1.666270 104 | H 0.714650 -2.848192 1.568616 105 | 11 106 | -26.835910 107 | H -0.199367 0.594071 0.743886 108 | C -0.406177 -0.339059 1.276602 109 | C 0.861057 -0.806908 1.990997 110 | H -1.213188 -0.171154 1.996216 111 | H 1.151566 -0.073057 2.756819 112 | O 1.871013 -0.965231 0.997958 113 | H 2.714716 -1.129941 1.447299 114 | O 0.302362 -2.251487 3.857383 115 | C 0.596264 -2.137509 2.688994 116 | H -0.732447 -1.085849 0.544263 117 | H 0.688106 -3.020176 2.014252 118 | -------------------------------------------------------------------------------- /TEST/methanolFormaldehydeHydTransfer/mopac/de-gsm/stringfile.standard.fr: -------------------------------------------------------------------------------- 1 | 11 2 | 3 | H -0.351903 -0.148585 0.361989 4 | C -0.328870 -0.216962 1.435915 5 | C 0.938342 -0.675554 2.111141 6 | H -1.064777 0.328351 1.991568 7 | H 1.257067 -0.155880 3.027492 8 | O 1.985211 -0.675991 1.137653 9 | H 2.834259 -0.958079 1.549178 10 | O -0.041727 -2.456822 3.418630 11 | C 0.370913 -2.092781 2.313705 12 | H -0.841740 -1.632925 1.603866 13 | H 0.727175 -2.835079 1.577362 14 | 11 15 | 16 | H -0.329227 -0.092794 0.355220 17 | C -0.308691 -0.167614 1.428260 18 | C 0.926484 -0.662446 2.094527 19 | H -1.047840 0.372421 1.987658 20 | H 1.242637 -0.158530 3.022751 21 | O 1.979764 -0.666423 1.130689 22 | H 2.819279 -0.952095 1.548376 23 | O -0.060373 -2.450741 3.441762 24 | C 0.345547 -2.097429 2.284369 25 | H -0.798281 -1.796464 1.666270 26 | H 0.714650 -2.848192 1.568616 27 | 11 28 | 29 | H -0.306920 -0.033962 0.347192 30 | C -0.290397 -0.116611 1.419220 31 | C 0.912396 -0.649869 2.077276 32 | H -1.032408 0.419351 1.981630 33 | H 1.224676 -0.161866 3.017475 34 | O 1.972313 -0.657323 1.123502 35 | H 2.801968 -0.945823 1.547256 36 | O -0.077889 -2.447412 3.466224 37 | C 0.318098 -2.108167 2.254761 38 | H -0.738910 -1.951775 1.733496 39 | H 0.701022 -2.866849 1.560467 40 | 11 41 | 42 | H -0.318026 -0.043148 0.363612 43 | C -0.314389 -0.165511 1.432695 44 | C 0.925601 -0.652826 2.094956 45 | H -1.076039 0.326511 2.005846 46 | H 1.247352 -0.145589 3.019876 47 | O 1.976148 -0.648083 1.127787 48 | H 2.794989 -1.022142 1.517493 49 | O -0.088437 -2.426415 3.438667 50 | C 0.350589 -2.090173 2.287836 51 | H -0.775772 -1.801681 1.632322 52 | H 0.761933 -2.851251 1.607410 53 | 11 54 | 55 | H -0.329227 -0.092794 0.355220 56 | C -0.308691 -0.167614 1.428260 57 | C 0.926484 -0.662446 2.094527 58 | H -1.047840 0.372421 1.987658 59 | H 1.242637 -0.158530 3.022751 60 | O 1.979764 -0.666423 1.130689 61 | H 2.819279 -0.952095 1.548376 62 | O -0.060373 -2.450741 3.441762 63 | C 0.345547 -2.097429 2.284369 64 | H -0.798281 -1.796464 1.666270 65 | H 0.714650 -2.848192 1.568616 66 | 11 67 | 68 | H -0.340269 -0.142213 0.349163 69 | C -0.301830 -0.170116 1.423786 70 | C 0.927760 -0.672306 2.094753 71 | H -1.017453 0.416599 1.966845 72 | H 1.237750 -0.171754 3.026439 73 | O 1.984630 -0.685643 1.135476 74 | H 2.838053 -0.880573 1.575932 75 | O -0.032608 -2.475371 3.443117 76 | C 0.340611 -2.104521 2.280873 77 | H -0.819344 -1.790957 1.700092 78 | H 0.666649 -2.843452 1.532022 79 | 11 80 | 81 | H -0.298769 -0.036264 0.346633 82 | C -0.298887 -0.171207 1.413243 83 | C 0.928299 -0.665979 2.091062 84 | H -1.073688 0.311354 1.979336 85 | H 