├── src ├── out.data ├── __init__.py ├── min.rst ├── control ├── test.in └── in.lj ├── README.md ├── lib ├── qm_charge.dat ├── inp ├── output_ndx.py ├── test.png ├── qm_ener.dat ├── __init__.py ├── unit_test.sh ├── copy_ff.py ├── g03.xyz ├── README ├── e_gaussian.py ├── epydoc.cfg ├── todo ├── g03.geo ├── e_poscar_2_geo.py ├── g03.gjf ├── test.py ├── e_2_reaxData.py ├── e_t_ldh.py ├── e_2_csv.py ├── e_2_multi_geo.py ├── config.conf └── e_2_trainset.py ├── tools ├── __init__.py ├── vasp │ ├── POTCAR │ ├── kpoints │ │ └── note │ ├── sum_energy.sh │ ├── vtotav │ ├── freq │ │ └── vasp_freq │ ├── dptools │ │ └── __init__.py │ ├── subvasp.sh │ ├── charges │ │ ├── atoms.dat │ │ └── index.ndx │ ├── ana-fe.sh │ ├── xdat2pdb.py │ ├── get_kpoints_kplib.py │ ├── gen.sh │ ├── gen-tao.sh │ ├── note-compile.txt │ ├── ana-fe.py │ ├── fe │ │ └── ti_get_poscar.py │ ├── wall.py │ ├── raman │ │ └── vasp_raman.gnuplot.sh │ ├── refine-ab.py │ ├── any2vasp │ ├── eos-ase │ │ └── ana-eos.py │ ├── get_oszicar.py │ ├── gather_poscars.py │ ├── fix-atoms.py.1 │ ├── gether_poscar │ ├── select_frame.py │ ├── vasp2.zwicky │ ├── fix-atoms.py │ ├── dimer │ │ └── readme │ ├── vasp2 │ └── get_homo_lumo_gap.py ├── g03 │ ├── __init__.py │ ├── qm_ener.dat │ ├── angles │ ├── bonds │ ├── gout2pdb │ ├── qm_charge.dat │ ├── test.gjf │ ├── freq.gjf │ └── N2O.gjf ├── kmc │ ├── run │ ├── note │ ├── 00-ref │ │ ├── jacs.9b13694.pdf │ │ └── s41929-022-00846-8.pdf │ ├── 02-her │ │ ├── species.dat │ │ ├── species.template │ │ └── rxn.csv │ ├── 03-solvent │ │ ├── species.dat │ │ ├── species.template │ │ └── rxn.csv │ ├── 04-her │ │ ├── species.dat │ │ ├── species.template │ │ └── rxn.csv │ ├── 05-her │ │ ├── species.dat │ │ ├── species.template │ │ └── rxn.csv │ ├── species.dat │ ├── 01-acs │ │ ├── species.dat │ │ └── species.template │ ├── de │ ├── eact │ ├── species.template │ └── rxn ├── linux │ ├── __init__.py │ ├── pushgit │ ├── password-6.py │ ├── realpath │ ├── pdb2bgf_babel.py │ ├── dos2unix │ ├── g4z │ ├── pwdw │ ├── occ │ ├── getscihub │ ├── tocheng-zwicky │ ├── ion │ │ └── getcheng.py │ ├── pwdu-ubuntu │ ├── pwdu │ ├── ave.py │ └── html2docx ├── reax │ ├── __init__.py │ ├── lianchi │ │ └── __init__.py │ ├── ff │ │ ├── ffield.reax.065.unkown │ │ ├── ffield.reax.2021X12.HO │ │ ├── ffield.reax.054.CHO_image │ │ ├── ffield.reax.090.CHONSi_image │ │ └── ffield.reax.2008X3.Au │ ├── reax2 │ │ ├── C_C.png │ │ ├── C_H.png │ │ ├── C_N.png │ │ ├── C_O.png │ │ ├── C_S.png │ │ ├── H_H.png │ │ ├── H_N.png │ │ ├── H_O.png │ │ ├── H_S.png │ │ ├── N_N.png │ │ ├── N_S.png │ │ ├── O_N.png │ │ ├── O_O.png │ │ ├── O_S.png │ │ ├── S_S.png │ │ ├── C_Si.png │ │ ├── H_Si.png │ │ ├── N_Si.png │ │ ├── O_Si.png │ │ ├── S_Si.png │ │ └── Si_Si.png │ ├── fort │ │ └── getBo.py │ ├── functions │ │ └── pbo3 │ │ │ └── plot.py │ ├── mo.py │ └── addcharge.py ├── builder │ ├── __init__.py │ └── inp_tpl.py ├── caltech │ ├── __init__.py │ ├── dat │ │ ├── WAT │ │ │ ├── .lcd │ │ │ ├── Meso.bgf │ │ │ ├── mW.bgf │ │ │ ├── F3C.bgf │ │ │ ├── F3C_OPT.bgf │ │ │ ├── dreiding3Wat.bgf │ │ │ ├── tip3.bgf │ │ │ └── tip3_charmm.bgf │ │ └── LAMMPS │ │ │ ├── in.lammps.solv.atom.eng │ │ │ ├── in.lammps.solv.atom.eng.rigidSolu │ │ │ ├── in.lammps.atom.eng │ │ │ └── in.lammps.solv.2pt │ └── Packages │ │ ├── Math │ │ ├── FFT │ │ │ ├── FFT.bs │ │ │ └── FFT.so │ │ ├── Macopt.bs │ │ ├── Macopt │ │ │ ├── Macopt.bs │ │ │ └── Macopt.so │ │ ├── Polynomial │ │ │ └── .exists │ │ ├── FFT.so │ │ ├── Macopt.so │ │ └── Matrix.pm │ │ ├── auto │ │ └── Math │ │ │ ├── FFT │ │ │ ├── FFT.bs │ │ │ ├── FFT.so │ │ │ └── .packlist │ │ │ ├── FFT32 │ │ │ ├── FFT32.bs │ │ │ ├── FFT32.so │ │ │ └── .packlist │ │ │ └── FFT64 │ │ │ ├── FFT64.bs │ │ │ └── FFT64.so │ │ ├── Term │ │ └── Size │ │ │ └── Unix │ │ │ ├── .exists │ │ │ ├── Unix.bs │ │ │ └── Unix.so │ │ └── FSearch │ │ ├── test.pl │ │ ├── a.out │ │ ├── Fsearch.so │ │ ├── Fsearch_wrap.o │ │ ├── FSearch-大小写冲突-chengtao.so │ │ ├── Fsearch.h │ │ ├── create_info.dat │ │ └── Fsearch.i ├── lammps │ ├── __init__.py │ ├── find_half_life.py │ ├── xrd │ │ ├── xrd.in │ │ ├── lammps.data │ │ ├── log.cite │ │ ├── log.lammps │ │ └── plot-xrd.py │ └── neb │ │ └── get_coords.py ├── network │ ├── 101900.log │ ├── 104008.log │ └── netscan.sh ├── project │ ├── __init__.py │ ├── ldh │ │ ├── __init__.py │ │ └── sintering_model.py │ └── li │ │ └── cry.py ├── sas │ ├── example │ │ ├── low.dat │ │ ├── ndx.dat │ │ ├── sur_sas.dat │ │ ├── UFF.atoms │ │ ├── min.rst │ │ ├── lammps.etor.0 │ │ ├── lammps.ecoa.0 │ │ ├── lammps.ehb.0 │ │ ├── lammps.epen.0 │ │ ├── lammps.eval.0 │ │ ├── lammps.econ.0 │ │ ├── cn.inp │ │ ├── input.dat │ │ ├── sas.inp │ │ └── cn.log │ ├── example-3 │ │ ├── sur_sas.dat │ │ ├── UFF.atoms │ │ └── input.dat │ ├── example-nlist │ │ ├── low.dat │ │ ├── ndx.dat │ │ ├── UFF.atoms │ │ ├── min.rst │ │ ├── lammps.etor.0 │ │ ├── lammps.ecoa.0 │ │ ├── lammps.ehb.0 │ │ ├── lammps.epen.0 │ │ ├── lammps.eval.0 │ │ ├── lammps.econ.0 │ │ ├── cn.inp │ │ ├── sas.inp │ │ ├── input.dat │ │ └── cn.log │ ├── sas │ ├── al │ │ ├── rhombi │ │ ├── distance │ │ ├── surface │ │ ├── rhombi_old │ │ ├── surface_old │ │ ├── rhombi.inp │ │ ├── surface_atom.inp │ │ └── compile.sh │ ├── sas-nlist │ ├── sas.03162016 │ ├── html │ │ ├── crarr.png │ │ ├── api-objects.txt │ │ ├── index.html │ │ └── frames.html │ ├── share │ │ ├── UFF.atoms │ │ ├── cn.inp │ │ └── sas.inp │ ├── compile.sh │ ├── cn.inp │ ├── filter.py │ ├── input.dat │ ├── nl.py │ ├── remove-low-coordinated.py │ └── example-2 │ │ └── input.dat ├── gromacs │ ├── mols │ │ ├── benzene │ │ │ ├── log │ │ │ ├── state.cpt │ │ │ ├── topol.tpr │ │ │ └── state_prev.cpt │ │ └── ifpsc-de │ │ │ ├── supergroups │ │ │ ├── masses │ │ │ ├── state.cpt │ │ │ ├── topol.tpr │ │ │ ├── state_prev.cpt │ │ │ ├── .traj.trr_offsets.npz │ │ │ ├── any2pdb.py │ │ │ ├── get_ave_box.py │ │ │ ├── setup_groups.py │ │ │ ├── input │ │ │ ├── log │ │ │ └── pbs │ ├── 2pt │ │ ├── supergroups │ │ ├── masses │ │ ├── run.sh │ │ ├── dos-r.png │ │ ├── dos-t.png │ │ ├── dos-v.png │ │ ├── dos.png │ │ ├── topol.tpr │ │ ├── log_opt │ │ ├── setup_groups.py │ │ ├── entropy_gas │ │ ├── entropy_solid │ │ ├── fluidicity │ │ └── input │ ├── topol.top.opls │ ├── get_ave_box.py │ └── npt-to-nvt.py ├── deepmd │ ├── reaxff-ml │ │ ├── type.raw │ │ ├── KPOINTS │ │ ├── pbs.gpu │ │ └── merge.py │ ├── gen_set.py │ ├── vasp2raw-dp.py │ ├── run.sh │ ├── trj2pdb.py │ ├── sp │ │ └── run.sh │ ├── merge-lammps.py │ └── get-sp.sh ├── inprogress │ ├── test.py │ ├── csv.py │ ├── parse_molid.py │ └── parse_molatom.py ├── nanocut │ ├── ot.png │ ├── to.png │ ├── vmdscene.tga │ ├── icosahedron │ │ ├── icosahedron-030.xyz.gz │ │ ├── icosahedron-036.xyz.gz │ │ └── icosahedron.py │ ├── decahedron │ │ └── decahedron.py │ ├── pt_to │ │ └── run.sh │ └── nw │ │ └── to_13_4.ini ├── fftool │ ├── oplsaa.ff.gromacs │ │ ├── forcefield.doc │ │ ├── aminoacids.r2b │ │ └── watermodels.dat │ └── convert_gromacs.py ├── garffield │ ├── crystal.py │ └── check_geo.py ├── jdft │ └── inp_jdft │ │ ├── cu │ │ ├── ce.in │ │ ├── u0.in │ │ ├── u1.in │ │ ├── kpoints │ │ └── common │ │ └── pt │ │ ├── ce.in │ │ ├── u0.in │ │ ├── u1.in │ │ ├── u2.in │ │ ├── kpoints │ │ └── common ├── crystal09 │ └── gaustocry │ │ ├── a.out │ │ └── gaustocry ├── dftb │ ├── uv │ │ └── uv-vis-gaussian.pdf │ ├── any2gen │ ├── gen2pdb │ ├── scan.py │ └── dftb-uv.py ├── fftool-git │ ├── fftool-master.zip │ └── fftool-master │ │ └── examples │ │ ├── opc.zmat │ │ ├── spc.zmat │ │ ├── spce.zmat │ │ ├── co2.zmat │ │ ├── opc3.zmat │ │ ├── tip4p.zmat │ │ ├── tip4pew.zmat │ │ ├── methanol.zmat │ │ ├── ethanol.zmat │ │ ├── co2.ff │ │ ├── vc.zmat │ │ ├── ethane.zmat │ │ ├── opc3.ff │ │ ├── spc.ff │ │ ├── spce.ff │ │ ├── ethyleneglycol.zmat │ │ ├── DMSO.zmat │ │ ├── tip4p.ff │ │ ├── urea.xyz │ │ ├── benzene.zmat │ │ ├── opc.ff │ │ ├── tip4pew.ff │ │ └── dmf.zmat ├── hun │ ├── Atom.dic │ ├── Cutoff.dic │ ├── frag.sh │ └── toVmd.py ├── ase │ ├── png.py │ ├── u2s.py │ ├── build-bulk.py │ ├── pdb2vasp.py │ ├── any2pdb.py │ ├── extract_atoms.py │ ├── any2png.py │ ├── center-com.py │ ├── move-atom-center.py │ ├── trj2pdb.py │ ├── estimate_nmol.py │ └── ase-translate.py ├── chemistry │ └── CPK-JmolPeriodicTable.pdf ├── cif │ ├── run.sh │ └── any2cif ├── wham │ ├── note │ └── lammps │ │ └── r00 │ │ ├── plumed.dat │ │ └── pbs.lammps ├── math │ ├── ave_std_s1.py │ ├── ave.py │ ├── int.py │ └── shapely-point-in-polygon.py ├── align │ └── v1 │ │ └── au.xyz ├── movies │ ├── length.py │ ├── rename.py │ └── merge.sh ├── ical │ └── test.py ├── pic │ └── crop.py ├── onyx │ ├── getback.py │ └── tocheng ├── c │ └── makefile.auto ├── vmd │ └── merge.py ├── msi2lmp │ └── replace_xx.py ├── puremd │ └── out.py ├── plot │ └── hist.py ├── pygen │ └── p2c ├── rdkit │ └── mol2xyz.py ├── maestro │ └── mae.py └── intermol │ └── gmx2lmp ├── test ├── glycine │ ├── fort.2 │ ├── fort.9 │ ├── bondchange.out │ ├── fort.35 │ ├── fort.13 │ ├── fort.20 │ ├── conti.gjf │ ├── fort.74 │ ├── qm_ener.dat │ ├── fort.72 │ ├── summary.txt │ ├── fort.99 │ ├── dipole.out │ ├── fort.55 │ ├── fort.56 │ ├── fort.71 │ ├── fort.73 │ ├── glycine.gjf │ ├── glycine.xyz │ ├── qm_charge.dat │ ├── freq.gjf │ ├── fort.91 │ └── molfra.out └── configParser │ ├── config │ ├── config.ini │ └── next.ini ├── examples ├── 05_vasp_raman │ ├── results │ │ ├── CHG │ │ ├── CHGCAR │ │ ├── REPORT │ │ ├── WAVECAR │ │ ├── phonon │ │ │ ├── CHG │ │ │ ├── CHGCAR │ │ │ ├── REPORT │ │ │ ├── WAVECAR │ │ │ ├── KPOINTS │ │ │ ├── PCDAT │ │ │ ├── IBZKPT │ │ │ ├── INCAR │ │ │ ├── POSCAR │ │ │ └── CONTCAR │ │ ├── POTCAR │ │ ├── KPOINTS │ │ ├── OUTCAR.phon │ │ ├── POSCAR.phon │ │ ├── DYNMAT │ │ ├── inp │ │ │ ├── KPOINTS │ │ │ └── POSCAR │ │ ├── vasp.nodes │ │ ├── LOG │ │ ├── log │ │ ├── PCDAT │ │ ├── XDATCAR │ │ ├── INCAR │ │ ├── POSCAR │ │ ├── vasp_raman.dat │ │ ├── IBZKPT │ │ └── CONTCAR │ ├── working_folder │ │ └── inp │ │ │ ├── KPOINTS │ │ │ └── POSCAR │ └── doc │ │ ├── raman-cal.pdf │ │ ├── raman-wiki.pdf │ │ └── readme.txt ├── 01_cut_a_sphere │ ├── README │ └── inp └── 03_xyz2cfg │ └── lammps_input ├── arc ├── linux_tools │ ├── scan │ │ ├── testcopy.log │ │ └── read.py │ ├── xrd │ │ └── modifyResidue.py │ ├── xtob │ ├── packmol │ ├── SerialReax │ ├── molfraanal │ ├── SerialReax_p │ ├── puremd-intel │ ├── puremd-openmpi │ ├── dffforcefield │ │ ├── dff2gmx.jar │ │ └── group_0709.py │ ├── qs_towhee │ ├── readcry.py │ ├── vle │ ├── sub_undernodes.py │ ├── qdelm │ ├── qsgrompp_l │ ├── old │ │ ├── changeCharge.py │ │ └── generateCoordXvg.py │ ├── cmdall │ ├── rm_m_size │ ├── cmdall2 │ ├── readpdb.py │ ├── subfolder │ ├── node.py │ ├── rm_m │ ├── dos2unix_all │ ├── gulp │ │ └── change.py │ ├── parse_xvg.py │ ├── qsgrompp │ └── lammps │ │ └── read_lmplog.py └── simulation_tools_py │ ├── template │ ├── water │ │ ├── towhee_ostwald │ │ ├── .svn │ │ │ └── text-base │ │ │ │ ├── towhee_ostwald.svn-base │ │ │ │ ├── towhee_coords.svn-base │ │ │ │ ├── water_coords.svn-base │ │ │ │ ├── box_01_step_00000000000000.pdb.svn-base │ │ │ │ └── box_01_step_00000000000200.pdb.svn-base │ │ ├── towhee_coords │ │ └── water_coords │ └── .svn │ │ ├── all-wcprops │ │ └── entries │ ├── docs │ ├── .svn │ │ ├── prop-base │ │ │ ├── crarr.png.svn-base │ │ │ └── uml_class_diagram_for_pdb_pdb.gif.svn-base │ │ └── text-base │ │ │ ├── crarr.png.svn-base │ │ │ └── uml_class_diagram_for_pdb_pdb.gif.svn-base │ ├── crarr.png │ ├── uml_class_diagram_for_pdb_pdb.gif │ ├── frames.html │ └── index.html │ ├── test.py │ ├── epydoc.cfg │ └── pre │ ├── opls.py │ ├── .svn │ └── text-base │ │ └── opls.py.svn-base │ ├── tools │ └── .svn │ │ └── all-wcprops │ ├── parser │ ├── eth.gro │ ├── hist.py │ └── dipole.py │ └── ifpsc │ └── .svn │ └── all-wcprops ├── setup.py ├── doc ├── html │ ├── crarr.png │ ├── frames.html │ └── index.html ├── tools │ ├── crarr.png │ ├── frames.html │ └── index.html └── config.conf ├── __init__.py ├── data └── reaxFF │ ├── HE_lg │ └── config.ini │ ├── LDH │ └── config.ini │ └── CLP │ └── config.ini ├── molecules └── ase │ └── get_mol.py └── .gitattributes /src/out.data: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /lib/qm_charge.dat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/vasp/POTCAR: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /test/glycine/fort.2: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /test/glycine/fort.9: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/g03/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/kmc/run: -------------------------------------------------------------------------------- 1 | 0 2 | -------------------------------------------------------------------------------- /tools/linux/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/reax/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /lib/inp: -------------------------------------------------------------------------------- 1 | 292 292 5000 2 | -------------------------------------------------------------------------------- /test/glycine/bondchange.out: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/builder/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/caltech/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/caltech/dat/WAT/.lcd: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/lammps/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/network/101900.log: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/network/104008.log: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/project/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/sas/example/low.dat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/sas/example/ndx.dat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /test/glycine/fort.35: -------------------------------------------------------------------------------- 1 | 234535.1 2 | -------------------------------------------------------------------------------- /tools/gromacs/mols/benzene/log: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/project/ldh/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/reax/lianchi/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/sas/example-3/sur_sas.dat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/sas/example-nlist/low.dat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/sas/example-nlist/ndx.dat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/sas/example/sur_sas.dat: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/CHG: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/CHGCAR: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/REPORT: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/WAVECAR: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /test/glycine/fort.13: -------------------------------------------------------------------------------- 1 | 0.0000 2 | -------------------------------------------------------------------------------- /tools/caltech/Packages/Math/FFT/FFT.bs: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/caltech/Packages/Math/Macopt.bs: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/reax/ff/ffield.reax.065.unkown: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/reax/ff/ffield.reax.2021X12.HO: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /arc/linux_tools/scan/testcopy.log: -------------------------------------------------------------------------------- 1 | ii 2 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/phonon/CHG: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/caltech/Packages/auto/Math/FFT/FFT.bs: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/gromacs/2pt/supergroups: -------------------------------------------------------------------------------- 1 | 1-176 2 | -------------------------------------------------------------------------------- /tools/reax/ff/ffield.reax.054.CHO_image: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/reax/ff/ffield.reax.090.CHONSi_image: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/phonon/CHGCAR: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/phonon/REPORT: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/phonon/WAVECAR: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /lib/output_ndx.py: -------------------------------------------------------------------------------- 1 | """ in develop 2 | """ 3 | -------------------------------------------------------------------------------- /tools/caltech/Packages/Math/Macopt/Macopt.bs: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/caltech/Packages/Math/Polynomial/.exists: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/caltech/Packages/Term/Size/Unix/.exists: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/caltech/Packages/Term/Size/Unix/Unix.bs: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/caltech/Packages/auto/Math/FFT32/FFT32.bs: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/caltech/Packages/auto/Math/FFT64/FFT64.bs: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tools/gromacs/mols/ifpsc-de/supergroups: -------------------------------------------------------------------------------- 1 | 1-50 2 | -------------------------------------------------------------------------------- /arc/linux_tools/xrd/modifyResidue.py: -------------------------------------------------------------------------------- 1 | f = open 2 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/template/water/towhee_ostwald: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/POTCAR: -------------------------------------------------------------------------------- 1 | ./phonon/POTCAR -------------------------------------------------------------------------------- /tools/deepmd/reaxff-ml/type.raw: -------------------------------------------------------------------------------- 1 | 0 2 | 1 3 | 1 4 | -------------------------------------------------------------------------------- /tools/gromacs/2pt/masses: -------------------------------------------------------------------------------- 1 | C3H 12.011 2 | H 1.008 3 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/KPOINTS: -------------------------------------------------------------------------------- 1 | ./phonon/KPOINTS -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/OUTCAR.phon: -------------------------------------------------------------------------------- 1 | ./phonon/OUTCAR -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/POSCAR.phon: -------------------------------------------------------------------------------- 1 | ./phonon/POSCAR -------------------------------------------------------------------------------- /tools/gromacs/mols/ifpsc-de/masses: -------------------------------------------------------------------------------- 1 | C 12.011 2 | H 1.008 3 | -------------------------------------------------------------------------------- /tools/kmc/note: -------------------------------------------------------------------------------- 1 | https://doi.org/10.1021/jacs.9b13694 2 | 3 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import setup 2 | setup(name='simpy2') 3 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/DYNMAT: -------------------------------------------------------------------------------- 1 | 1 2 0 2 | 12.011 3 | -------------------------------------------------------------------------------- /tools/vasp/kpoints/note: -------------------------------------------------------------------------------- 1 | http://muellergroup.jhu.edu/K-Points.html 2 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/template/water/.svn/text-base/towhee_ostwald.svn-base: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /test/glycine/fort.20: -------------------------------------------------------------------------------- 1 | 0 0: Normal run 1: Force field optimization 2 | -------------------------------------------------------------------------------- /tools/caltech/Packages/FSearch/test.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/perl -w 2 | use Fsearch; 3 | -------------------------------------------------------------------------------- /tools/inprogress/test.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | sys.stdout.write('Dive in') 4 | -------------------------------------------------------------------------------- /tools/linux/pushgit: -------------------------------------------------------------------------------- 1 | git add . 2 | git commit -m "bugfix" 3 | git push 4 | 5 | -------------------------------------------------------------------------------- /lib/test.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ensemble-learning/simpy/HEAD/lib/test.png -------------------------------------------------------------------------------- /src/min.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ensemble-learning/simpy/HEAD/src/min.rst -------------------------------------------------------------------------------- /tools/sas/example-3/UFF.atoms: -------------------------------------------------------------------------------- 1 | Pt 3.000 2 | O 3.0 3 | H 3.0 4 | EOF 5 | -------------------------------------------------------------------------------- /lib/qm_ener.dat: -------------------------------------------------------------------------------- 1 | g03 HF 0.00000000 2 | g03 ZPE 0.00000000 3 | -------------------------------------------------------------------------------- /tools/gromacs/2pt/run.sh: -------------------------------------------------------------------------------- 1 | DoSPT 2 | python2 ~/soft/simpy/tools/dos2pt/plot_dos.py 3 | -------------------------------------------------------------------------------- /tools/sas/sas: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ensemble-learning/simpy/HEAD/tools/sas/sas -------------------------------------------------------------------------------- /tools/vasp/sum_energy.sh: -------------------------------------------------------------------------------- 1 | cmdall "grep F= OSZICAR | tail -1 | cut -b 8-22" > results 2 | -------------------------------------------------------------------------------- /test/glycine/conti.gjf: -------------------------------------------------------------------------------- 1 | 2 | 3 | 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etor total 3 | -------------------------------------------------------------------------------- /data/reaxFF/HE_lg/config.ini: -------------------------------------------------------------------------------- 1 | [Description] 2 | system = High energy material 3 | element = C H O N S Si X 4 | [ Update ] 5 | -------------------------------------------------------------------------------- /tools/caltech/Packages/Math/FFT.so: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ensemble-learning/simpy/HEAD/tools/caltech/Packages/Math/FFT.so -------------------------------------------------------------------------------- /tools/dftb/uv/uv-vis-gaussian.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ensemble-learning/simpy/HEAD/tools/dftb/uv/uv-vis-gaussian.pdf -------------------------------------------------------------------------------- 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4 | password = data*1e6 5 | print "%06d"%password 6 | -------------------------------------------------------------------------------- /tools/sas/example-nlist/lammps.etor.0: -------------------------------------------------------------------------------- 1 | step: 0 2 | atom1 atom2 atom3 atom4 phi bo(23) etor total 3 | -------------------------------------------------------------------------------- /tools/sas/example/lammps.ecoa.0: -------------------------------------------------------------------------------- 1 | step: 0 2 | atom1 atom2 atom3 angle bo(12) bo(23) ecoa total 3 | -------------------------------------------------------------------------------- /tools/sas/example/lammps.ehb.0: -------------------------------------------------------------------------------- 1 | step: 0 2 | atom1 atom2 atom3 r(23) angle bo(12) ehb total 3 | -------------------------------------------------------------------------------- /tools/sas/example/lammps.epen.0: 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accessible_surface_area_read_nlist.f90 -o sas-nlist 2 | gfortran accessible_surface_area.f90 -o sas 3 | -------------------------------------------------------------------------------- /tools/sas/example-nlist/lammps.ecoa.0: -------------------------------------------------------------------------------- 1 | step: 0 2 | atom1 atom2 atom3 angle bo(12) bo(23) ecoa total 3 | -------------------------------------------------------------------------------- /tools/sas/example-nlist/lammps.ehb.0: -------------------------------------------------------------------------------- 1 | step: 0 2 | atom1 atom2 atom3 r(23) angle bo(12) ehb total 3 | -------------------------------------------------------------------------------- /tools/sas/example-nlist/lammps.epen.0: -------------------------------------------------------------------------------- 1 | step: 0 2 | atom1 atom2 atom3 angle bo(12) bo(23) epen total 3 | -------------------------------------------------------------------------------- /tools/vasp/dptools/__init__.py: -------------------------------------------------------------------------------- 1 | from dptools.bandout import * 2 | from dptools.gen import * 3 | from dptools.xyz import * 4 | 5 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/docs/.svn/prop-base/crarr.png.svn-base: -------------------------------------------------------------------------------- 1 | K 13 2 | svn:mime-type 3 | V 24 4 | application/octet-stream 5 | END 6 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/docs/crarr.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ensemble-learning/simpy/HEAD/arc/simulation_tools_py/docs/crarr.png -------------------------------------------------------------------------------- /data/reaxFF/LDH/config.ini: -------------------------------------------------------------------------------- 1 | [Description] 2 | system = clay force field 3 | element = Ca Si Al S 4 | [ Update ] 5 | 20130828 = new test 6 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/LOG: -------------------------------------------------------------------------------- 1 | Running on GPUs: GPU-6a2e5546-f507-741e-f7e8-b291a4e804a3,GPU-230df04e-4f52-dcdd-65ba-3df65d7e2565 2 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/log: -------------------------------------------------------------------------------- 1 | Running on GPUs: GPU-6a2e5546-f507-741e-f7e8-b291a4e804a3,GPU-230df04e-4f52-dcdd-65ba-3df65d7e2565 2 | -------------------------------------------------------------------------------- /tools/ase/png.py: -------------------------------------------------------------------------------- 1 | from ase.io import read, write 2 | 3 | data = read("CONTCAR") 4 | write("test.png", data, rotation="-60z, 120x") 5 | -------------------------------------------------------------------------------- /tools/caltech/Packages/Math/FFT/FFT.so: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ensemble-learning/simpy/HEAD/tools/caltech/Packages/Math/FFT/FFT.so -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/co2.zmat: -------------------------------------------------------------------------------- 1 | CO2 2 | 3 | O 4 | C 1 1.1490 5 | O 2 1.1490 1 180.00 6 | 7 | co2.ff 8 | -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/opc3.zmat: -------------------------------------------------------------------------------- 1 | OPC3 2 | 3 | Hw 4 | Ow 1 0.9789 5 | Hw 2 0.9789 1 109.47 6 | 7 | opc3.ff 8 | 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/tools/caltech/Packages/auto/Math/FFT32/FFT32.so: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ensemble-learning/simpy/HEAD/tools/caltech/Packages/auto/Math/FFT32/FFT32.so -------------------------------------------------------------------------------- /tools/caltech/Packages/auto/Math/FFT64/FFT64.so: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ensemble-learning/simpy/HEAD/tools/caltech/Packages/auto/Math/FFT64/FFT64.so -------------------------------------------------------------------------------- /tools/cif/run.sh: -------------------------------------------------------------------------------- 1 | python mismatch.py 3.51 3.51 5.76 5.76 > li_li2s.log # li li2s 2 | #python mismatch.py 3.51 3.51 5.76 5.76 > li_li2s.log # li li2s 3 | -------------------------------------------------------------------------------- /tools/sas/example-nlist/lammps.econ.0: -------------------------------------------------------------------------------- 1 | step:0 2 | atom1 atom2 atom3 atom4 phi bo(12) bo(23) bo(34) econ total 3 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/doc/readme.txt: -------------------------------------------------------------------------------- 1 | run the job: 2 | 1. gen_raman 3 | 2. qsub pbs 4 | 5 | note: 6 | It seems that no "selective dynamics" is allowed. 7 | -------------------------------------------------------------------------------- /lib/copy_ff.py: -------------------------------------------------------------------------------- 1 | import os 2 | from ffield import Ffield 3 | from output_ff import toFfield 4 | 5 | ff = Ffield("ffield") 6 | toFfield(ff, "ffield.new") 7 | -------------------------------------------------------------------------------- /tools/gromacs/2pt/log_opt: -------------------------------------------------------------------------------- 1 | 0 0.44843051351591123 2 | 1 0.44842988044568788 3 | 2 0.44843006382077549 4 | -------------------------------------------------------------------------------- /tools/gromacs/mols/ifpsc-de/.traj.trr_offsets.npz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ensemble-learning/simpy/HEAD/tools/gromacs/mols/ifpsc-de/.traj.trr_offsets.npz -------------------------------------------------------------------------------- /tools/kmc/04-her/species.dat: -------------------------------------------------------------------------------- 1 | H3O 0.1000 2 | H2O 1.0000 3 | H* 0.0000 4 | H2 0.0000 5 | e 1.0000 6 | -------------------------------------------------------------------------------- /tools/kmc/05-her/species.dat: -------------------------------------------------------------------------------- 1 | H3O 0.1000 2 | H2O 1.0000 3 | H* 0.0000 4 | H2 0.0000 5 | e 1.0000 6 | -------------------------------------------------------------------------------- /tools/nanocut/icosahedron/icosahedron-030.xyz.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ensemble-learning/simpy/HEAD/tools/nanocut/icosahedron/icosahedron-030.xyz.gz -------------------------------------------------------------------------------- /tools/nanocut/icosahedron/icosahedron-036.xyz.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ensemble-learning/simpy/HEAD/tools/nanocut/icosahedron/icosahedron-036.xyz.gz -------------------------------------------------------------------------------- /tools/sas/al/surface_atom.inp: -------------------------------------------------------------------------------- 1 | test_surface_atom.xyz 2 | .TRUE. 3 | 0.6 4 | 5 | ! coordination file (xyz file format) 6 | ! pbc_flag 7 | ! vector cut off 8 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/docs/.svn/prop-base/uml_class_diagram_for_pdb_pdb.gif.svn-base: -------------------------------------------------------------------------------- 1 | K 13 2 | svn:mime-type 3 | V 24 4 | application/octet-stream 5 | END 6 | -------------------------------------------------------------------------------- /tools/fftool/oplsaa.ff.gromacs/aminoacids.r2b: -------------------------------------------------------------------------------- 1 | ; rtp residue to rtp building block table 2 | ;GMX Force-field 3 | CYS CYSH 4 | LYS LYSH 5 | LYSN LYS 6 | -------------------------------------------------------------------------------- /tools/kmc/04-her/species.template: -------------------------------------------------------------------------------- 1 | H3O 0.0000 2 | e 0.0000 3 | H2O 0.0000 4 | H* 0.0000 5 | H2 0.0000 6 | -------------------------------------------------------------------------------- /tools/kmc/05-her/species.template: -------------------------------------------------------------------------------- 1 | H2O 0.0000 2 | e 0.0000 3 | OH- 0.0000 4 | H* 0.0000 5 | H2 0.0000 6 | -------------------------------------------------------------------------------- /data/reaxFF/CLP/config.ini: -------------------------------------------------------------------------------- 1 | [Description] 2 | system = CO2 capture 3 | element = C H O Ca Si Al S X 4 | [Update] 5 | version = ffield.00000 6 | 20130828 = new test 7 | -------------------------------------------------------------------------------- /lib/g03.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | Title Card Required 3 | N 0.0000 0.0000 -1.1984 4 | N 0.0000 0.0000 -0.0721 5 | O 0.0000 0.0000 1.1117 6 | -------------------------------------------------------------------------------- /tools/g03/gout2pdb: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import sys 4 | from ase.io import read, write 5 | 6 | atoms = read(sys.argv[1]) 7 | write('opt.pdb', atoms) 8 | 9 | -------------------------------------------------------------------------------- /tools/jdft/inp_jdft/cu/u0.in: -------------------------------------------------------------------------------- 1 | include coords 2 | include kpoints 3 | include common 4 | 5 | initial-state ce.$VAR 6 | target-mu -0.163167 7 | dump End None 8 | 9 | -------------------------------------------------------------------------------- /tools/jdft/inp_jdft/cu/u1.in: -------------------------------------------------------------------------------- 1 | include coords 2 | include kpoints 3 | include common 4 | 5 | initial-state ce.$VAR 6 | target-mu -0.119068 7 | dump End None 8 | 9 | -------------------------------------------------------------------------------- /tools/jdft/inp_jdft/pt/u0.in: -------------------------------------------------------------------------------- 1 | include coords 2 | include kpoints 3 | include common 4 | 5 | initial-state ce.$VAR 6 | target-mu -0.163167 7 | dump End None 8 | 9 | -------------------------------------------------------------------------------- /tools/jdft/inp_jdft/pt/u1.in: -------------------------------------------------------------------------------- 1 | include coords 2 | include kpoints 3 | include common 4 | 5 | initial-state ce.$VAR 6 | target-mu -0.185167 7 | dump End None 8 | 9 | -------------------------------------------------------------------------------- /tools/jdft/inp_jdft/pt/u2.in: -------------------------------------------------------------------------------- 1 | include coords 2 | include kpoints 3 | include common 4 | 5 | initial-state ce.$VAR 6 | target-mu -0.207266 7 | dump End None 8 | 9 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/template/.svn/all-wcprops: -------------------------------------------------------------------------------- 1 | K 25 2 | svn:wc:ra_dav:version-url 3 | V 63 4 | /svn/ms-tools-python~source-code-repository/!svn/ver/8/template 5 | END 6 | -------------------------------------------------------------------------------- /tools/caltech/Packages/FSearch/FSearch-大小写冲突-chengtao.so: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ensemble-learning/simpy/HEAD/tools/caltech/Packages/FSearch/FSearch-大小写冲突-chengtao.so -------------------------------------------------------------------------------- /tools/caltech/dat/WAT/Meso.bgf: -------------------------------------------------------------------------------- 1 | HETATM 1 WAT WAT B 1 0.000 0.000 0.000 Xe 0 0 0.0000 0 0 1.600 2 | FORMAT CONECT (a6,12i6) 3 | CONECT 1 4 | -------------------------------------------------------------------------------- /tools/g03/qm_charge.dat: -------------------------------------------------------------------------------- 1 | scan_01 1 1 -0.578105 # N 2 | scan_01 1 2 -1.693606 # N 3 | scan_01 1 3 2.271711 # O 4 | -------------------------------------------------------------------------------- /tools/gromacs/2pt/setup_groups.py: -------------------------------------------------------------------------------- 1 | print 1408, 176 2 | 3 | for i in range(0,1408): 4 | print 8,2 5 | print 8*i+1, 8*i+2, 8*i+3, 8*i+4, 8*i+5, 8*i+6, 8*i+7, 8*i+8 6 | -------------------------------------------------------------------------------- /tools/jdft/inp_jdft/cu/kpoints: -------------------------------------------------------------------------------- 1 | #Brillouin zone sampling 2 | kpoint-folding 1 1 1 # 3x3x1 uniform k-mesh 3 | kpoint 0 0 0 1 # gamma-centered k-point mesh 4 | 5 | -------------------------------------------------------------------------------- /tools/jdft/inp_jdft/pt/kpoints: -------------------------------------------------------------------------------- 1 | #Brillouin zone sampling 2 | kpoint-folding 1 1 1 # 3x3x1 uniform k-mesh 3 | kpoint 0 0 0 1 # gamma-centered k-point mesh 4 | 5 | -------------------------------------------------------------------------------- /tools/linux/pdb2bgf_babel.py: -------------------------------------------------------------------------------- 1 | import os 2 | import sys 3 | 4 | fname = sys.argv[1] 5 | 6 | CMD = "babel -ipdb %s.pdb -obgf %s.bgf"%(fname, fname) 7 | os.system(CMD) 8 | -------------------------------------------------------------------------------- /tools/wham/note: -------------------------------------------------------------------------------- 1 | http://membrane.urmc.rochester.edu/sites/default/files/wham/wham_talk.pdf 2 | http://www.alchemistry.org/wiki/Weighted_Histogram_Analysis_Method 3 | 4 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/docs/.svn/text-base/crarr.png.svn-base: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ensemble-learning/simpy/HEAD/arc/simulation_tools_py/docs/.svn/text-base/crarr.png.svn-base -------------------------------------------------------------------------------- /arc/simulation_tools_py/docs/uml_class_diagram_for_pdb_pdb.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ensemble-learning/simpy/HEAD/arc/simulation_tools_py/docs/uml_class_diagram_for_pdb_pdb.gif -------------------------------------------------------------------------------- /tools/ase/u2s.py: -------------------------------------------------------------------------------- 1 | import ase.io.vasp 2 | 3 | struct = ase.io.vasp.read_vasp('002-mp-126-sur-111.vasp') 4 | ase.io.vasp.write_vasp('POSCAR', struct*(2,2,1),direct=True, vasp5=True) 5 | 6 | -------------------------------------------------------------------------------- /tools/vasp/subvasp.sh: -------------------------------------------------------------------------------- 1 | python ~/soft/simpy/tools/vasp/get_potcar.py 2 | python ~/soft/simpy/tools/vasp/get_kpoint.py 3 | python ~/soft/simpy/tools/vasp/incar.py 4 | genpbs_vasp 5 | 6 | -------------------------------------------------------------------------------- /tools/wham/lammps/r00/plumed.dat: -------------------------------------------------------------------------------- 1 | 2 | UNITS LENGTH=A ENERGY=kcal/mol 3 | dd: DISTANCE ATOMS=1,2 4 | RESTRAINT ARG=dd KAPPA=25.0000 AT=2.5000 5 | PRINT ARG=dd FILE=colvar STRIDE=100 6 | -------------------------------------------------------------------------------- /lib/README: -------------------------------------------------------------------------------- 1 | 2012-12-31 12:04:51 2 | ADD 3 | getVol() : in Class System 4 | return the volume of the system 5 | 6 | toDO: 7 | 8 | 1. documentation 9 | 2. unit test 10 | -------------------------------------------------------------------------------- /tools/caltech/Packages/FSearch/Fsearch.h: -------------------------------------------------------------------------------- 1 | double Abs(double); 2 | void setResidual(int *, int, int, int, double *, int *); 3 | int getResidual(int, double **, double *, int *, int, int); 4 | -------------------------------------------------------------------------------- /tools/linux/dos2unix: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import sys 4 | filename = sys.argv[1] 5 | text = open(filename, 'rb').read().replace('\r\n', '\n') 6 | open(filename, 'wb').write(text) 7 | -------------------------------------------------------------------------------- /tools/math/ave_std_s1.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import sys 3 | 4 | if len(sys.argv) > 1: 5 | data = np.loadtxt(sys.argv[1]) 6 | print(np.average(data)) 7 | print(np.std(data)) 8 | -------------------------------------------------------------------------------- /tools/vasp/charges/atoms.dat: -------------------------------------------------------------------------------- 1 | 11 11 11 11 11 11 11 11 11 11 2 | 11 11 11 11 11 11 11 11 11 11 3 | 11 11 11 11 11 11 11 11 11 11 4 | 11 11 11 11 11 11 11 11 11 11 5 | 11 11 11 11 11 11 11 11 6 | -------------------------------------------------------------------------------- /examples/01_cut_a_sphere/README: -------------------------------------------------------------------------------- 1 | Generate a sphere from the pdb file 2 | 3 | run: 4 | python /home/tao/Nutstore/code/simupy/tools/build/sphere.py 5 | 6 | The details can be set in "inp" file 7 | -------------------------------------------------------------------------------- /tools/align/v1/au.xyz: -------------------------------------------------------------------------------- 1 | 5 2 | 3 | Au 5.0 5.0 1.0 4 | Au 5.0 -5.0 1.0 5 | Au -5.0 5.0 1.0 6 | Au -5.0 -5.0 1.0 7 | Au 0.0 0.0 1.0 8 | -------------------------------------------------------------------------------- /tools/vasp/ana-fe.sh: -------------------------------------------------------------------------------- 1 | cmdall "tar -xvzf *.tar.gz" 2 | cmdall "cd 5* && python ~/Soft/simpy/tools/vasp/fe_slow.py " 3 | cat ./*/5*/ave*.dat > fe.dat 4 | python ~/Soft/simpy/tools/math/int.py 5 | 6 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/epydoc.cfg: -------------------------------------------------------------------------------- 1 | [epydoc] 2 | name: scipy 3 | 4 | modules: mol.py, pdb.py, msd.py 5 | output: html 6 | target: ./docs/ 7 | graph: all 8 | dotpath: /usr/bin/dot 9 | 10 | 11 | -------------------------------------------------------------------------------- /tools/vasp/xdat2pdb.py: -------------------------------------------------------------------------------- 1 | from ase.io import read, write 2 | 3 | atoms = read('../POSCAR') 4 | write('input.pdb', atoms) 5 | 6 | traj = read('../XDATCAR', index='') 7 | write('output.pdb', traj) 8 | 9 | -------------------------------------------------------------------------------- /tools/kmc/03-solvent/rxn.csv: -------------------------------------------------------------------------------- 1 | # reaction , dE, dS , dE_act, dS_act 2 | H3O <--> H2O + H , -1.0 , -0.001965, 0.001 , 0.00 3 | H + H <--> H2 , -1.0 , -0.001965, 0.5 , -0.0005133 4 | -------------------------------------------------------------------------------- /tools/math/ave.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import sys 3 | 4 | fname = sys.argv[1] 5 | 6 | data = np.loadtxt(fname) 7 | data = data.transpose() 8 | 9 | for i in data: 10 | print(np.average(i)) 11 | -------------------------------------------------------------------------------- /tools/movies/length.py: -------------------------------------------------------------------------------- 1 | import os 2 | for i in os.listdir("."): 3 | if i.endswith(".mp4"): 4 | cmd = "ffmpeg -i %s 2>&1 | grep Duration | cut -d ' ' -f 4 | sed s/,//"%i 5 | os.system(cmd) 6 | -------------------------------------------------------------------------------- /tools/ical/test.py: -------------------------------------------------------------------------------- 1 | a = 3.5 2 | b = 2.55 3 | 4 | c = 1.4 5 | d = 1.1 6 | 7 | import math 8 | s1 = math.sqrt(a*a + b*b) 9 | s2 = math.sqrt(c*c + d*d) 10 | 11 | nstep = 1000 12 | print (s2-s1)/nstep 13 | 14 | -------------------------------------------------------------------------------- /molecules/ase/get_mol.py: -------------------------------------------------------------------------------- 1 | from ase.build import molecule 2 | from ase.collections import g2 3 | from ase.io import write 4 | 5 | for i in g2.names: 6 | atoms = molecule(i) 7 | write(i+'.pdb', atoms) 8 | 9 | -------------------------------------------------------------------------------- /tools/linux/g4z: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os 4 | import sys 5 | 6 | tfile = sys.argv[1] 7 | 8 | cmd = "scp -r tcheng@zwicky.cacr.caltech.edu:%s ."%tfile 9 | os.system(cmd) 10 | print cmd 11 | 12 | -------------------------------------------------------------------------------- /test/glycine/dipole.out: -------------------------------------------------------------------------------- 1 | System identifier:glycine 2 | Dipole moment (Debye): 2.2230 Location: 39.8231 40.2618 39.9999 Direction (-side): -49582.9058 -1555.2676 -1.0000 3 | -------------------------------------------------------------------------------- /tools/ase/build-bulk.py: -------------------------------------------------------------------------------- 1 | from ase.build import bulk 2 | from ase.io import write 3 | 4 | for i in ['Pt', 'Ir', 'Pd', 'Rh']: 5 | atoms = bulk(i, 'fcc', cubic=True) 6 | write('%s.vasp'%i, atoms, vasp5=True) 7 | 8 | -------------------------------------------------------------------------------- /tools/kmc/02-her/rxn.csv: -------------------------------------------------------------------------------- 1 | # reaction , dE, dS , dE_act, dS_act 2 | H3O + * <--> H2O + H* , -1.0 , -0.001965, 0.2 , -0.0005133 3 | H* + H* <--> H2 + * + * , -1.0 , -0.001965, 0.5 , -0.0005133 4 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/docs/.svn/text-base/uml_class_diagram_for_pdb_pdb.gif.svn-base: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ensemble-learning/simpy/HEAD/arc/simulation_tools_py/docs/.svn/text-base/uml_class_diagram_for_pdb_pdb.gif.svn-base -------------------------------------------------------------------------------- /tools/gromacs/2pt/entropy_gas: -------------------------------------------------------------------------------- 1 | 2 | # Supergroup; Entropies in eV/K [trans, rot, vib]; number of DoF [trans, rot, vib] 3 | 1 1.27718808E-01 1.22932148E-01 0.00000000E+00 3.40181280E+02 4.60690203E+02 0.00000000E+00 4 | -------------------------------------------------------------------------------- /tools/sas/share/cn.inp: -------------------------------------------------------------------------------- 1 | [GLOBAL] 2 | r_ref_0 = 2.788 3 | r_ref_1 = 3.944 4 | r_ref_2 = 4.830 5 | 6 | n_atoms = 745 7 | # cut_off_func = 1(cut-off) 2(cn function) 8 | cut_off_func = 1 9 | r_cut_range = 1.8 10 | n_cut_off = 4 11 | -------------------------------------------------------------------------------- /test/glycine/fort.55: -------------------------------------------------------------------------------- 1 | 1 0.000000 2 | 2 0.000000 3 | 3 0.000000 4 | 4 0.000000 5 | 5 0.000000 6 | 6 0.000000 7 | 7 0.000000 8 | 8 0.000000 9 | 9 0.000000 10 | 10 0.000000 11 | -------------------------------------------------------------------------------- /test/glycine/fort.56: -------------------------------------------------------------------------------- 1 | 1 -0.636405 2 | 2 -0.429665 3 | 3 -0.156979 4 | 4 0.160214 5 | 5 0.160270 6 | 6 0.454769 7 | 7 0.359392 8 | 8 -0.469909 9 | 9 0.279097 10 | 10 0.279217 11 | -------------------------------------------------------------------------------- /tools/caltech/Packages/FSearch/create_info.dat: -------------------------------------------------------------------------------- 1 | ~huskeypm/source/swig-1.3.34/swig -perl5 Fsearch.i 2 | g++ -fpic -c -Dbool=char -I/usr/lib/perl5/5.8.0/i386-linux-thread-multi/CORE Fsearch_wrap.c 3 | g++ -shared Fsearch_wrap.o -o Fsearch.so 4 | -------------------------------------------------------------------------------- /tools/gromacs/2pt/entropy_solid: -------------------------------------------------------------------------------- 1 | 2 | # Supergroup; Entropies in eV/K [trans, rot, vib]; number of DoF [trans, rot, vib] 3 | 1 4.48657807E-02 1.13131999E-02 1.82804948E-02 1.91280524E+02 6.32686906E+01 1.67921820E+03 4 | -------------------------------------------------------------------------------- /tools/sas/example/cn.inp: -------------------------------------------------------------------------------- 1 | [GLOBAL] 2 | r_ref_0 = 2.788 3 | r_ref_1 = 3.944 4 | r_ref_2 = 4.830 5 | 6 | n_atoms = 201 7 | # cut_off_func = 1(cut-off) 2(cn function) 8 | cut_off_func = 1 9 | r_cut_range = 1.8 10 | n_cut_off = 4 11 | -------------------------------------------------------------------------------- /src/control: -------------------------------------------------------------------------------- 1 | [MC] 2 | 3 | swap = 1 4 | swap group 1 = Ca1 Ca2 Ca3 5 | swap group 2 = Al1 Al2 Al3 6 | mc steps = 9999 7 | 8 | [RUN] 9 | code = /net/hulk/home6/chengtao/soft/lammps-12Apr13/src/lmp_openmpi 10 | mpi = 60 11 | 12 | 13 | -------------------------------------------------------------------------------- /tools/sas/cn.inp: -------------------------------------------------------------------------------- 1 | [GLOBAL] 2 | r_ref_0 = 2.788 3 | r_ref_1 = 3.944 4 | r_ref_2 = 4.830 5 | 6 | n_atoms = 8183 7 | # cut_off_func = 1(cut-off) 2(cn function) 8 | cut_off_func = 1 9 | r_cut_range = 1.2 10 | n_cut_off = 4 11 | 12 | 13 | -------------------------------------------------------------------------------- /tools/sas/example-nlist/cn.inp: -------------------------------------------------------------------------------- 1 | [GLOBAL] 2 | r_ref_0 = 2.788 3 | r_ref_1 = 3.944 4 | r_ref_2 = 4.830 5 | 6 | n_atoms = 201 7 | # cut_off_func = 1(cut-off) 2(cn function) 8 | cut_off_func = 1 9 | r_cut_range = 1.8 10 | n_cut_off = 4 11 | -------------------------------------------------------------------------------- /tools/caltech/Packages/FSearch/Fsearch.i: -------------------------------------------------------------------------------- 1 | %module Fsearch 2 | %include "typemaps.i" 3 | %{ 4 | #include "Fsearch.h" 5 | %} 6 | void setResidual(int *, int, int, int, double *, int *); 7 | int getResidual(int, double **, double *, int *, int, int); 8 | -------------------------------------------------------------------------------- /tools/g03/test.gjf: -------------------------------------------------------------------------------- 1 | %mem=800MB 2 | # freq b3lyp/6-311g(d,p) 3 | 4 | scan_00 5 | 6 | 0 1 7 | N 0.00000 0.00000 -1.06259 8 | N 0.00000 0.00000 0.18447 9 | O 0.00000 0.00000 0.76835 10 | 11 | 12 | 13 | 14 | 15 | -------------------------------------------------------------------------------- /test/configParser/config: -------------------------------------------------------------------------------- 1 | [SectionOne] 2 | Status: Single 3 | Name: Derek 4 | Value: Yes 5 | Age: 29 6 | Single: True 7 | 8 | [SectionTwo] 9 | FavoriteColor=Green 10 | [SectionThree] 11 | FamilyName: Johnson 12 | 13 | [Others] 14 | Route: 66 15 | -------------------------------------------------------------------------------- /tools/project/li/cry.py: -------------------------------------------------------------------------------- 1 | a = 5.76 2 | b = 3.51 3 | for i in range(1,6): 4 | for j in range(1,12): 5 | val = abs((a*i - b*j)/(a*i)) 6 | if val < 0.05: 7 | print i, j, a*i - b*j, a*i, val 8 | 9 | 10 | -------------------------------------------------------------------------------- /lib/e_gaussian.py: -------------------------------------------------------------------------------- 1 | import os 2 | from g03 import G03tools 3 | 4 | os.chdir("d:\\Nut1\\work\\cement\\crystal_new\\Belite\\reactions\\scan\\a9\\") 5 | for i in range(10): 6 | b = G03tools('scan%d.log'%i) 7 | print b.getEnergy() 8 | 9 | 10 | 11 | -------------------------------------------------------------------------------- /src/test.in: -------------------------------------------------------------------------------- 1 | #PBS -S /bin/tcsh 2 | #PBS -l nodes=1:ppn=64,walltime=0020:00:00 3 | #PBS -q workq 4 | #PBS -N test 5 | #PBS -M chengtao@wag.caltech.edu 6 | #PBS -m e 7 | 8 | cd /net/hulk/home6/chengtao/soft/simpy/src 9 | 10 | epdpy mc_swap.py > log 11 | -------------------------------------------------------------------------------- /test/configParser/config.ini: -------------------------------------------------------------------------------- 1 | [SectionOne] 2 | Status: Single 3 | Name: Derek 4 | Value: Yes 5 | Age: 29 6 | Single: True 7 | 8 | [SectionTwo] 9 | FavoriteColor=Green 10 | [SectionThree] 11 | FamilyName: Johnson 12 | 13 | [Others] 14 | Route: 66 15 | -------------------------------------------------------------------------------- /tools/pic/crop.py: -------------------------------------------------------------------------------- 1 | import os, sys 2 | 3 | lx = 360 4 | ly = 300 5 | x0 = 600 6 | y0 = 150 7 | 8 | for i in sys.argv[1:]: 9 | fname = i 10 | cmd = "convert %s -crop %dx%d+%d+%d ../%s"%(fname, lx, ly, x0, y0, fname) 11 | os.system(cmd) 12 | 13 | -------------------------------------------------------------------------------- /test/glycine/fort.71: -------------------------------------------------------------------------------- 1 | glycine 2 | Iter. Nmol Epot Ekin Etot T(K) Eaver(block) Eaver(total) Taver Tmax Pres(GPa) sdev(Epot) sdev(Eaver) Tset Timestep RMSG Totaltime 3 | -------------------------------------------------------------------------------- /tools/ase/pdb2vasp.py: -------------------------------------------------------------------------------- 1 | import sys 2 | from ase.io import read, write 3 | 4 | if len(sys.argv) > 1: 5 | pdbfile = sys.argv[1] 6 | atoms = read(pdbfile) 7 | vaspfile = pdbfile.split('.')[0] + '.vasp' 8 | write(vaspfile, atoms, vasp5=True) 9 | 10 | -------------------------------------------------------------------------------- /tools/g03/freq.gjf: -------------------------------------------------------------------------------- 1 | %mem=800MB 2 | # freq b3lyp/6-311g(d,p) 3 | 4 | scan_01 5 | 6 | 0 3 7 | N 0.00000 0.00000 -1.72451 8 | N 0.00000 0.00000 0.46240 9 | O 0.00000 0.00000 1.10434 10 | 11 | 12 | B 2 3 0.6419 F 13 | 14 | 15 | 16 | -------------------------------------------------------------------------------- /tools/onyx/getback.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os 4 | import sys 5 | import shutil 6 | 7 | f = open("jobinfo", "r") 8 | lines = f.readlines() 9 | job_path = lines[-1].strip() 10 | os.system("cp %s . -r"%job_path) 11 | print job_path 12 | 13 | 14 | -------------------------------------------------------------------------------- /tools/vasp/get_kpoints_kplib.py: -------------------------------------------------------------------------------- 1 | import os 2 | o = open('PRECALC', 'w') 3 | o.write("""MINDISTANCE=24.99999999872511509929 4 | INCLUDEGAMMA=TRUE 5 | HEADER=Verbose 6 | """) 7 | o.close() 8 | 9 | os.system('demo_kplib POSCAR PRECALC > KPOINTS') 10 | 11 | 12 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/template/water/towhee_coords: -------------------------------------------------------------------------------- 1 | -0.255600 -0.194200 -0.212500 o_2w -0.847600 2 | 0.709600 -0.068500 -0.442200 h_1w 0.423800 3 | -0.454000 0.262700 0.654600 h_1w 0.423800 4 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/template/water/water_coords: -------------------------------------------------------------------------------- 1 | -0.255600 -0.194200 -0.212500 o_2w -0.847600 2 | 0.709600 -0.068500 -0.442200 h_1w 0.423800 3 | -0.454000 0.262700 0.654600 h_1w 0.423800 4 | -------------------------------------------------------------------------------- /tools/builder/inp_tpl.py: -------------------------------------------------------------------------------- 1 | """packmol input template 2 | """ 3 | 4 | INP = """# 5 | tolerance 2.0 6 | 7 | filetype pdb 8 | 9 | output sim.pdb 10 | 11 | structure %pdbfile% 12 | number %n% 13 | inside box 0. 0. 0. %l% %l% %l% 14 | end structure 15 | 16 | """ 17 | -------------------------------------------------------------------------------- /tools/deepmd/gen_set.py: -------------------------------------------------------------------------------- 1 | import os, math 2 | 3 | n = 0 4 | f = open("force.raw", 'r') 5 | for i in f: 6 | if len(i.strip())> 0: 7 | n += 1 8 | f.close() 9 | 10 | n_set = math.ceil(n*2/3.0) 11 | os.system('~/soft/simpy/tools/deepmd/raw_to_set.sh %d'%n_set) 12 | -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/methanol.zmat: -------------------------------------------------------------------------------- 1 | methanol 2 | 3 | 1 CTO 4 | 2 H1O 1 1.09 5 | 3 H1O 1 1.09 2 109.5 6 | 4 H1O 1 1.09 2 109.5 3 120.0 7 | 5 OH 1 1.41 2 109.5 3 240.0 8 | 6 HO 5 0.945 1 109.5 2 180.0 9 | 10 | oplsaa.ff 11 | -------------------------------------------------------------------------------- /tools/movies/rename.py: -------------------------------------------------------------------------------- 1 | import os 2 | for i in os.listdir("."): 3 | if i.endswith(".mp4"): 4 | tokens = i.strip().split() 5 | new_name = "%02d"%(int(tokens[0]))+"-"+"%02d"%(int(tokens[2])) 6 | new_name += ".mp4" 7 | os.rename(i, new_name) 8 | 9 | -------------------------------------------------------------------------------- /tools/sas/al/compile.sh: -------------------------------------------------------------------------------- 1 | rm ./distance ./rhombi_old ./rhombi ./surface_old ./surface 2 | 3 | gfortran distances.f -o distance 4 | gfortran rhombi_new.f -o rhombi_old 5 | gfortran rhombi_pbc.f -o rhombi 6 | gfortran surface.f -o surface_old 7 | gfortran surface_pbc.f -o surface 8 | -------------------------------------------------------------------------------- /tools/gromacs/topol.top.opls: -------------------------------------------------------------------------------- 1 | #include "./oplsaa.ff/forcefield.itp" 2 | #include "c15.itp" 3 | #include "spc.itp" 4 | #include "cu.itp" 5 | #include "br.itp" 6 | 7 | [ system ] 8 | mixture 9 | 10 | [ molecules ] 11 | Cu 1440 12 | c15 18 13 | Br 18 14 | SOL 1000 15 | 16 | 17 | -------------------------------------------------------------------------------- /tools/nanocut/icosahedron/icosahedron.py: -------------------------------------------------------------------------------- 1 | from ase.cluster.icosahedron import Icosahedron 2 | from ase.io import write 3 | 4 | ns = 36 5 | atoms = Icosahedron('Cu', noshells=ns) 6 | 7 | print('#atoms = {}'.format(len(atoms))) 8 | write('icosahedron-%03d.xyz'%ns, atoms) 9 | 10 | -------------------------------------------------------------------------------- /tools/vasp/charges/index.ndx: -------------------------------------------------------------------------------- 1 | 1 2 3 4 5 6 7 8 9 10 2 | 11 12 13 14 15 16 17 18 19 20 3 | 21 22 23 24 25 26 27 28 29 30 4 | 31 32 33 34 35 36 37 38 39 40 5 | 41 42 43 44 45 46 47 48 6 | -------------------------------------------------------------------------------- /tools/kmc/species.dat: -------------------------------------------------------------------------------- 1 | OH* 0.00 2 | NO* 0.00 3 | O* 0.00 4 | N* 0.00 5 | NH* 0.00 6 | NH2* 0.00 7 | NH3* 0.00 8 | H2O* 0.00 9 | H* 0.00 10 | NO2* 0.00 11 | NOH* 0.00 12 | HNO* 0.00 13 | HNOH* 0.00 14 | N2H4* 0.00 15 | N2H4 0.0 16 | NH3 0.0 17 | HNO2 0.03 18 | H2 0.02 19 | H2O 1.00 20 | -------------------------------------------------------------------------------- /tools/kmc/01-acs/species.dat: -------------------------------------------------------------------------------- 1 | OH* 0.00 2 | NO* 0.00 3 | O* 0.00 4 | N* 0.00 5 | NH* 0.00 6 | NH2* 0.00 7 | NH3* 0.00 8 | H2O* 0.00 9 | H* 0.00 10 | NO2* 0.00 11 | NOH* 0.00 12 | HNO* 0.00 13 | HNOH* 0.00 14 | N2H4* 0.00 15 | N2H4 0.0 16 | NH3 0.0 17 | HNO2 0.03 18 | H2 0.02 19 | H2O 1.00 20 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/pre/opls.py: -------------------------------------------------------------------------------- 1 | DFF2OPLS = { 2 | "C(A6)C~C2" : ["opls_145",-0.115], 3 | "C(A6)H~C2" : ["opls_145",-0.115], 4 | "CC2H2":["opls_136",-0.120], 5 | "CC3H":["opls_149",0.055], 6 | "CCH3":["opls_135",-0.180], 7 | "HC":["opls_140",0.060], 8 | "H[C=H]":["opls_146",0.115], 9 | } 10 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/template/water/.svn/text-base/towhee_coords.svn-base: -------------------------------------------------------------------------------- 1 | -0.255600 -0.194200 -0.212500 o_2w -0.847600 2 | 0.709600 -0.068500 -0.442200 h_1w 0.423800 3 | -0.454000 0.262700 0.654600 h_1w 0.423800 4 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/template/water/.svn/text-base/water_coords.svn-base: -------------------------------------------------------------------------------- 1 | -0.255600 -0.194200 -0.212500 o_2w -0.847600 2 | 0.709600 -0.068500 -0.442200 h_1w 0.423800 3 | -0.454000 0.262700 0.654600 h_1w 0.423800 4 | -------------------------------------------------------------------------------- /tools/vasp/gen.sh: -------------------------------------------------------------------------------- 1 | python ~/soft/simpy/tools/vasp/get_potcar.py 2 | python ~/soft/simpy/tools/vasp/get_kpoint.py 3 | python ~/soft/simpy/tools/vasp/incar.py 4 | 5 | # for vasp 5.2 6 | #genpbs_vasp 7 | 8 | # for vasp 5.3 9 | python /project/source/VASP/vasp.5.3.5/bin/genVASPpbs.py 1 4 24:00:00 vasp 10 | -------------------------------------------------------------------------------- /tools/kmc/04-her/rxn.csv: -------------------------------------------------------------------------------- 1 | # reaction , dE, dS , dE_act, dS_act 2 | H3O + * + e <--> H2O + H* , -1.0 , -0.001965, 0.4 , -0.0005133 3 | H* + H* <--> H2 + * + * , -1.0 , -0.001965, 0.4 , -0.0005133 4 | H3O + H* + e <--> H2 + * + H2O, -1.0 , -0.001965, 0.4 , -0.0005133 5 | -------------------------------------------------------------------------------- /tools/kmc/05-her/rxn.csv: -------------------------------------------------------------------------------- 1 | # reaction , dE, dS , dE_act, dS_act 2 | H2O + * + e <--> OH- + H* , 0.1 , -0.001965, 0.6 , -0.0005133 3 | H* + H* <--> H2 + * + * , 0.17 , -0.001965, 0.78 , -0.0005133 4 | H2O + H* + e <--> H2 + * + OH- , 0.07 , -0.001965, 0.73 , -0.0005133 5 | -------------------------------------------------------------------------------- /tools/linux/pwdw: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | """ 4 | convert linux path to windows format 5 | """ 6 | 7 | import os 8 | 9 | cmd = os.getcwd() 10 | wcmd = cmd 11 | if "/temp1/jobs/" in cmd: 12 | wcmd = wcmd.replace("/temp1/jobs/", "e:\\") 13 | wcmd = wcmd.replace("/", "\\") 14 | print wcmd 15 | 16 | -------------------------------------------------------------------------------- /tools/reax/fort/getBo.py: -------------------------------------------------------------------------------- 1 | """get specified bond order from fort.8 2 | """ 3 | 4 | f = open("fort.8", "r") 5 | 6 | n = 1 7 | 8 | for i in range(n): 9 | f.readline() 10 | 11 | tokens = f.readline().strip().split() 12 | 13 | o = open("bo", "w") 14 | o.write(tokens[13] + '\n') 15 | o.close() 16 | 17 | -------------------------------------------------------------------------------- /tools/vasp/gen-tao.sh: -------------------------------------------------------------------------------- 1 | python ~/Soft/simpy/tools/vasp/get_potcar.py 2 | python ~/Soft/simpy/tools/vasp/get_kpoint.py 3 | python ~/Soft/simpy/tools/vasp/incar.py 4 | 5 | # for vasp 5.2 6 | #genpbs_vasp 7 | 8 | # for vasp 5.3 9 | #python /project/source/VASP/vasp.5.3.5/bin/genVASPpbs.py 1 4 24:00:00 vasp 10 | -------------------------------------------------------------------------------- /arc/linux_tools/qs_towhee: -------------------------------------------------------------------------------- 1 | #/bin/sh 2 | # It qsub the job of GROMACS 3 | echo "#!