1.245026 -0.139954 3.006650 86 | O 1.988199 -0.683052 1.130762 87 | H 2.828038 -0.940608 1.563403 88 | O -0.037049 -2.451834 3.458021 89 | C 0.349298 -2.098613 2.294898 90 | H -0.809396 -1.801048 1.698217 91 | H 0.662879 -2.843100 1.546273 92 | 11 93 | 94 | H -0.329227 -0.092794 0.355220 95 | C -0.308691 -0.167614 1.428260 96 | C 0.926484 -0.662446 2.094527 97 | H -1.047840 0.372421 1.987658 98 | H 1.242637 -0.158530 3.022751 99 | O 1.979764 -0.666423 1.130689 100 | H 2.819279 -0.952095 1.548376 101 | O -0.060373 -2.450741 3.441762 102 | C 0.345547 -2.097429 2.284369 103 | H -0.798281 -1.796464 1.666270 104 | H 0.714650 -2.848192 1.568616 105 | 11 106 | 107 | H -0.360991 -0.149179 0.367896 108 | C -0.318139 -0.164197 1.443603 109 | C 0.924768 -0.659157 2.098189 110 | H -1.020774 0.430874 1.991869 111 | H 1.240406 -0.178212 3.038802 112 | O 1.971741 -0.649577 1.130889 113 | H 2.810479 -0.963299 1.532574 114 | O -0.083493 -2.449661 3.424464 115 | C 0.341925 -2.095930 2.273081 116 | H -0.786742 -1.790949 1.634190 117 | H 0.764770 -2.851018 1.592942 118 | -------------------------------------------------------------------------------- /TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/gscreate: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | file=molecule 4 | 5 | #nl $file > tmp.mole 6 | #nl link > tmp.link 7 | #join tmp.mole tmp.link > tmp.geom2 8 | #awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom 9 | 10 | #cat qstart tmp.geom qend > qcin 11 | #cat qstart molecule$1 qend > scratch/qcin$1 12 | cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 13 | 14 | #rm tmp.geom tmp.geom2 tmp.link tmp.mole 15 | -------------------------------------------------------------------------------- /TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/inpfileq: -------------------------------------------------------------------------------- 1 | 2 | # FSM/GSM/SSM inpfileq 3 | 4 | ------------- QCHEM Scratch Info ------------------------ 5 | $QCSCRATCH/ # path for scratch dir. end with "/" 6 | GSM_go1q # name of run 7 | --------------------------------------------------------- 8 | 9 | ------------ String Info -------------------------------- 10 | SM_TYPE GSM # SSM, FSM or GSM 11 | RESTART 0 # read restart.xyz 12 | MAX_OPT_ITERS 80 # maximum iterations 13 | STEP_OPT_ITERS 30 # for FSM/SSM 14 | CONV_TOL 0.0005 # perp grad 15 | ADD_NODE_TOL 0.1 # for GSM 16 | SCALING 1.0 # for opt steps 17 | SSM_DQMAX 0.8 # add step size 18 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 19 | INT_THRESH 2.0 # intermediate detection 20 | MIN_SPACING 5.0 # node spacing SSM 21 | BOND_FRAGMENTS 1 # make IC's for fragments 22 | INITIAL_OPT 0 # opt steps first node 23 | FINAL_OPT 150 # opt steps last SSM node 24 | PRODUCT_LIMIT 100.0 # kcal/mol 25 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 26 | NNODES 9 # including endpoints 27 | --------------------------------------------------------- 28 | -------------------------------------------------------------------------------- /TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/qend: -------------------------------------------------------------------------------- 1 | $end 2 | -------------------------------------------------------------------------------- /TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/qstart: -------------------------------------------------------------------------------- 1 | $rem 2 | JOBTYPE FORCE 3 | EXCHANGE B3LYP 4 | ! CORRELATION PBE 5 | ! UNRESTRICTED TRUE 6 | SCF_ALGORITHM rca_diis 7 | SCF_MAX_CYCLES 150 8 | BASIS 6-31G* 9 | ! BASIS LANL2DZ 10 | ! ECP LANL2DZ 11 | WAVEFUNCTION_ANALYSIS FALSE 12 | GEOM_OPT_MAX_CYCLES 300 13 | 14 | scf_convergence 6 15 | 16 | SYM_IGNORE TRUE 17 | SYMMETRY FALSE 18 | 19 | molden_format true 20 | $end 21 | 22 | 23 | $molecule 24 | 0 1 25 | -------------------------------------------------------------------------------- /TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/scratch/initial0001.xyz: -------------------------------------------------------------------------------- 1 | 11 2 | Step 5 3 | H 0.41797324 0.94736684 -0.39562105 4 | C 0.23463898 1.11282329 0.66131673 5 | C 0.64075280 0.23925801 1.58339559 6 | H -0.28695375 2.01445005 0.96002081 7 | H 0.46045309 0.40790985 2.64613421 8 | O 1.30089798 -0.91413688 1.27688069 9 | H 1.50257557 -1.39412410 2.10286864 10 | O 1.19203118 -2.73369610 3.40309101 11 | C 0.37322499 -3.45250540 2.86892341 12 | H -0.00656927 -4.36236697 3.36949173 13 | H -0.02689882 -3.23019659 1.86359922 14 | 11 15 | Step 20 16 | H -0.19936743 0.59407144 0.74388584 17 | C -0.40617656 -0.33905946 1.27660171 18 | C 0.86105725 -0.80690813 1.99099738 19 | H -1.21318809 -0.17115368 1.99621611 20 | H 1.15156591 -0.07305690 2.75681870 21 | O 1.87101317 -0.96523074 0.99795803 22 | H 2.71471571 -1.12994105 1.44729950 23 | O 0.30236175 -2.25148677 3.85738347 24 | C 0.59626418 -2.13750850 2.68899351 25 | H -0.73244687 -1.08584907 0.54426337 26 | H 0.68810598 -3.02017613 2.01425240 27 | -------------------------------------------------------------------------------- /TEST/methanolFormaldehydeHydTransfer/qchem/de-gsm/stringfile.standard: -------------------------------------------------------------------------------- 1 | 11 2 | 0.000000 3 | H 0.417973 0.947367 -0.395621 4 | C 0.234639 1.112823 0.661317 5 | C 0.640753 0.239258 1.583396 6 | H -0.286954 2.014450 0.960021 7 | H 0.460453 0.407910 2.646134 8 | O 1.300898 -0.914137 1.276881 9 | H 1.502576 -1.394124 2.102869 10 | O 1.192031 -2.733696 3.403091 11 | C 0.373225 -3.452505 2.868923 12 | H -0.006569 -4.362367 3.369492 13 | H -0.026899 -3.230197 1.863599 14 | 11 15 | 1.183521 16 | H 0.057002 0.595267 -0.191130 17 | C -0.003387 0.777347 0.877206 18 | C 0.767280 0.117186 1.739984 19 | H -0.691662 1.534591 1.233738 20 | H 0.712088 0.300942 2.813275 21 | O 1.686864 -0.814643 1.352529 22 | H 1.942388 -1.329380 2.138683 23 | O 1.117218 -2.702732 3.393627 24 | C 0.280384 -3.182516 2.658215 25 | H -0.523511 -3.834894 3.046809 26 | H 0.280934 -2.989098 1.571132 27 | 11 28 | 3.663935 29 | H -0.141515 0.244769 -0.001183 30 | C -0.134575 0.455592 1.063644 31 | C 0.847870 0.021751 1.852666 32 | H -0.929025 1.068741 1.473122 33 | H 0.864516 0.235909 2.920953 34 | O 1.912398 -0.696155 1.380422 35 | H 2.285659 -1.202061 2.120241 36 | O 1.001392 -2.735069 3.388092 37 | C 0.197633 -2.957360 2.508592 38 | H -0.863993 -3.183675 2.729672 39 | H 0.478390 -2.946580 1.439877 40 | 11 41 | 6.299598 42 | H -0.253855 -0.027399 0.166073 43 | C -0.180174 0.200305 1.225459 44 | C 0.932752 -0.050198 1.914933 