/bin/bash" >> towhee.sh 4 | echo "#PBS -l nodes=1:ppn=1" >> towhee.sh 5 | echo "cd $PWD" >> towhee.sh 6 | echo "cp towhee_final towhee_initial" 7 | echo "towhee > result1.log" >> towhee.sh 8 | qsub towhee.sh 9 | rm towhee.sh 10 | -------------------------------------------------------------------------------- /lib/epydoc.cfg: -------------------------------------------------------------------------------- 1 | [epydoc] 2 | name: simpy 3 | 4 | modules: cons.py data.py dump.py ffield.py fort.py g03.py geo.py msd.py mytype.py output_conf.py output_ff.py pdb.py poscar.py utilities.py 5 | output: html 6 | target: /home/tao/Nutstore/code/simpy/docs 7 | graph: all 8 | dotpath: /usr/bin/dot 9 | 10 | 11 | -------------------------------------------------------------------------------- /tools/gromacs/2pt/fluidicity: -------------------------------------------------------------------------------- 1 | # Supergroup no.; effective deg. of freedom [CM; rot; vib]; Voronoi volume (nm^3); fluidicity f [CM; rot; vib]; HS diameters (nm) [CM, rot, vib]; weight 2 | 1 553.3328 538.4467 1679.2749 30.4222 0.6240 0.9276 0.0166 0.4484 0.4484 2.5006 176.00000 3 | -------------------------------------------------------------------------------- /tools/hun/Cutoff.dic: -------------------------------------------------------------------------------- 1 | H H 0.4000 2 | H C 0.4000 3 | H O 0.4000 4 | H N 0.4000 5 | C C 0.4000 6 | C O 0.4000 7 | C N 0.4000 8 | O O 0.4000 9 | O N 0.4000 10 | N N 0.4000 11 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/pre/.svn/text-base/opls.py.svn-base: -------------------------------------------------------------------------------- 1 | DFF2OPLS = { 2 | "C(A6)C~C2" : ["opls_145",-0.115], 3 | "C(A6)H~C2" : ["opls_145",-0.115], 4 | "CC2H2":["opls_136",-0.120], 5 | "CC3H":["opls_149",0.055], 6 | "CCH3":["opls_135",-0.180], 7 | "HC":["opls_140",0.060], 8 | "H[C=H]":["opls_146",0.115], 9 | } 10 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/PCDAT: -------------------------------------------------------------------------------- 1 | 1 2 1 0 0.3200866E+02 0.1000000E-03 2 | CAR 3 | raman 4 | 0 0 0 5 | 1 1 6 | 256 256 256 7 | 256 8 | 0.1000000E-09 9 | 0.6250000E-11 10 | 0 11 | 0.5000000E-15 0.2481949E-09 0.2481949E-09 0.1200000E-08 12 | -------------------------------------------------------------------------------- /tools/ase/any2pdb.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | from ase.io import read, write 4 | import sys 5 | 6 | outfile = "output.pdb" 7 | 8 | if len(sys.argv) > 1: 9 | infile = sys.argv[1] 10 | if len(sys.argv) > 2: 11 | outfile = sys.argv[2] 12 | data = read(infile) 13 | write(outfile, data) 14 | -------------------------------------------------------------------------------- /tools/vasp/note-compile.txt: -------------------------------------------------------------------------------- 1 | vasp 编译 vtst solv gpu on caltech hpc 2 | 3 | VTST_OBJS = bfgs.o dynmat.o instanton.o lbfgs.o sd.o cg.o dimer.o bbm.o \ 4 | fire.o lanczos.o neb.o qm.o opt.o chain.o 5 | 6 | and then add those objects after hamil_rot.o, as in: 7 | 8 | hamil_rot.o \ 9 | $(VTST_OBJS) \ 10 | dyna.o \ 11 | -------------------------------------------------------------------------------- /arc/linux_tools/readcry.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | import os 3 | 4 | for i in range(84, 100,4): 5 | for j in range(84, 100, 4): 6 | os.chdir("a%03d_%03d"%(i,j)) 7 | os.system("echo %d %d >> ../cryinfor.log"%(i,j)) 8 | os.system("cry.py >> ../cryinfor.log") 9 | os.chdir("../") 10 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/pre/tools/.svn/all-wcprops: -------------------------------------------------------------------------------- 1 | K 25 2 | svn:wc:ra_dav:version-url 3 | V 64 4 | /svn/ms-tools-python~source-code-repository/!svn/ver/3/pre/tools 5 | END 6 | plot.py 7 | K 25 8 | svn:wc:ra_dav:version-url 9 | V 72 10 | /svn/ms-tools-python~source-code-repository/!svn/ver/3/pre/tools/plot.py 11 | END 12 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/phonon/PCDAT: -------------------------------------------------------------------------------- 1 | 1 2 1 0 0.3200866E+02 0.1000000E-03 2 | CAR 3 | phonon 4 | 0 0 0 5 | 1 1 6 | 256 256 256 7 | 256 8 | 0.1000000E-09 9 | 0.6250000E-11 10 | 1 11 | 0.1000000E-16 0.2481949E-09 0.2481949E-09 0.1200000E-08 12 | -------------------------------------------------------------------------------- /lib/todo: -------------------------------------------------------------------------------- 1 | @todo @description @input date 2 | pbc 01-11-2012 3 | degree2matrix cell parameters 01-11-2012 4 | toData 01-11-2012 5 | 6 | -------------------------------------------------------------------------------- /test/configParser/next.ini: -------------------------------------------------------------------------------- 1 | [Others] 2 | route = 66 3 | 4 | [SectionThree] 5 | familyname = Johnson 6 | 7 | [SectionOne] 8 | status = Single 9 | name = Derek 10 | age = 29 11 | value = Yes 12 | single = True 13 | 14 | [Person] 15 | haseyes = True 16 | age = 50 17 | 18 | [SectionTwo] 19 | favoritecolor = Green 20 | 21 | -------------------------------------------------------------------------------- /tools/linux/occ: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import time 4 | import sys 5 | 6 | time_start = time.time() 7 | time_limit = float(sys.argv[1])*3600 8 | 9 | while(1): 10 | time_now = time.time() 11 | dt = time_now - time_start 12 | if dt > time_limit: 13 | break 14 | 15 | print time_limit 16 | 17 | -------------------------------------------------------------------------------- /tools/linux/getscihub: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import sys, time 4 | from scihub import SciHub 5 | doi = sys.argv[1] 6 | #doi = "https://doi.org/10.1002/jcc.25860" 7 | sh = SciHub() 8 | result = sh.fetch(doi) 9 | fname = "lit%d.pdf"%(int(time.time())) 10 | with open(fname, 'wb+') as fd: 11 | fd.write(result['pdf']) 12 | -------------------------------------------------------------------------------- /tools/ase/extract_atoms.py: -------------------------------------------------------------------------------- 1 | from ase.io import read, write 2 | 3 | atoms = read('POSCAR') 4 | selected = [119, 168, 49, 50, 51, 52, 53, 54] 5 | remove = [] 6 | for i in range(len(atoms)): 7 | if not i+1 in selected: 8 | remove.append(i) 9 | 10 | del(atoms[remove]) 11 | write('out.vasp', atoms, vasp5=True, direct=True) 12 | -------------------------------------------------------------------------------- /tools/gromacs/mols/ifpsc-de/any2pdb.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | from ase.io import read, write 4 | import sys 5 | 6 | outfile = "output.xyz" 7 | 8 | if len(sys.argv) > 1: 9 | infile = sys.argv[1] 10 | if len(sys.argv) > 2: 11 | outfile = sys.argv[2] 12 | data = read(infile) 13 | write(outfile, data) 14 | -------------------------------------------------------------------------------- /tools/ase/any2png.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | from ase.io import read, write 4 | import sys 5 | 6 | outfile = "output.png" 7 | 8 | if len(sys.argv) > 1: 9 | infile = sys.argv[1] 10 | if len(sys.argv) > 2: 11 | outfile = sys.argv[2] 12 | data = read(infile) 13 | write(outfile, data, rotation="-60z, 120x") 14 | -------------------------------------------------------------------------------- /tools/lammps/find_half_life.py: -------------------------------------------------------------------------------- 1 | nhalf = 15 2 | 3 | f = open("N3H.dat", "r") 4 | 5 | for i in f: 6 | tokens = i.strip().split() 7 | if len(tokens) == 2: 8 | step = int(tokens[0]) 9 | nmol = int(tokens[1]) 10 | if nmol <= nhalf: 11 | print step 12 | break 13 | 14 | f.close() 15 | -------------------------------------------------------------------------------- /tools/sas/example-3/input.dat: -------------------------------------------------------------------------------- 1 | UFF.atoms 2 | out.music 3 | 1.400 4 | 5000 5 | 11.8750 11.8750 11.8750 6 | 1.0004 7 | 8 | 9 | ! file containing the atom types + diameters 10 | ! file containing the coordinates 11 | ! probe size in A 12 | ! number of insertions 13 | ! length of unitcell 14 | ! crystal density in g / cm3 15 | -------------------------------------------------------------------------------- /tools/vasp/ana-fe.py: -------------------------------------------------------------------------------- 1 | import os, socket 2 | 3 | hostname = socket.gethostname() 4 | if 1: 5 | #os.system('cmdall "tar -xvzf *.tar.gz"') 6 | os.system('cmdall "cd 2* && python2 ~/soft/simpy/tools/vasp/fe_slow.py "') 7 | os.system('cat ./*/2*/ave*.dat > fe.dat') 8 | os.system('python2 ~/soft/simpy/tools/math/int.py') 9 | 10 | -------------------------------------------------------------------------------- /tools/caltech/Packages/auto/Math/FFT/.packlist: -------------------------------------------------------------------------------- 1 | /ul/tpascal/scripts/Packages/Math/FFT.pm 2 | /ul/tpascal/scripts/Packages/Math/FFT/FFT.bs 3 | /ul/tpascal/scripts/Packages/Math/FFT/FFT.so 4 | /ul/tpascal/scripts/Packages/auto/Math/FFT/FFT.bs 5 | /ul/tpascal/scripts/Packages/auto/Math/FFT/FFT.so 6 | /ul/tpascal/scripts/Packages/share/man/man3/Math::FFT.3pm 7 | -------------------------------------------------------------------------------- /lib/g03.geo: -------------------------------------------------------------------------------- 1 | BIOGRF 200 2 | DESCRP Title Card Required 3 | REMARK generated by simulation python 4 | HETATM 1 N 0.00000 0.00000 -1.19843 N 0 0 0.00000 5 | HETATM 2 N 0.00000 0.00000 -0.07214 N 0 0 0.00000 6 | HETATM 3 O 0.00000 0.00000 1.11174 O 0 0 0.00000 7 | END 8 | 9 | -------------------------------------------------------------------------------- /tools/caltech/dat/WAT/mW.bgf: -------------------------------------------------------------------------------- 1 | BIOGRF 200 2 | DESCRP F3C 3 | REMARK BGF file created by Cerius2 4 | FORCEFIELD DREIDING 5 | FORMAT ATOM (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5,f10.5) 6 | ATOM 1 O WAT 1 1 0.38770 0.02814 0.02554 O_mW 0 2 0.00000 7 | FORMAT CONECT (a6,12i6) 8 | CONECT 1 9 | END 10 | -------------------------------------------------------------------------------- /tools/gromacs/get_ave_box.py: -------------------------------------------------------------------------------- 1 | """ 2 | @note: 3 | """ 4 | 5 | import os, sys 6 | 7 | cmd = 'echo Box-X | gmx_mpi energy' 8 | f = os.popen(cmd) 9 | for i in f: 10 | if 'Box-X' in i: 11 | tokens = i.strip().split() 12 | f.close() 13 | 14 | box_x = float(tokens[1]) 15 | os.system("gmx_mpi editconf -f conf.gro -o conf.gro -box %.5f"%box_x) 16 | -------------------------------------------------------------------------------- /tools/gromacs/npt-to-nvt.py: -------------------------------------------------------------------------------- 1 | import os 2 | os.system('echo Box-X | gmx energy | grep Box-X > box-x.dat') 3 | 4 | if os.path.exists('box-x.dat'): 5 | f = open('box-x.dat', 'r') 6 | lines = f.readlines() 7 | f.close() 8 | 9 | tokens = lines[0].strip().split() 10 | os.system('gmx editconf -f confout.gro -o conf.gro -box %s'%tokens[1]) 11 | 12 | -------------------------------------------------------------------------------- /arc/linux_tools/vle: -------------------------------------------------------------------------------- 1 | cd $PWD 2 | cat ./*/result.log > result.log 3 | echo "Density" > vle.log 4 | grep "Specific Density g/ml 1 " result.log >> vle.log 5 | echo "Hv" >> vle.log 6 | grep "H_vap (Direct) kJ/mol" result.log >> vle.log 7 | echo "Pressure" >> vle.log 8 | grep "Thermodynamic Pressure kPa 2" result.log >> vle.log 9 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/XDATCAR: -------------------------------------------------------------------------------- 1 | raman 2 | 1 3 | 2.481949 0.000000 0.000000 4 | -1.240974 2.149431 0.000000 5 | 0.000000 0.000000 12.000000 6 | C 7 | 2 8 | Direct configuration= 1 9 | 0.00328338 0.00176573 0.14167004 10 | 0.33004024 0.66489935 0.14167024 11 | -------------------------------------------------------------------------------- /tools/inprogress/csv.py: -------------------------------------------------------------------------------- 1 | import csv 2 | with open('eggs.csv', 'wb') as csvfile: 3 | spamwriter = csv.writer(csvfile, delimiter=' ', 4 | quotechar='|', quoting=csv.QUOTE_MINIMAL) 5 | spamwriter.writerow(['Spam'] * 5 + ['Baked Beans']) 6 | spamwriter.writerow(['Spam', 'Lovely Spam', 'Wonderful Spam']) 7 | -------------------------------------------------------------------------------- /tools/gromacs/mols/ifpsc-de/get_ave_box.py: -------------------------------------------------------------------------------- 1 | """ 2 | @note: 3 | """ 4 | 5 | import os, sys 6 | 7 | cmd = 'echo Box-X | gmx_mpi energy' 8 | f = os.popen(cmd) 9 | for i in f: 10 | if 'Box-X' in i: 11 | tokens = i.strip().split() 12 | f.close() 13 | 14 | box_x = float(tokens[1]) 15 | os.system("gmx_mpi editconf -f conf.gro -o conf.gro -box %.5f"%box_x) 16 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/template/water/.svn/text-base/box_01_step_00000000000000.pdb.svn-base: -------------------------------------------------------------------------------- 1 | ATOM 1 O 0 0.198 0.000 0.230 3.17 1.00 O -0.8476 2 | ATOM 2 H 0 1.164 0.126 0.000 0.00 1.00 H 0.4238 3 | ATOM 3 H 0 0.000 0.457 1.097 0.00 1.00 H 0.4238 4 | TER 5 | END 6 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/template/water/.svn/text-base/box_01_step_00000000000200.pdb.svn-base: -------------------------------------------------------------------------------- 1 | ATOM 1 O 0 0.430 0.848 0.000 3.17 1.00 O -0.8476 2 | ATOM 2 H 0 0.000 0.000 0.326 0.00 1.00 H 0.4238 3 | ATOM 3 H 0 0.660 1.437 0.718 0.00 1.00 H 0.4238 4 | TER 5 | END 6 | -------------------------------------------------------------------------------- /lib/e_poscar_2_geo.py: -------------------------------------------------------------------------------- 1 | """ read the geo file and output to data (LAMMPS), geo and xyz file. 2 | """ 3 | import os 4 | from mytype import System, Molecule, Atom 5 | from poscar import Poscar 6 | from output_conf import toXyz, toGeo 7 | 8 | os.chdir("/home/tao/Documents/wag/alpha/opt") 9 | a = Poscar("alpha1.vasp") 10 | b = a.parser() 11 | toXyz(b) 12 | toGeo(b) 13 | 14 | -------------------------------------------------------------------------------- /tools/gromacs/2pt/input: -------------------------------------------------------------------------------- 1 | # Number of points in the trajectory (5001) 2 | points = 5001 3 | # Trajectory period in ps (20) 4 | tau = 20. 5 | # Size of the box in nm 6 | cell = 3.12174 3.12174 3.12174 7 | # Temperature in K 8 | temperature = 298.15 9 | # Trajectory info 10 | format = gro 11 | # Estimate velocities from positions 12 | estimate_velocities = .true. 13 | -------------------------------------------------------------------------------- /tools/gromacs/mols/ifpsc-de/setup_groups.py: -------------------------------------------------------------------------------- 1 | o = open('groups', 'w') 2 | n_atoms = 1400 3 | n_mol = 50 4 | n_mol_atoms = int(n_atoms/n_mol) 5 | o.write('%d %d\n'%(n_atoms, n_mol)) 6 | for i in range(n_mol): 7 | o.write('%d 1\n'%n_mol_atoms) 8 | for j in range(n_mol_atoms): 9 | o.write('%d '%(i*n_mol_atoms+1+j)) 10 | o.write('\n') 11 | o.close() 12 | -------------------------------------------------------------------------------- /tools/linux/tocheng-zwicky: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os 4 | import sys 5 | 6 | cmd = "scp -r " 7 | 8 | files = "" 9 | if len(sys.argv) > 1: 10 | for i in range(1, len(sys.argv)): 11 | files += sys.argv[i] + " " 12 | cmd += files 13 | cmd += "tao@131.215.26.220:/home/tao/Dropbox" 14 | print cmd 15 | os.system(cmd) 16 | 17 | 18 | -------------------------------------------------------------------------------- /lib/g03.gjf: -------------------------------------------------------------------------------- 1 | # opt=modredundant b3lyp/6-311g(d,p) geom=connectivity 2 | 3 | Title Card Required 4 | 5 | 0 1 6 | N 0.00000000 0.00000000 -1.19842600 7 | N 0.00000000 0.00000000 -0.07213700 8 | O 0.00000000 0.00000000 1.11174200 9 | 10 | 1 2 3.0 11 | 2 3 2.0 12 | 3 13 | 14 | B 2 3 1.183880 F 15 | 16 | -------------------------------------------------------------------------------- /tools/deepmd/vasp2raw-dp.py: -------------------------------------------------------------------------------- 1 | from dpdata import System, LabeledSystem, MultiSystems 2 | 3 | #s = System('POSCAR', fmt='poscar') 4 | #print(s) 5 | ls=LabeledSystem('OUTCAR', fmt='outcar') 6 | """ 7 | if len(ls)%2==0: 8 | size = int(len(ls)/2) 9 | else: 10 | size = int(len(ls)/2) + 1 11 | """ 12 | ls.to_deepmd_raw('.') 13 | #ls.to_deepmd_npy('deepmd', set_size=size) 14 | -------------------------------------------------------------------------------- /tools/linux/ion/getcheng.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os 4 | import sys 5 | 6 | cmd = "scp -r " 7 | 8 | files = "" 9 | if len(sys.argv) > 1: 10 | for i in range(1, len(sys.argv)): 11 | files += sys.argv[i] + " " 12 | cmd += "tao@131.215.26.219:" 13 | cmd += files 14 | cmd += " ." 15 | print cmd 16 | os.system(cmd) 17 | 18 | 19 | -------------------------------------------------------------------------------- /tools/fftool/oplsaa.ff.gromacs/watermodels.dat: -------------------------------------------------------------------------------- 1 | tip4p TIP4P TIP 4-point, recommended 2 | tip4pew TIP4PEW TIP 4-point with Ewald 3 | tip3p TIP3P TIP 3-point 4 | tip5p TIP5P TIP 5-point (see http://redmine.gromacs.org/issues/1348 for issues) 5 | tip5pe TIP5P TIP 5-point improved for Ewald sums 6 | spc SPC simple point charge 7 | spce SPC/E extended simple point charge 8 | -------------------------------------------------------------------------------- /tools/gromacs/mols/ifpsc-de/input: -------------------------------------------------------------------------------- 1 | # Number of points in the trajectory (5001) 2 | points = 5001 3 | # Trajectory period in ps (20) 4 | tau = 20. 5 | # Size of the box in nm 6 | cell = 2.38751 2.38751 2.38751 7 | # Temperature in K 8 | temperature = 311.00 9 | # Trajectory info 10 | format = gro 11 | # Estimate velocities from positions 12 | estimate_velocities = .true. 13 | -------------------------------------------------------------------------------- /arc/linux_tools/sub_undernodes.py: -------------------------------------------------------------------------------- 1 | import os 2 | import os.path 3 | dirList = os.listdir("./") 4 | 5 | for i in dirList: 6 | if os.path.isdir(i): 7 | os.chdir(i) 8 | os.system("grompp_mpi -np 6 -f run.mdp -c run -p 2,3-dimethylbutane -o run") 9 | os.system("/opt/openmpi/bin/mpirun -np 6 mdrun_mpi -s run -c runi") 10 | os.chdir("../") 11 | 12 | 13 | -------------------------------------------------------------------------------- /test/glycine/fort.73: -------------------------------------------------------------------------------- 1 | glycine 2 | Iter. Ebond Eatom Elp Emol Eval Ecoa Ehbo Etors Econj Evdw Ecoul Echarge Efield 3 | 502 -1371.37 -31.07 -0.00 0.00 14.93 0.00 -0.70 -1.07 -2.61 451.67 -180.05 112.83 0.00 4 | -------------------------------------------------------------------------------- /tools/g03/N2O.gjf: -------------------------------------------------------------------------------- 1 | # opt=modredundant b3lyp/6-311g(d,p) geom=connectivity 2 | 3 | Title Card Required 4 | 5 | 0 1 6 | N 0.00000000 0.00000000 -1.19842600 7 | N 0.00000000 0.00000000 -0.07213700 8 | O 0.00000000 0.00000000 1.11174200 9 | 10 | 1 2 3.0 11 | 2 3 2.0 12 | 3 13 | 14 | A 2 3 1 1.183880 F 15 | 16 | -------------------------------------------------------------------------------- /tools/vasp/fe/ti_get_poscar.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import shutil 3 | import os 4 | 5 | data = np.loadtxt("../lammps/windows.dat") 6 | for i in range(len(data)): 7 | n = int(data[i][0]) + 1 8 | pos = "POSCAR_%06d"%n 9 | folder = "run_%02d"%i 10 | if not os.path.exists(folder): 11 | os.mkdir(folder) 12 | shutil.copy("../poscars/%s"%pos, folder) 13 | 14 | -------------------------------------------------------------------------------- /lib/test.py: -------------------------------------------------------------------------------- 1 | from mytype import System, Molecule, Atom 2 | from poscar import Poscar 3 | from output_conf import toPoscar 4 | 5 | import sys 6 | 7 | if len(sys.argv) > 1: 8 | fname = sys.argv[1] 9 | else: 10 | fname = "CONTCAR" 11 | a = Poscar(fname) 12 | b = a.parser() 13 | b.assignAtomTypes() 14 | b.assignEleTypes() 15 | print b.getVol() 16 | 17 | toPoscar(b) 18 | 19 | 20 | -------------------------------------------------------------------------------- /tools/c/makefile.auto: -------------------------------------------------------------------------------- 1 | all: main 2 | 3 | main: main.o populator.o 4 | gcc $^ -o $@ 5 | 6 | clean: 7 | -rm main *.o 8 | 9 | .PHONY: clean 10 | 11 | sources = main.c populator.c 12 | 13 | include $(sources:.c=.d) 14 | 15 | %.d: %.c 16 | set -e; rm -f $@; \ 17 | $(CC) -MM $(CPPFLAGS) $< > $@.$$$$; \ 18 | sed 's,\($*\)\.o[ :]*,\1.o $@ : ,g' < $@.$$$$ > $@; \ 19 | rm -f $@.$$$$ 20 | -------------------------------------------------------------------------------- /tools/dftb/any2gen: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | """ 4 | Convert any file format (with correct ext) to .gen. 5 | @Note: need ase. 6 | any2gen infile 7 | """ 8 | 9 | import sys 10 | from ase.io import read, write 11 | 12 | if len(sys.argv) > 1: 13 | infile = sys.argv[1] 14 | atoms = read(infile) 15 | write("geo_start.gen", atoms) 16 | else: 17 | print(__doc__) 18 | 19 | -------------------------------------------------------------------------------- /tools/dftb/gen2pdb: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | """ 4 | Convert any file format (with correct ext) to .gen. 5 | @Note: need ase. 6 | any2gen infile 7 | """ 8 | 9 | import sys 10 | from ase.io import read, write 11 | 12 | if len(sys.argv) > 1: 13 | infile = sys.argv[1] 14 | atoms = read(infile) 15 | write("geo_start.pdb", atoms) 16 | else: 17 | print(__doc__) 18 | 19 | -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/ethanol.zmat: -------------------------------------------------------------------------------- 1 | ethanol 2 | 3 | 1 C3H 4 | 2 CTO 1 1.47 5 | 3 H 2 1.09 1 109.5 6 | 4 H 1 1.09 2 109.5 3 180.0 7 | 5 H 2 1.09 1 109.5 4 60.0 8 | 6 H 1 1.09 2 109.5 5 180.0 9 | 7 OH 2 1.41 1 109.5 6 60.0 10 | 8 H 1 1.09 2 109.5 7 180.0 11 | 9 HO 7 0.945 2 109.5 1 180.0 12 | 13 | oplsaa.ff 14 | -------------------------------------------------------------------------------- /tools/gromacs/mols/ifpsc-de/log: -------------------------------------------------------------------------------- 1 | 2 | Statistics over 2000001 steps [ 0.0000 through 1000.0000 ps ], 1 data sets 3 | All statistics are over 20001 points 4 | 5 | Energy Average Err.Est. RMSD Tot-Drift 6 | ------------------------------------------------------------------------------- 7 | Density 1112.02 1.4 9.09496 9.90541 (kg/m^3) 8 | -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/co2.ff: -------------------------------------------------------------------------------- 1 | # EPM2 CO2 2 | 3 | ATOMS 4 | # type m/amu q/e pot pars 5 | O O 15.999 -0.3256 lj 3.033 0.66938 6 | C C 12.011 0.6512 lj 2.757 0.23388 7 | 8 | BONDS 9 | # i j pot re/A kr/kJmol-1 10 | C O cons 1.149 2845.0 11 | 12 | ANGLES 13 | # i j k pot th/deg ka/kjmol-1 14 | O C O harm 180.0 1236.0 15 | -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/vc.zmat: -------------------------------------------------------------------------------- 1 | vinylcarb 2 | 3 | 1 C_2 4 | 2 O_2 1 1.229 5 | 3 OS 1 1.327 2 125.6 6 | 4 OS 1 1.327 2 -125.6 3 0.0 7 | 5 CM 3 1.438 1 107.0 2 180.0 8 | 6 CM 4 1.438 1 107.0 2 180.0 9 | 7 HCM 5 1.080 3 125.7 2 180.0 10 | 8 HCM 6 1.080 4 125.7 2 180.0 11 | 12 | connect 5 6 13 | 14 | oplsaa.ff 15 | -------------------------------------------------------------------------------- /tools/network/netscan.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | network=$1 3 | time=$(date +%H%M%S) 4 | 5 | for i in $(seq $2 $3) 6 | do 7 | ping -c 1 -w 2 $network.$i > /dev/null 8 | if [ $? -eq 0 ]; then 9 | arp $network.$i | grep ":" | awk '{print $1,$3}' >> $time.log 10 | echo "host $network.$i is up" 11 | else 12 | echo "host $network.$i is down" 13 | fi 14 | done 15 | -------------------------------------------------------------------------------- /tools/sas/filter.py: -------------------------------------------------------------------------------- 1 | """ 2 | """ 3 | import numpy as np 4 | import sys 5 | 6 | cut_off = 0.04 7 | if len(sys.argv) > 1: 8 | cut_off = float(sys.argv[1]) 9 | data = np.loadtxt("frac_atom.dat") 10 | sur = np.where(data > cut_off, 1, 0) 11 | n_sur = np.sum(sur) 12 | n_total = len(data) 13 | print n_sur, n_total 14 | print n_sur*100.0/n_total 15 | np.savetxt("sur_sas.dat", sur, fmt="%.6f") 16 | -------------------------------------------------------------------------------- /tools/caltech/dat/LAMMPS/in.lammps.solv.atom.eng: -------------------------------------------------------------------------------- 1 | shakeOpts 2 | kspace_style ewald 1e-04 3 | compute atomPE all pe/atom 4 | compute atomKE all ke/atom 5 | variable atomEng atom c_atomPE+c_atomKE 6 | dump 4 all custom 10000 ${sname}.2pt.atom.eng id v_atomEng 7 | run 0 8 | undump 4 9 | uncompute atomPE 10 | uncompute atomKE 11 | 12 | -------------------------------------------------------------------------------- /tools/sas/input.dat: -------------------------------------------------------------------------------- 1 | UFF.atoms 2 | pt_201.music 3 | 1.400 4 | 5000 5 | 26.00000 26.00000 26.00000 6 | 0.59 7 | 0.0 8 | cn.dat 9 | nlist.dat 10 | 11 | 12 | 13 | ! file containing the atom types + diameters 14 | ! file containing the coordinates 15 | ! probe size in A 16 | ! number of insertions 17 | ! length of unitcell 18 | ! crystal density in g / cm3 19 | ! scale factor cut off 20 | -------------------------------------------------------------------------------- /tools/vasp/wall.py: -------------------------------------------------------------------------------- 1 | o = open("HILLSPOT", "w") 2 | 3 | cv1 = 5.0 4 | cv2 = 5.0 5 | 6 | hd = 0.1 7 | hh = 0.5 8 | 9 | x = 0 10 | step = 0.05 11 | 12 | while(x-cv1 <= step): 13 | o.write("%8.4f%8.4f%8.4f%8.4f\n"%(x, cv2, hd, hh)) 14 | x += step 15 | 16 | x = 0 17 | while(x-cv2 <= step): 18 | o.write("%8.4f%8.4f%8.4f%8.4f\n"%(cv1, x, hd, hh)) 19 | x += step 20 | 21 | o.close() 22 | 23 | -------------------------------------------------------------------------------- /tools/wham/lammps/r00/pbs.lammps: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | #SBATCH -A wag 4 | #SBATCH -J jobs 5 | #SBATCH --mem-per-cpu=4G # memory per CPU core 6 | #SBATCH -o gromacs%j.%N.out 7 | #SBATCH --time=2:00:00 # walltime 8 | #SBATCH --ntasks=1 # number of processor cores (i.e. tasks) 9 | #SBATCH --nodes=1 10 | 11 | 12 | cd $SLURM_SUBMIT_DIR 13 | ~/soft/lammps/lammps-3Mar20/src/lmp_mpi -in in.lmp > log 14 | -------------------------------------------------------------------------------- /tools/ase/center-com.py: -------------------------------------------------------------------------------- 1 | from ase.io import read, write 2 | from ase.build import sort 3 | 4 | atoms = read('pt.pdb') 5 | com = atoms.get_center_of_mass() 6 | cell = atoms.get_cell() 7 | dx = [] 8 | for i in range(3): 9 | dx.append(-com[i] + cell[i][i]/2) 10 | 11 | atoms.translate(dx) 12 | atoms = sort(atoms) 13 | 14 | write('input.pdb', atoms) 15 | write('POSCAR', atoms, vasp5=True, direct=True) 16 | -------------------------------------------------------------------------------- /tools/caltech/dat/LAMMPS/in.lammps.solv.atom.eng.rigidSolu: -------------------------------------------------------------------------------- 1 | shakeOpts 2 | kspace_style ewald 1e-04 3 | compute atomPE all pe/atom 4 | compute atomKE all ke/atom 5 | variable atomEng atom c_atomPE+c_atomKE 6 | dump 4 all custom 10000 ${sname}.2pt.atom.eng id v_atomEng 7 | run 0 8 | undump 4 9 | uncompute atomPE 10 | uncompute atomKE 11 | 12 | -------------------------------------------------------------------------------- /tools/sas/example/input.dat: -------------------------------------------------------------------------------- 1 | UFF.atoms 2 | out.music 3 | 1.400 4 | 5000 5 | 26.00000 26.00000 26.00000 6 | 0.59 7 | 0.0 8 | cn.dat 9 | nlist.dat 10 | 11 | 12 | 13 | ! file containing the atom types + diameters 14 | ! file containing the coordinates 15 | ! probe size in A 16 | ! number of insertions 17 | ! length of unitcell 18 | ! crystal density in g / cm3 19 | ! scale factor cut off 20 | -------------------------------------------------------------------------------- /arc/linux_tools/qdelm: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os 4 | import sys 5 | 6 | if __name__ == "__main__": 7 | if len(sys.argv) < 3: 8 | print "warning no job to delete" 9 | else: 10 | start = int(sys.argv[1]) 11 | end = int(sys.argv[2]) + 1 12 | for i in range(start, end): 13 | os.system('qdel %d'%i) 14 | print "job %d is being killed"%i 15 | -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/ethane.zmat: -------------------------------------------------------------------------------- 1 | ethane 2 | 3 | 1 C3H 4 | 2 C3H 1 rCC 5 | 3 H 2 rCH 1 aHCC 6 | 4 H 1 rCH 2 aHCC 3 d1 7 | 5 H 2 rCH 1 aHCC 4 d2 8 | 6 H 1 rCH 2 aHCC 5 d1 9 | 7 H 2 rCH 1 aHCC 6 d2 10 | 8 H 1 rCH 2 aHCC 7 d1 11 | 12 | rCC = 1.47 13 | rCH = 1.07 14 | aHCC = 109.5 15 | d1 = 180.0 16 | d2 = 60.0 17 | 18 | oplsaa.ff 19 | -------------------------------------------------------------------------------- /tools/sas/example/sas.inp: -------------------------------------------------------------------------------- 1 | UFF.atoms 2 | out.music 3 | 1.400 4 | 5000 5 | 200.00000 150.00000 442.00000 6 | 0.59 7 | 0.0 8 | 0.15 9 | cn.dat 10 | nlist.dat 11 | 12 | 13 | ! file containing the atom types + diameters 14 | ! file containing the coordinates 15 | ! probe size in A 16 | ! number of insertions 17 | ! length of unitcell 18 | ! crystal density in g / cm3 19 | ! scale factor cut off 20 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/phonon/IBZKPT: -------------------------------------------------------------------------------- 1 | Automatically generated mesh 2 | 4 3 | Reciprocal lattice 4 | 0.00000000000000 0.00000000000000 0.00000000000000 1 5 | 0.33333333333333 0.00000000000000 0.00000000000000 4 6 | 0.33333333333333 0.33333333333333 0.00000000000000 2 7 | -0.33333333333333 0.33333333333333 0.00000000000000 2 8 | -------------------------------------------------------------------------------- /lib/e_2_reaxData.py: -------------------------------------------------------------------------------- 1 | """ read the geo file and output to data (LAMMPS), geo and xyz file. 2 | """ 3 | from mytype import System, Molecule, Atom 4 | from geo import Geo 5 | from output_conf import toData 6 | from output_conf import toGeo 7 | from output_conf import toXyz 8 | 9 | testfile = "../../debug/geo" 10 | a = Geo(testfile) 11 | b = a.parser() 12 | b.assignAtomTypes() 13 | toData(b) 14 | toGeo(b) 15 | toXyz(b) 16 | -------------------------------------------------------------------------------- /tools/sas/example-nlist/sas.inp: -------------------------------------------------------------------------------- 1 | UFF.atoms 2 | out.music 3 | 1.400 4 | 5000 5 | 200.00000 150.00000 442.00000 6 | 0.59 7 | 0.0 8 | 0.15 9 | cn.dat 10 | nlist.dat 11 | 12 | 13 | ! file containing the atom types + diameters 14 | ! file containing the coordinates 15 | ! probe size in A 16 | ! number of insertions 17 | ! length of unitcell 18 | ! crystal density in g / cm3 19 | ! scale factor cut off 20 | -------------------------------------------------------------------------------- /examples/01_cut_a_sphere/inp: -------------------------------------------------------------------------------- 1 | [SPHERE] 2 | pdbfile = ca12.pdb ; input pdb file 3 | center = 23.978 23.978 23.978 ; center of the sphere, usually we use the center of the box 4 | radius = 12.8 ; radius of the sphere (in A) 5 | atoms = Ca Al O ; Atom names in the pdb file 6 | natoms = 12 14 33 ; Desired ratio 7 | outfile = caalo_128.pdb ; Output pdb file 8 | -------------------------------------------------------------------------------- /tools/math/int.py: -------------------------------------------------------------------------------- 1 | import sys 2 | import numpy as np 3 | from scipy import integrate 4 | 5 | #datafile = sys.argv[1] 6 | datafile = "fe.dat" 7 | 8 | data = np.loadtxt(datafile) 9 | data = data.transpose() 10 | 11 | x = data[0] 12 | y = data[1] 13 | 14 | y_int = integrate.cumtrapz(y, x, initial=0) 15 | 16 | o = open("fe-int.dat", "w") 17 | for i in range(len(x)): 18 | o.write("%12.4f%12.4f\n"%(x[i], y_int[i])) 19 | 20 | -------------------------------------------------------------------------------- /tools/vasp/raman/vasp_raman.gnuplot.