45 | H -1.019093 0.687100 1.709026 46 | H 1.023311 0.199107 2.971869 47 | O 2.052544 -0.582489 1.336137 48 | H 2.566238 -1.036694 2.022298 49 | O 0.668716 -2.821995 3.482140 50 | C 0.091401 -2.785276 2.418695 51 | H -0.998230 -2.600422 2.335908 52 | H 0.613797 -2.947456 1.456165 53 | 11 54 | 12.231001 55 | H -0.328973 -0.139184 0.311313 56 | C -0.169929 -0.026186 1.378893 57 | C 1.040320 -0.175315 1.918571 58 | H -0.996282 0.315677 1.992176 59 | H 1.230496 0.106031 2.954067 60 | O 2.147984 -0.415065 1.144090 61 | H 2.817807 -0.859211 1.686625 62 | O -0.098206 -2.722568 3.564587 63 | C -0.053975 -2.579661 2.363167 64 | H -0.928880 -2.277058 1.755283 65 | H 0.807390 -2.874021 1.725809 66 | 11 67 | 59.288766 68 | H -0.310861 -0.214025 0.327418 69 | C -0.230984 -0.268496 1.410483 70 | C 1.023767 -0.517903 2.016150 71 | H -1.040617 0.143102 2.002421 72 | H 1.214175 -0.126767 3.014798 73 | O 2.102103 -0.561651 1.133236 74 | H 2.839307 -1.009742 1.576376 75 | O -0.210611 -2.315636 3.447231 76 | C 0.153329 -2.046875 2.294736 77 | H -0.755680 -1.807787 1.458835 78 | H 0.773773 -2.633029 1.600648 79 | 11 80 | -0.135269 81 | H -0.259437 -0.056381 0.284885 82 | C -0.369852 -0.287633 1.347242 83 | C 0.925920 -0.670216 2.076262 84 | H -1.096195 0.293488 1.916078 85 | H 1.110077 -0.162447 3.032330 86 | O 1.992644 -0.710165 1.150390 87 | H 2.788336 -1.110441 1.551736 88 | O 0.026206 -2.470974 3.511575 89 | C 0.454322 -2.093047 2.442330 90 | H -0.881014 -1.300029 1.285868 91 | H 0.906805 -2.788826 1.687472 92 | 11 93 | -19.289558 94 | H -0.120638 0.233386 0.407561 95 | C -0.433465 -0.336229 1.287044 96 | C 0.801128 -0.778072 2.076685 97 | H -1.113592 0.260693 1.900105 98 | H 0.998322 -0.122524 2.936271 99 | O 1.901943 -0.817993 1.166210 100 | H 2.691693 -1.086987 1.664403 101 | O 0.597693 -2.514138 3.770487 102 | C 0.600849 -2.193486 2.603488 103 | H -0.987107 -1.213194 0.928529 104 | H 0.547124 -2.951762 1.787715 105 | 11 106 | -21.526454 107 | H -0.199367 0.594071 0.743886 108 | C -0.406177 -0.339059 1.276602 109 | C 0.861057 -0.806908 1.990997 110 | H -1.213188 -0.171154 1.996216 111 | H 1.151566 -0.073057 2.756819 112 | O 1.871013 -0.965231 0.997958 113 | H 2.714716 -1.129941 1.447299 114 | O 0.302362 -2.251487 3.857383 115 | C 0.596264 -2.137509 2.688994 116 | H -0.732447 -1.085849 0.544263 117 | H 0.688106 -3.020176 2.014252 118 | -------------------------------------------------------------------------------- /TPLsList.cmake: -------------------------------------------------------------------------------- 1 | TRIBITS_REPOSITORY_DEFINE_TPLS( 2 | MKL cmake/TPLS PT 3 | ) 4 | -------------------------------------------------------------------------------- /Version.cmake: -------------------------------------------------------------------------------- 1 | # 2 | # Single file that needs to be changed on when branching 3 | # 4 | IF("${REPOSITORY_NAME}" STREQUAL "") 5 | # Need to set the repository name 6 | SET(REPOSITORY_NAME molecularGSM) 7 | ENDIF() 8 | 9 | # Version info 10 | SET(${REPOSITORY_NAME}_VERSION 0.0.1) 11 | SET(${REPOSITORY_NAME}_MAJOR_VERSION 00) 12 | SET(${REPOSITORY_NAME}_MAJOR_MINOR_VERSION 000000) 13 | SET(${REPOSITORY_NAME}_VERSION_STRING "0.0.1 (Dev)") 14 | -------------------------------------------------------------------------------- /athena.pbs: -------------------------------------------------------------------------------- 1 | ##!/bin/bash 2 | ##This file was created on 12/12/2016 3 | 4 | #this is a pbs script for Athena HPC, change accordingly 5 | PBS -l nodes=1:ppn=4 -l walltime=18:00:00 6 | PBS -N test 7 | PBS -o test.o 8 | PBS -e test.e 9 | 10 | cd $PBS_O_WORKDIR 11 | module load CMake 12 | #module load Intel/13.x 13 | pwd 14 | echo $MKLROOT 15 | echo $LD_LIBRARY_PATH 16 | export OMP_NUM_THREADS=1 17 | #source /export/zimmerman/paulzim/qchem/qchemapr272016/paul.set.local 18 | source /export/zimmerman/craldaz/bin/qchem.source 19 | echo "working on ctest" 20 | ctest -V 21 | 22 | -------------------------------------------------------------------------------- /cmake/FindMKL.cmake: -------------------------------------------------------------------------------- 1 | ################################################################################ 2 | # 3 | # \file cmake/FindMKL.cmake 4 | # \author J. Bakosi 5 | # \copyright 2012-2015, Jozsef Bakosi, 2016, Los Alamos National Security, LLC. 6 | # \brief Find the Math Kernel Library from Intel 7 | # \date Thu 26 Jan 2017 02:05:50 PM MST 8 | # 9 | ################################################################################ 10 | 11 | # Find the Math Kernel Library from Intel 12 | # 13 | # MKL_FOUND - System has MKL 14 | # MKL_INCLUDE_DIRS - MKL include files directories 15 | # MKL_LIBRARIES - The MKL libraries 16 | # MKL_INTERFACE_LIBRARY - MKL interface library 17 | # MKL_SEQUENTIAL_LAYER_LIBRARY - MKL sequential layer library 18 | # MKL_CORE_LIBRARY - MKL core library 19 | # 20 | # The environment variables MKLROOT and INTEL are used to find the library. 21 | # Everything else is ignored. If MKL is found "-DMKL_ILP64" is added to 22 | # CMAKE_C_FLAGS and CMAKE_CXX_FLAGS. 23 | # 24 | # Example usage: 25 | # 26 | # find_package(MKL) 27 | # if(MKL_FOUND) 28 | # target_link_libraries(TARGET ${MKL_LIBRARIES}) 29 | # endif() 30 | 31 | # If already in cache, be silent 32 | if (MKL_INCLUDE_DIRS AND MKL_LIBRARIES AND MKL_INTERFACE_LIBRARY AND 33 | MKL_SEQUENTIAL_LAYER_LIBRARY AND MKL_CORE_LIBRARY) 34 | set (MKL_FIND_QUIETLY TRUE) 35 | endif() 36 | 37 | if(NOT BUILD_SHARED_LIBS) 38 | if (WIN32) 39 | set(INT_LIB "mkl_intel_ilp64.lib") 40 | set(SEQ_LIB "mkl_sequential.lib") 41 | set(THR_LIB "mkl_intel_thread.lib") 42 | set(COR_LIB "mkl_core.lib") 43 | else() 44 | set(INT_LIB "libmkl_intel_ilp64.a") 45 | set(SEQ_LIB "libmkl_sequential.a") 46 | set(THR_LIB "libmkl_intel_thread.a") 47 | set(COR_LIB "libmkl_core.a") 48 | endif() 49 | else() 50 | set(INT_LIB "mkl_intel_ilp64") 51 | set(SEQ_LIB "mkl_sequential") 52 | set(THR_LIB "mkl_intel_thread") 53 | set(COR_LIB "mkl_core") 54 | endif() 55 | 56 | if(MSVC) 57 | set(ProgramFilesx86 "ProgramFiles(x86)") 58 | set(INTEL_ROOT_DEFAULT $ENV{${ProgramFilesx86}}/IntelSWTools/compilers_and_libraries/windows) 59 | else() 60 | set(INTEL_ROOT_DEFAULT "/opt/intel") 61 | endif() 62 | set(INTEL_ROOT ${INTEL_ROOT_DEFAULT} CACHE PATH "Folder contains intel libs") 63 | find_path(MKL_ROOT include/mkl.h PATHS $ENV{MKLROOT} ${INTEL_ROOT}/mkl 64 | DOC "Folder contains MKL") 65 | 66 | find_path(MKL_INCLUDE_DIR NAMES mkl.h HINTS ${MKL_ROOT}/include /usr/include/mkl) 67 | 68 | 69 | find_library(MKL_INTERFACE_LIBRARY 70 | NAMES ${INT_LIB} 71 | PATHS ${MKL_ROOT}/lib 72 | ${MKL_ROOT}/lib/intel64 73 | ${MKL_ROOT}/lib/intel64_win 74 | ${INTEL_ROOT}/mkl/lib/intel64) 75 | 76 | find_library(MKL_SEQUENTIAL_LAYER_LIBRARY 77 | NAMES ${SEQ_LIB} 78 | PATHS ${MKL_ROOT}/lib 79 | ${MKL_ROOT}/lib/intel64 80 | ${INTEL_ROOT}/mkl/lib/intel64) 81 | 82 | find_library(MKL_CORE_LIBRARY 83 | NAMES ${COR_LIB} 84 | PATHS ${MKL_ROOT}/lib 85 | ${MKL_ROOT}/lib/intel64 86 | ${INTEL_ROOT}/mkl/lib/intel64) 87 | 88 | set(MKL_INCLUDE_DIRS ${MKL_INCLUDE_DIR}) 89 | set(MKL_LIBRARIES ${MKL_INTERFACE_LIBRARY} ${MKL_SEQUENTIAL_LAYER_LIBRARY} ${MKL_CORE_LIBRARY}) 90 | 91 | if(NOT WIN32 AND NOT APPLE) 92 | # Added -Wl block to avoid circular dependencies. 93 | # https://stackoverflow.com/questions/5651869/what-are-the-start-group-and-end-group-command-line-options 94 | # https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor 95 | set(MKL_LIBRARIES -Wl,--start-group ${MKL_LIBRARIES} -Wl,--end-group) 96 | elseif(APPLE) 97 | # MacOS does not support --start-group and --end-group 98 | set(MKL_LIBRARIES -Wl,${MKL_LIBRARIES} -Wl,) 99 | endif() 100 | 101 | # message("1 ${MKL_INCLUDE_DIR}") 102 | # message("2 ${MKL_INTERFACE_LIBRARY}") 103 | # message("3 ${MKL_SEQUENTIAL_LAYER_LIBRARY}") 104 | # message("4 ${MKL_CORE_LIBRARY}") 105 | 106 | if (MKL_INCLUDE_DIR AND 107 | MKL_INTERFACE_LIBRARY AND 108 | MKL_SEQUENTIAL_LAYER_LIBRARY AND 109 | MKL_CORE_LIBRARY) 110 | 111 | 112 | if (NOT DEFINED ENV{CRAY_PRGENVPGI} AND 113 | NOT DEFINED ENV{CRAY_PRGENVGNU} AND 114 | NOT DEFINED ENV{CRAY_PRGENVCRAY} AND 115 | NOT DEFINED ENV{CRAY_PRGENVINTEL} AND 116 | NOT MSVC) 117 | set(ABI "-m64") 118 | endif() 119 | 120 | set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DMKL_ILP64 ${ABI}") 121 | set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DMKL_ILP64 ${ABI}") 122 | 123 | else() 124 | set(MKL_INCLUDE_DIRS "") 125 | set(MKL_LIBRARIES "") 126 | set(MKL_INTERFACE_LIBRARY "") 127 | set(MKL_SEQUENTIAL_LAYER_LIBRARY "") 128 | set(MKL_CORE_LIBRARY "") 129 | 130 | endif() 131 | 132 | # Handle the QUIETLY and REQUIRED arguments and set MKL_FOUND to TRUE if 133 | # all listed variables are TRUE. 134 | INCLUDE(FindPackageHandleStandardArgs) 135 | FIND_PACKAGE_HANDLE_STANDARD_ARGS(MKL DEFAULT_MSG MKL_LIBRARIES MKL_INCLUDE_DIRS MKL_INTERFACE_LIBRARY MKL_SEQUENTIAL_LAYER_LIBRARY MKL_CORE_LIBRARY) 136 | 137 | MARK_AS_ADVANCED(MKL_INCLUDE_DIRS MKL_LIBRARIES MKL_INTERFACE_LIBRARY MKL_SEQUENTIAL_LAYER_LIBRARY MKL_CORE_LIBRARY) 138 | 139 | -------------------------------------------------------------------------------- /cmake/tribits: -------------------------------------------------------------------------------- 1 | ../TriBITS/tribits -------------------------------------------------------------------------------- /docs/CMakeLists.txt: -------------------------------------------------------------------------------- 1 | ################################################################################ 2 | # Documentation Generation 3 | # 4 | # Build documentation using Doxygen (www.doxygen.org) 5 | # Builds the docs in the docs/ directory (HTML and LaTeX formats for a .pdf) 6 | ################################################################################ 