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | gnuplot << EOF 4 | reset 5 | set terminal postscript enhanced "Helvetica" 20 6 | set output "Raman.ps" 7 | set xrange[0:4000] 8 | set style line 1 lt 1 lc -1 lw 4 9 | set title "Off-resonance Raman PBE/PAW_h level" 10 | #set nokey 11 | set xlabel "Frequency, cm^{-1}" 12 | set ylabel "Intensity, a.u." 13 | 14 | plot "vasp_raman.dat-broaden.dat" u 1:2 w l ls 1 15 | EOF -------------------------------------------------------------------------------- /tools/vasp/refine-ab.py: -------------------------------------------------------------------------------- 1 | f = open('ML_AB.0', 'r') 2 | lines = f.readlines() 3 | f.close() 4 | 5 | nc = 0 6 | for n, i in enumerate(lines): 7 | if i.strip().startswith('Configuration num'): 8 | nc += 1 9 | lines[n] = ' Configuration num.%7d\n'%nc 10 | print(lines[n]) 11 | lines[4] = '%11d\n'%nc 12 | 13 | o = open('ML_AB', 'w') 14 | for i in lines: 15 | o.write(i) 16 | o.close() 17 | 18 | 19 | -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/opc3.ff: -------------------------------------------------------------------------------- 1 | # OPC3 water (kJ/mol, A, deg) 2 | 3 | ATOMS 4 | # type m/uma q/e pot pars 5 | Ow Ow 15.999 -0.8952 lj 3.17427 0.68369 6 | Hw Hw 1.008 0.4476 lj 0.00000 0.00000 7 | 8 | BONDS 9 | # i j pot re/A ka/kJmol-1 10 | Ow Hw cons 0.9789 4331.53 11 | 12 | ANGLES 13 | # i j k pot th/deg ka/kjmol-1 14 | Hw Ow Hw cons 109.47 317.57 15 | -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/spc.ff: -------------------------------------------------------------------------------- 1 | # SPC water (kJ/mol, A, deg) 2 | 3 | ATOMS 4 | # type m/uma q/e pot pars 5 | Ow Ow 15.999 -0.82 lj 3.1655 0.6503 6 | Hw Hw 1.008 0.41 lj 0.0000 0.0000 7 | 8 | BONDS 9 | # i j pot re/A ka/kJmol-1 10 | Ow Hw cons 1.000 4331.53 11 | 12 | ANGLES 13 | # i j k pot th/deg ka/kjmol-1 14 | Hw Ow Hw cons 109.47 317.57 15 | -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/spce.ff: -------------------------------------------------------------------------------- 1 | # SPC/E water (kJ/mol, A, deg) 2 | 3 | ATOMS 4 | # type m/uma q/e pot pars 5 | Ow Ow 15.999 -0.8476 lj 3.1655 0.6503 6 | Hw Hw 1.008 0.4238 lj 0.0000 0.0000 7 | 8 | BONDS 9 | # i j pot re/A ka/kJmol-1 10 | Ow Hw cons 1.000 4331.53 11 | 12 | ANGLES 13 | # i j k pot th/deg ka/kjmol-1 14 | Hw Ow Hw harm 109.47 317.57 15 | -------------------------------------------------------------------------------- /arc/linux_tools/qsgrompp_l: -------------------------------------------------------------------------------- 1 | #/bin/sh 2 | # It qsub the job of GROMACS 3 | # $1 for cpu core 4 | # $2 input gro file 5 | # $3 input top file 6 | 7 | echo "#!/bin/bash" > grompp.sh 8 | #echo "#PBS -l nodes=1:ppn=$1" >> grompp.sh 9 | echo "cd \$PWD" >> grompp.sh 10 | echo "grompp_mpi -np $1 -f equil.mdp -c $2 -p $3 -o equil" >> grompp.sh 11 | echo "mpirun -np $1 mdrun_mpi -s equil" >> grompp.sh 12 | bash grompp.sh & 13 | rm grompp.sh 14 | -------------------------------------------------------------------------------- /tools/linux/pwdu-ubuntu: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | """ 4 | convert linux path to windows format 5 | """ 6 | 7 | import os 8 | 9 | cmd = os.getcwd() 10 | wcmd = cmd 11 | if "Disk/pmd" in cmd: 12 | wcmd = wcmd.replace("/home/tao/Disk/pmd/", "/net/hulk/PMD/tcheng/") 13 | elif "giant12" in cmd: 14 | wcmd = wcmd.replace( "/home/tao/Disk/giant12/", "/temp1/jobs/") 15 | 16 | #wcmd = wcmd.replace("/", "\\") 17 | print wcmd 18 | 19 | -------------------------------------------------------------------------------- /arc/linux_tools/old/changeCharge.py: -------------------------------------------------------------------------------- 1 | f = open("crystal.top", 'r') 2 | o = open("crystal_1.top", 'w') 3 | 4 | for i in f: 5 | i = i.replace("-0.3146", "-0.4520") 6 | i = i.replace(" 0.9429", " 0.3411") 7 | i = i.replace("-0.3137", " 0.2424") 8 | i = i.replace(" 0.3063", " 0.4039") 9 | i = i.replace("-0.9967", "-0.8109") 10 | i = i.replace(" 0.3841", " 0.3236") 11 | o.write(i) 12 | 13 | f.close() 14 | o.close() 15 | 16 | -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/ethyleneglycol.zmat: -------------------------------------------------------------------------------- 1 | ethyleneglycol 2 | 3 | 1 CTO 4 | 2 CTO 1 1.52 5 | 3 OH2 1 1.47 2 109.5 6 | 4 H 1 1.09 2 109.5 3 240.0 7 | 5 H 1 1.09 2 109.5 3 120.0 8 | 6 H 2 1.09 1 109.5 3 300.0 9 | 7 OH2 2 1.47 1 109.5 3 180.0 10 | 8 H 2 1.09 1 109.5 3 60.0 11 | 9 HO2 3 1.00 1 109.5 2 180.0 12 | 10 HO2 7 1.00 2 109.5 1 180.0 13 | 14 | oplsaa.ff 15 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/INCAR: -------------------------------------------------------------------------------- 1 | ! general 2 | SYSTEM = raman 3 | ISTART = 0 4 | NWRITE = 3 5 | ICHARG = 2 6 | PREC = N 7 | ENCUT = 400.0 8 | NELMIN = 4 9 | EDIFF = 1.0E-4 10 | ISMEAR = 1 11 | SIGMA = 0.2 12 | LWAVE = .FALSE. 13 | LCHARG = .FALSE. 14 | LREAL = Auto 15 | IALGO = 38 16 | ADDGRID = .TRUE. 17 | ! raman 18 | LEPSILON=.TRUE. 19 | ! parallelisation 20 | NPAR = 7 21 | ISYM = 0 22 | ! output 23 | LELF = .FALSE. 24 | LVTOT = .FALSE. 25 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/POSCAR: -------------------------------------------------------------------------------- 1 | OUTCAR.0006.+1.out 1.0e-02 2 | 1.00000000000000 3 | 2.4819487690084672 0.0000000000000000 0.0000000000000000 4 | -1.2409743845546799 2.1494306848475140 0.0000000000000000 5 | 0.0000000000000010 0.0000000000000010 12.0000000000000000 6 | C 7 | 2 8 | Cartesian 9 | 0.0059579644 0.0037953072 1.7000404639 10 | -0.0059800955 1.4291550594 1.7000428205 11 | -------------------------------------------------------------------------------- /src/in.lj: -------------------------------------------------------------------------------- 1 | # 3d Lennard-Jones melt 2 | 3 | units lj 4 | atom_style atomic 5 | atom_modify map array 6 | 7 | lattice fcc 0.8442 8 | region box block 0 4 0 4 0 4 9 | create_box 1 box 10 | create_atoms 1 box 11 | mass 1 1.0 12 | 13 | velocity all create 1.44 87287 loop geom 14 | 15 | pair_style lj/cut 2.5 16 | pair_coeff 1 1 1.0 1.0 2.5 17 | 18 | neighbor 0.3 bin 19 | neigh_modify delay 0 every 20 check no 20 | 21 | fix 1 all nve 22 | 23 | 24 | -------------------------------------------------------------------------------- /test/glycine/glycine.gjf: -------------------------------------------------------------------------------- 1 | 10 2 | glycine 3 | O 0.5746 1.2556 0.0001 4 | O 1.6767 -0.7037 -0.0001 5 | C -0.7431 -0.7561 0.0001 6 | H -0.7612 -1.4193 0.8704 7 | H -0.7612 -1.4200 -0.8696 8 | C 0.6360 -0.0991 -0.0001 9 | H 1.4921 1.5679 0.0001 10 | N -1.9270 0.0853 -0.0001 11 | H -1.9247 0.6950 0.8108 12 | H -1.9245 0.6950 -0.8111 13 | -------------------------------------------------------------------------------- /test/glycine/glycine.xyz: -------------------------------------------------------------------------------- 1 | 10 2 | glycine 3 | O 0.5746 1.2556 0.0001 4 | O 1.6767 -0.7037 -0.0001 5 | C -0.7431 -0.7561 0.0001 6 | H -0.7612 -1.4193 0.8704 7 | H -0.7612 -1.4200 -0.8696 8 | C 0.6360 -0.0991 -0.0001 9 | H 1.4921 1.5679 0.0001 10 | N -1.9270 0.0853 -0.0001 11 | H -1.9247 0.6950 0.8108 12 | H -1.9245 0.6950 -0.8111 13 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/vasp_raman.dat: -------------------------------------------------------------------------------- 1 | # mode freq(cm-1) alpha beta2 activity 2 | 001 861.97778 0.0150179 0.0292079 0.2146042 3 | 002 2.26454 0.0428732 0.0049035 0.1170395 4 | 003 1.11446 -0.0139644 0.0182394 0.1364511 5 | 004 0.05250 -0.0007840 0.0004816 0.0033990 6 | 005 1835.12945 -77.4139673 244642882.6771160 1712769860.2449503 7 | 006 1837.98946 -5065.7511104 224425390.6333053 2725760278.4892015 8 | -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/DMSO.zmat: -------------------------------------------------------------------------------- 1 | DMSO 2 | 3 | 1 OY 4 | 2 SZ 1 1.530 5 | 3 CSZ 2 1.790 1 107.0 6 | 4 CSZ 2 1.790 3 96.0 1 110.0 7 | 5 H 3 1.090 2 109.5 1 75.0 8 | 6 H 3 1.090 2 109.5 5 120.0 9 | 7 H 3 1.090 2 109.5 5 240.0 10 | 8 H 4 1.090 2 109.5 1 -75.0 11 | 9 H 4 1.090 2 109.5 8 120.0 12 | 10 H 4 1.090 2 109.5 8 240.0 13 | 14 | oplsaa.ff 15 | -------------------------------------------------------------------------------- /tools/sas/nl.py: -------------------------------------------------------------------------------- 1 | from ase.io import read, write 2 | from ase.neighborlist import NeighborList 3 | from ase.neighborlist import natural_cutoffs 4 | 5 | nt = [0]*32 6 | atoms = read('run-01.pdb') 7 | nl = NeighborList(natural_cutoffs(atoms, 1.35)) 8 | nl.update(atoms) 9 | 10 | o = open('nl.dat', 'w') 11 | for i in range(len(atoms)): 12 | indices, offsets = nl.get_neighbors(i) 13 | nt[len(indices)] += 1 14 | o.write('%d\n'%len(indices)) 15 | 16 | -------------------------------------------------------------------------------- /tools/vasp/any2vasp: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env /exec/python/pythonEPD-6.3-2-rh3-x86/bin/python 2 | 3 | """ 4 | Convert any file format (with correct ext) to POSCAR. 5 | @Note: need ase. 6 | any2vasp infile 7 | """ 8 | 9 | import sys 10 | from ase.io import read, write 11 | 12 | if len(sys.argv) > 1: 13 | infile = sys.argv[1] 14 | atoms = read(infile) 15 | outfile = "POSCAR" 16 | write(outfile, atoms) 17 | else: 18 | print __doc__ 19 | 20 | 21 | -------------------------------------------------------------------------------- /tools/vmd/merge.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | r1 = np.loadtxt("r1.dat") 4 | r1 = r1.transpose() 5 | 6 | r2 = np.loadtxt("r2.dat") 7 | r2 = r2.transpose() 8 | 9 | r = [] 10 | 11 | for i in range(len(r1[1])): 12 | if r1[1][i] < r2[1][i]: 13 | val = r1[1][i] 14 | else: 15 | val = r2[1][i] 16 | r.append(val) 17 | 18 | o = open("r.dat", "w") 19 | for i in range(len(r)): 20 | o.write("%20.8f\n"%r[i]) 21 | o.close() 22 | 23 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/phonon/INCAR: -------------------------------------------------------------------------------- 1 | ! general 2 | SYSTEM = phonon 3 | ISTART = 0 4 | ICHARG = 2 5 | PREC = N 6 | ENCUT = 400.0 7 | NELMIN = 4 8 | EDIFF = 1.0E-4 9 | IBRION = 5 10 | ISMEAR = 1 11 | SIGMA = 0.2 12 | LWAVE = .FALSE. 13 | LCHARG = .FALSE. 14 | LREAL = Auto 15 | IALGO = 48 16 | ADDGRID = .TRUE. 17 | ! phonon 18 | POTIM = 0.01 19 | ! parallelisation 20 | NPAR = 7 21 | ! output 22 | LELF = .FALSE. 23 | LVTOT = .FALSE. 24 | NWRITE=3 25 | -------------------------------------------------------------------------------- /tools/caltech/Packages/auto/Math/FFT32/.packlist: -------------------------------------------------------------------------------- 1 | /ul/tpascal/scripts/Packages/Math/FFT.pm 2 | /ul/tpascal/scripts/Packages/Math/FFT/FFT.bs 3 | /ul/tpascal/scripts/Packages/Math/FFT/FFT.so 4 | /ul/tpascal/scripts/Packages/auto/Math/FFT/FFT.bs 5 | /ul/tpascal/scripts/Packages/auto/Math/FFT/FFT.so 6 | /ul/tpascal/scripts/Packages/auto/Math/FFT32/FFT32.bs 7 | /ul/tpascal/scripts/Packages/auto/Math/FFT32/FFT32.so 8 | /ul/tpascal/scripts/Packages/share/man/man3/Math::FFT.3pm 9 | -------------------------------------------------------------------------------- /tools/vasp/eos-ase/ana-eos.py: -------------------------------------------------------------------------------- 1 | from ase.io import read 2 | from ase.units import kJ 3 | from ase.eos import EquationOfState 4 | configs = read('eos.traj@0:11') # read 5 configurations 5 | # Extract volumes and energies: 6 | volumes = [ag.get_volume() for ag in configs] 7 | energies = [ag.get_potential_energy() for ag in configs] 8 | eos = EquationOfState(volumes, energies) 9 | v0, e0, B = eos.fit() 10 | print(B / kJ * 1.0e24, 'GPa') 11 | eos.plot('eos.png') 12 | -------------------------------------------------------------------------------- /arc/linux_tools/dffforcefield/group_0709.py: -------------------------------------------------------------------------------- 1 | GROUP =[ 2 | #'acetylene', 3 | #'acid', 4 | #'alcohols', 5 | #'aldehydes', 6 | #'alkane', 7 | #'alkene', 8 | #'amides', 9 | #'amine', 10 | 'benzenes', 11 | #'branched_alkanes', 12 | #'ether', 13 | #'fluoro', 14 | #'glycol', 15 | #'nitriles', 16 | #'nitroalkanes', 17 | #'noble_gas', 18 | #'silanes', 19 | #'siloxanes', 20 | #'small_molecules', 21 | #'sulfides', 22 | #'sulfur', 23 | #'thiols', 24 | ] 25 | -------------------------------------------------------------------------------- /tools/vasp/get_oszicar.py: -------------------------------------------------------------------------------- 1 | import os 2 | folder_name = os.path.basename(os.getcwd()) 3 | pe = [] 4 | f = open("OSZICAR", 'r') 5 | for i in f: 6 | if "E0" in i: 7 | tokens = i.strip().split() 8 | for j in tokens: 9 | if 'E0' in j: 10 | e0 = tokens[tokens.index(j)+1] 11 | pe.append(float(e0)) 12 | f.close() 13 | 14 | o = open('e0.dat', 'w') 15 | o.write('%s %.6f\n'%(folder_name, pe[-1])) 16 | o.close() 17 | -------------------------------------------------------------------------------- /arc/linux_tools/cmdall: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | import os 3 | import os.path 4 | import sys 5 | 6 | usage = """this 7 | """ 8 | 9 | cmd = "" 10 | try: 11 | len(sys.argv) < 2 12 | except: 13 | print usage 14 | 15 | cmd = " ".join([i for i in sys.argv[1:]]) 16 | allpath = [i for i in os.listdir(".")] 