7 | find_package(Doxygen) 8 | if(DOXYGEN_FOUND) 9 | configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY) 10 | add_custom_target(doc ALL ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} 11 | COMMENT "Generating API documentation with Doxygen" VERBATIM 12 | ) 13 | endif(DOXYGEN_FOUND) 14 | -------------------------------------------------------------------------------- /docs/assets/project_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ZimmermanGroup/molecularGSM/38156654295d3515a3e14dfd4e962e34bc059580/docs/assets/project_logo.png -------------------------------------------------------------------------------- /flux.pbs: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | ##This file was created on 12/12/2016 3 | #this is a pbs script for the FLUX HPC, change accordingly 4 | 5 | 6 | #### PBS preamble 7 | #PBS -N test 8 | #PBS -M craldaz@umich.edu 9 | #PBS -m abe 10 | 11 | # Change the number of cores (ppn=1), amount of memory, and walltime: 12 | #PBS -l nodes=1:ppn=1,mem=2000mb,walltime=00:30:20 13 | #PBS -j oe 14 | #PBS -V 15 | 16 | # Change "example_flux" to the name of your Flux allocation: 17 | #PBS -A ners590f16_fluxod 18 | #PBS -q fluxod 19 | #PBS -l qos=flux 20 | 21 | #### End PBS preamble 22 | 23 | # Show list of CPUs you ran on, if you're running under PBS 24 | if [ -n "$PBS_NODEFILE" ]; then cat $PBS_NODEFILE; fi 25 | 26 | # Change to the directory you submitted from 27 | if [ -n "$PBS_O_WORKDIR" ]; then cd $PBS_O_WORKDIR; fi 28 | 29 | # Put your job commands here: 30 | echo "Hello, world" 31 | module load intel/14.0.2 32 | #module load cmake 33 | #alias mopac='~/opt/mopac/MOPAC2016.exe' 34 | #export LD_LIBRARY_PATH=~/opt/mopac/ 35 | #export MOPAC_LICENSE=~/opt/mopac/ 36 | ctest -V 37 | 38 | -------------------------------------------------------------------------------- /pixi-build.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | # Exit immediately if any command fails 4 | set -e 5 | 6 | # Get the directory where this script is located 7 | REPO_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd ) 8 | 9 | # Activate the pixi environment using the manifest in the repository 10 | eval "$(pixi shell-hook --manifest-path ${REPO_DIR})" 11 | 12 | # Create a subshell to isolate the build process 13 | ( 14 | # Create BUILD directory if it doesn't exist 15 | mkdir -p BUILD 16 | # Change to the BUILD directory 17 | cd BUILD 18 | 19 | # Run CMake to configure the project 20 | # Uses the repository directory as source 21 | # Sets installation path to the active conda environment 22 | cmake ${REPO_DIR} -DCMAKE_INSTALL_PREFIX=${CONDA_PREFIX} 23 | 24 | # Compile the project 25 | make -j8 26 | # Install the compiled binaries and libraries 27 | make install 28 | ) 29 | -------------------------------------------------------------------------------- /pixi.toml: -------------------------------------------------------------------------------- 1 | [workspace] 2 | authors = ["Zimmerman Group, Andreas Copan (pixi environment)"] 3 | channels = ["conda-forge"] 4 | name = "molecularGSM" 5 | platforms = ["linux-64"] 6 | version = "0.1.0" 7 | 8 | [tasks] 9 | build = "pixi-build.sh" 10 | test = { cmd = "gsm", cwd = "TEST/dielsAlder/mopac/de-gsm" } 11 | 12 | [dependencies] 13 | cmake = "*" 14 | make = "*" 15 | cxx-compiler = "*" 16 | libstdcxx-ng = "*" 17 | mkl = "*" 18 | mkl-include = "*" 19 | mopac = "*" 20 | -------------------------------------------------------------------------------- /tutorial/geometryOptimization/getOptEnergy: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | list=`ls *.out` 4 | for item in $list 5 | do 6 | energyLine=`grep 'Final energy is' $item` 7 | counter=0 8 | for word in $energyLine 9 | do 10 | let counter=counter+1 11 | energy=$word 12 | done 13 | if [ $counter -eq 4 ]; 14 | then 15 | echo $energy $item >> optimized_energies_output_fromqchem.txt 16 | else 17 | echo "Energy N/A " $item >> optimized_energies_output_fromqchem.txt 18 | fi 19 | done 20 | 21 | -------------------------------------------------------------------------------- /tutorial/geometryOptimization/makeXYZ: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | qJobAry=`ls *.inp.out` 3 | mkdir xyzFiles 4 | 5 | for item in $qJobAry 6 | do 7 | lineEnd=`grep -n "END OF MOLDEN-FORMATTED" $item | grep -Eo '^[^:]+'` 8 | if [ -z "$lineEnd" ]; 9 | then 10 | continue 11 | fi 12 | 13 | lineEndm1=$(($lineEnd-1)) 14 | 15 | IFS='.' read -ra nameAry <<< "$item" 16 | counter=0 17 | 18 | for element in "${nameAry[@]}" 19 | do 20 | let counter=counter+1 21 | done 22 | 23 | counter2=0 24 | outFileName= 25 | for element in "${nameAry[@]}" 26 | do 27 | if [[ $counter2 -eq 0 || $counter2 -eq $(($counter-2)) ]]; 28 | then 29 | let counter2=counter2+1 30 | continue 31 | fi 32 | outFileName+=$element 33 | outFileName+="." 34 | let counter2=counter2+1 35 | done 36 | outFileName+="xyz" 37 | 38 | alist=`grep -A 1 "NAtoms" $item` 39 | 40 | x=0 41 | for thing in $alist 42 | do 43 | if [ $x -eq 8 ] 44 | then 45 | echo $thing 46 | numAtoms=$thing 47 | fi 48 | let x=x+1 49 | done 50 | 51 | let lineStart=lineEndm1-numAtoms-3 52 | 53 | lineStart=$(($lineEnd-$numAtoms-3)) 54 | csplit $item $lineStart $lineEndm1 55 | mv xx01 "xyzFiles/$outFileName" 56 | done 57 | 58 | rm xx* 59 | -------------------------------------------------------------------------------- /tutorial/geometryOptimization/q001.template.inp: -------------------------------------------------------------------------------- 1 | $rem 2 | JOBTYPE OPT 3 | EXCHANGE B3LYP 4 | ! CORRELATION PBE 5 | ! UNRESTRICTED TRUE 6 | SCF_ALGORITHM diis 7 | SCF_MAX_CYCLES 150 8 | BASIS LANL2DZ 9 | ECP LANL2DZ 10 | WAVEFUNCTION_ANALYSIS FALSE 11 | GEOM_OPT_MAX_CYCLES 300 12 | 13 | scf_convergence 6 14 | 15 | SYM_IGNORE TRUE 16 | SYMMETRY FALSE 17 | 18 | molden_format true 19 | $end 20 | 21 | 22 | $molecule 23 | 0 1 24 | 25 | $end 26 | -------------------------------------------------------------------------------- /tutorial/geometryOptimization/submitall.qsh: -------------------------------------------------------------------------------- 1 | #PBS -t 2 2 | #PBS -l nodes=1:ppn=1 -l pmem=2000MB -l walltime=24:00:00 3 | 4 | ID=`printf "%0*d\n" 3 ${PBS_ARRAYID}` 5 | #i=$PBS_ARRAYID 6 | 7 | source /export/zimmerman/paulzim/qchem/qchemjan42013c/paul.set.local 8 | 9 | cd $PBS_O_WORKDIR 10 | 11 | name=`ls q$ID*.inp` 12 | 13 | qchem -np 1 $name $name.out 14 | 15 | rm $QCSCRATCH 16 | 17 | #rm -f submitall.qsh.o* 18 | #rm -f submitall.qsh.e* 19 | --------------------------------------------------------------------------------