17 | allpath.sort() 18 | for i in allpath: 19 | if os.path.isdir(i): 20 | os.chdir(i) 21 | os.system(cmd) 22 | os.chdir("../") 23 | 24 | -------------------------------------------------------------------------------- /tools/caltech/dat/LAMMPS/in.lammps.atom.eng: -------------------------------------------------------------------------------- 1 | fix shakeH all shake shakeOpts 2 | kspace_style ewald 1e-04 3 | compute atomPE all pe/atom 4 | compute atomKE all ke/atom 5 | variable atomEng atom c_atomPE+c_atomKE 6 | dump 4 all custom 10000 ${sname}.2pt.atom.eng id v_atomEng 7 | dump_modify 4 append yes first yes 8 | run 0 9 | undump 4 10 | uncompute atomPE 11 | uncompute atomKE 12 | 13 | -------------------------------------------------------------------------------- /tools/msi2lmp/replace_xx.py: -------------------------------------------------------------------------------- 1 | import sys 2 | import shutil 3 | 4 | fname = sys.argv[1] 5 | 6 | f = open(fname, "r") 7 | o = open("tmp.car", "w") 8 | 9 | for i in f: 10 | line = i 11 | tokens = i.strip().split() 12 | if len(tokens) == 9: 13 | atom = tokens[7] 14 | line = i.replace("xx", "%-2s"%atom) 15 | o.write(line) 16 | 17 | o.close() 18 | f.close() 19 | 20 | shutil.copy(fname, "backup.car") 21 | shutil.copy("tmp.car", fname) 22 | -------------------------------------------------------------------------------- /tools/puremd/out.py: -------------------------------------------------------------------------------- 1 | """ 2 | 0: step 3 | 1: total energy 4 | 2: poten. energy 5 | 3: amd E 6 | 4: delta. energy 7 | 5: force. scale 8 | 6: kin. energy 9 | 7: temp. 10 | 8: target 11 | 9: volume 12 | 10: press. 13 | 11:target 14 | """ 15 | import numpy as np 16 | import os 17 | 18 | data = np.loadtxt("water.out", skiprows=1) 19 | data = data.transpose() 20 | np.savetxt("tempt.txt", data[7].transpose(), fmt="%.4f") 21 | -------------------------------------------------------------------------------- /tools/lammps/xrd/xrd.in: -------------------------------------------------------------------------------- 1 | atom_style charge 2 | boundary p p p 3 | 4 | units metal 5 | timestep 0.001 6 | 7 | read_data lammps.data 8 | pair_style none 9 | atom_modify sort 0 0 10 | 11 | # synchrotron 12 | compute XRD all xrd 1.0 Cu 2Theta 20 110 c 1 1 1 LP 1 echo 13 | 14 | fix 1 all ave/histo/weight 1 1 1 20 110 500 c_XRD[1] c_XRD[2] & 15 | mode vector file Cu.hist.xrd 16 | 17 | run 0 18 | 19 | -------------------------------------------------------------------------------- /tools/reax/functions/pbo3/plot.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import matplotlib.pyplot as plt 3 | 4 | data = np.loadtxt("data1") 5 | data = data.transpose() 6 | 7 | plt.plot(data[0], data[1], lw=2, color="blue") 8 | plt.plot(data[0], data[2], lw=2, color="blue", ls="--") 9 | 10 | data = np.loadtxt("data2") 11 | data = data.transpose() 12 | 13 | plt.plot(data[0], data[1], lw=2, color="green") 14 | plt.plot(data[0], data[2], lw=2, color="green", ls="--") 15 | 16 | plt.show() 17 | -------------------------------------------------------------------------------- /tools/sas/remove-low-coordinated.py: -------------------------------------------------------------------------------- 1 | f = open("cn.dat", "r") 2 | lines = f.readlines() 3 | f.close() 4 | 5 | f = open("out.xyz", "r") 6 | coords = f.readlines() 7 | f.close() 8 | 9 | new_coords = [] 10 | 11 | for i in range(len(lines)): 12 | nc = int(lines[i]) 13 | if nc > 5: 14 | new_coords.append(coords[2+i]) 15 | 16 | o = open("out.new.xyz", "w") 17 | o.write("%d\n\n"%len(new_coords)) 18 | for i in new_coords: 19 | o.write(i) 20 | o.close() 21 | 22 | -------------------------------------------------------------------------------- /tools/sas/html/api-objects.txt: -------------------------------------------------------------------------------- 1 | slice slice-module.html 2 | slice.read_data slice-module.html#read_data 3 | slice.main slice-module.html#main 4 | slice.LIB slice-module.html#LIB 5 | slice.write_lammps slice-module.html#write_lammps 6 | slice.__package__ slice-module.html#__package__ 7 | slice.read_ndx_coords slice-module.html#read_ndx_coords 8 | slice.get_slice slice-module.html#get_slice 9 | slice.DELTA_Z2 slice-module.html#DELTA_Z2 10 | slice.DELTA_Z1 slice-module.html#DELTA_Z1 11 | -------------------------------------------------------------------------------- /arc/linux_tools/rm_m_size: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os 4 | import os.path 5 | A1M = 1048576 6 | def parseFolder(folder): 7 | for i in os.listdir(folder): 8 | fullname = os.path.join(folder,i) 9 | if os.path.isdir(fullname): 10 | parseFolder(fullname) 11 | elif os.path.getsize(fullname) > 3*A1M: 12 | os.remove(fullname) 13 | else: 14 | pass 15 | 16 | if __name__ == "__main__": 17 | parseFolder('.') 18 | -------------------------------------------------------------------------------- /arc/linux_tools/scan/read.py: -------------------------------------------------------------------------------- 1 | import os 2 | os.system("ls ./*/*.edr > ls.log") 3 | os.system("echo '15' > in.log") 4 | os.system("echo '11' >> in.log") 5 | os.system("echo '14' >> in.log") 6 | os.system("echo '20' >> in.log") 7 | f = open("ls.log") 8 | for i in f: 9 | a = i[:-1] 10 | os.system("echo %s >> out.log"%a) 11 | os.system("g_energy_mpi -f %s < in.log >> out.log"%a) 12 | #os.system("grep './' > list.log") 13 | #os.system("grep 'dVpot/dlambda' > result.log") 14 | 15 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/template/.svn/entries: -------------------------------------------------------------------------------- 1 | 10 2 | 3 | dir 4 | 13 5 | https://svn.kenai.com/svn/ms-tools-python~source-code-repository/template 6 | https://svn.kenai.com/svn/ms-tools-python~source-code-repository 7 | 8 | 9 | 10 | 2011-08-04T09:22:54.578096Z 11 | 8 12 | chengtao@sjtu.edu.cn 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | c94ac6af-a9fb-c7db-cc57-a5ad3d5167db 28 | 29 | water 30 | dir 31 | 32 | zeolite 33 | dir 34 | 35 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/IBZKPT: -------------------------------------------------------------------------------- 1 | Automatically generated mesh 2 | 5 3 | Reciprocal lattice 4 | 0.00000000000000 0.00000000000000 0.00000000000000 1 5 | 0.33333333333333 0.00000000000000 0.00000000000000 2 6 | 0.00000000000000 0.33333333333333 0.00000000000000 2 7 | 0.33333333333333 0.33333333333333 0.00000000000000 2 8 | -0.33333333333333 0.33333333333333 0.00000000000000 2 9 | -------------------------------------------------------------------------------- /tools/inprogress/parse_molid.py: -------------------------------------------------------------------------------- 1 | dist = {} 2 | f = open("molid.out", "r") 3 | 4 | for i in f: 5 | tokens = i.strip().split() 6 | if i.strip().startswith("#"): 7 | pass 8 | else: 9 | if len(tokens) > 2: 10 | molname = tokens[2] 11 | if molname in dist.keys(): 12 | dist[molname] += 1 13 | else: 14 | dist[molname] = 1 15 | f.close() 16 | 17 | for i in dist.keys(): 18 | print i, dist[i] 19 | -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/tip4p.ff: -------------------------------------------------------------------------------- 1 | # TIP4P water (kJ/mol, A, deg) 2 | # add special M site using LAMMPS tip4p pair styles 3 | 4 | ATOMS 5 | # type m/uma q/e pot pars 6 | Ow Ow 15.999 -1.04 lj 3.1536 0.64852 7 | Hw Hw 1.008 0.52 lj 0.0000 0.00000 8 | 9 | BONDS 10 | # i j pot re/A ka/kJmol-1 11 | Ow Hw cons 0.9572 4331.53 12 | 13 | ANGLES 14 | # i j k pot th/deg ka/kjmol-1 15 | Hw Ow Hw harm 104.52 317.57 16 | -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/urea.xyz: -------------------------------------------------------------------------------- 1 | 8 2 | urea oplsaa.ff 3 | OU -0.69265 1.40835 -0.22910 4 | CU -1.29431 0.34754 -0.30568 5 | NU -1.44367 -0.25612 -1.50814 6 | NU -1.80763 -0.21721 0.81244 7 | HU -1.69355 0.24297 1.72783 8 | HU -2.31745 -1.11158 0.76328 9 | HU -1.05255 0.17444 -2.35923 10 | HU -1.94866 -1.15100 -1.58814 11 | -------------------------------------------------------------------------------- /tools/sas/share/sas.inp: -------------------------------------------------------------------------------- 1 | UFF.atoms 2 | out.music 3 | 1.400 4 | 5000 5 | 80.00000 80.00000 47.40000 6 | 0.59 7 | 0.0 8 | 0.04 9 | cn.dat 10 | nlist.dat 11 | 12 | 13 | 14 | ! file containing the atom types + diameters 15 | ! file containing the coordinates 16 | ! probe size in A 17 | ! number of insertions 18 | ! length of unitcell 19 | ! crystal density in g / cm3 20 | ! scale factor cut off 21 | ! surface atom cut off 22 | ! coordinatin files 23 | ! neighbor list files 24 | -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/benzene.zmat: -------------------------------------------------------------------------------- 1 | benzene 2 | 3 | CA 4 | CA 1 rCC 5 | CA 2 rCC 1 120.00 6 | CA 3 rCC 2 120.00 1 0 7 | CA 4 rCC 3 120.00 2 0 8 | CA 5 rCC 4 120.00 3 0 9 | HA 1 rCH 2 120.00 3 180 10 | HA 2 rCH 3 120.00 4 180 11 | HA 3 rCH 4 120.00 5 180 12 | HA 4 rCH 5 120.00 6 180 13 | HA 5 rCH 6 120.00 1 180 14 | HA 6 rCH 1 120.00 2 180 15 | 16 | rCC = 1.400 17 | rCH = 1.080 18 | 19 | connect 1 6 20 | 21 | oplsaa.ff 22 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/inp/POSCAR: -------------------------------------------------------------------------------- 1 | graphite 2 | 1.00000000000000 3 | 2.4819487690084672 0.0000000000000000 0.0000000000000000 4 | -1.2409743845546799 2.1494306848475140 0.0000000000000000 5 | 0.0000000000000010 0.0000000000000010 12.0000000000000000 6 | C 7 | 2 8 | Direct 9 | 0.0000000000000000 0.0000000000000000 0.1416700039999981 10 | 0.3333300050000005 0.6666700239999983 0.1416700039999981 11 | 12 | -------------------------------------------------------------------------------- /lib/e_t_ldh.py: -------------------------------------------------------------------------------- 1 | """ Replace the Ca in CaO crystal to creat a Ca-rich LDO (Ca:Al=7:1) 2 | This is for LDH project 3 | """ 4 | 5 | from data import ReaxData 6 | from output_conf import toReaxLammps 7 | from tools import LdhProject 8 | 9 | for i in range(100): 10 | testfile = "a666.data" 11 | a = ReaxData(testfile) 12 | b = a.parser() 13 | c = LdhProject(b) 14 | c.re_al = 8 15 | c.re1() 16 | b.assignAtomTypes() 17 | toReaxLammps(b, "case%02d.data"%i) 18 | 19 | 20 | 21 | -------------------------------------------------------------------------------- /tools/ase/move-atom-center.py: -------------------------------------------------------------------------------- 1 | from ase.io import read, write 2 | import sys 3 | from ase.build import sort 4 | 5 | fname = sys.argv[1] 6 | catom = int(sys.argv[2]) 7 | 8 | atoms = read(fname) 9 | sp = atoms.get_scaled_positions() 10 | dx = [0.5, 0.5, 0.5] - sp[catom-1] 11 | for n, i in enumerate(sp): 12 | sp[n] = sp[n] + dx 13 | atoms.set_scaled_positions(sp) 14 | sp = atoms.get_scaled_positions() 15 | atoms.wrap() 16 | atoms = sort(atoms) 17 | write('out.vasp', atoms, vasp5=True, direct=True) 18 | -------------------------------------------------------------------------------- /tools/ase/trj2pdb.py: -------------------------------------------------------------------------------- 1 | import os,sys 2 | from ase.io.trajectory import PickleTrajectory 3 | from ase import Atoms 4 | from ase.io.trajectory import Trajectory 5 | import ase.io 6 | 7 | 8 | #reading in the trajectory file created during dynamics 9 | traj = Trajectory('%s'%sys.argv[1]) 10 | 11 | o = open("flist", "w") 12 | 13 | ns = 0 14 | for atoms in traj: 15 | fname = "ase_%04d.pdb"%ns 16 | o.write("%s\n"%fname) 17 | ase.io.write(fname, atoms) 18 | ns += 1 19 | 20 | o.close() 21 | -------------------------------------------------------------------------------- /tools/sas/example-2/input.dat: -------------------------------------------------------------------------------- 1 | UFF.atoms 2 | out.music 3 | 1.400 4 | 5000 5 | 80.0000 80.0000 460.9100 6 | 0.59 7 | 0.03 8 | 0.1 9 | cn.dat 10 | nlist.dat 11 | 12 | 13 | 14 | ! file containing the atom types + diameters 15 | ! file containing the coordinates 16 | ! probe size in A 17 | ! number of insertions 18 | ! length of unitcell 19 | ! crystal density in g / cm3 20 | ! scale factor cut-off 21 | ! surface atom cut-off 22 | ! coordination number file 23 | ! neighbour list file 24 | -------------------------------------------------------------------------------- /tools/vasp/gather_poscars.py: -------------------------------------------------------------------------------- 1 | !/usr/bin/env python 2 | 3 | import os, shutil 4 | 5 | n = 0 6 | for i in os.listdir("."): 7 | if os.path.isdir(i): 8 | os.chdir(i) 9 | poscars = [] 10 | for j in os.listdir("."): 11 | if j.startswith("POSCAR"): 12 | poscars.append(j) 13 | poscars.sort() 14 | for k in poscars: 15 | shutil.copy(k, "../POSCAR_%06d"%n) 16 | n += 1 17 | os.chdir("..") 18 | 19 | 20 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/phonon/POSCAR: -------------------------------------------------------------------------------- 1 | graphite 2 | 1.00000000000000 3 | 2.4819487690084672 0.0000000000000000 0.0000000000000000 4 | -1.2409743845546799 2.1494306848475140 0.0000000000000000 5 | 0.0000000000000010 0.0000000000000010 12.0000000000000000 6 | C 7 | 2 8 | Direct 9 | 0.0000000000000000 0.0000000000000000 0.1416700039999981 10 | 0.3333300050000005 0.6666700239999983 0.1416700039999981 11 | 12 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/working_folder/inp/POSCAR: -------------------------------------------------------------------------------- 1 | graphite 2 | 1.00000000000000 3 | 2.4819487690084672 0.0000000000000000 0.0000000000000000 4 | -1.2409743845546799 2.1494306848475140 0.0000000000000000 5 | 0.0000000000000010 0.0000000000000010 12.0000000000000000 6 | C 7 | 2 8 | Direct 9 | 0.0000000000000000 0.0000000000000000 0.1416700039999981 10 | 0.3333300050000005 0.6666700239999983 0.1416700039999981 11 | 12 | -------------------------------------------------------------------------------- /tools/deepmd/run.sh: -------------------------------------------------------------------------------- 1 | #covert vasp output to raw file 2 | echo "converting vasp output to raw file ..." 3 | cmdall "python ~/soft/simpy/tools/deepmd/vasp2raw.py" 4 | 5 | mkdir ../data 6 | 7 | cat ./*/box.raw > ../data/box.raw 8 | cat ./*/coord.raw > ../data/coord.raw 9 | cat ./*/virial.raw > ../data/virial.raw 10 | cat ./*/force.raw > ../data/force.raw 11 | cat ./*/energy.raw > ../data/energy.raw 12 | 13 | cp ./type.raw ../data/ 14 | cp ~/soft/simpy/tools/deepmd/raw_to_set.sh ../data/ 15 | 16 | 17 | 18 | -------------------------------------------------------------------------------- /tools/deepmd/trj2pdb.py: -------------------------------------------------------------------------------- 1 | import os,sys 2 | from ase.io.trajectory import PickleTrajectory 3 | from ase import Atoms 4 | from ase.io.trajectory import Trajectory 5 | import ase.io 6 | 7 | 8 | #reading in the trajectory file created during dynamics 9 | traj = Trajectory('%s'%sys.argv[1]) 10 | 11 | o = open("flist", "w") 12 | 13 | ns = 0 14 | for atoms in traj: 15 | fname = "ase_%04d.pdb"%ns 16 | o.write("%s\n"%fname) 17 | ase.io.write(fname, atoms) 18 | 19 | ns += 1 20 | o.close() 21 | -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/opc.ff: -------------------------------------------------------------------------------- 1 | # OPC water (kJ/mol, A, deg) 2 | # add special M site at 0.1594 A from Ow using LAMMPS tip4p pair styles 3 | 4 | ATOMS 5 | # type m/uma q/e pot pars 6 | Ow Ow 15.999 -1.3582 lj 3.16655 0.89036 7 | Hw Hw 1.008 0.6791 lj 0.00000 0.00000 8 | 9 | BONDS 10 | # i j pot re/A ka/kJmol-1 11 | Ow Hw cons 0.8724 4331.53 12 | 13 | ANGLES 14 | # i j k pot th/deg ka/kjmol-1 15 | Hw Ow Hw cons 103.6 317.57 16 | -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/tip4pew.ff: -------------------------------------------------------------------------------- 1 | # TIP4P-Ew water (kJ/mol, A, deg) 2 | # add special M site using LAMMPS tip4p pair styles 3 | 4 | ATOMS 5 | # type m/uma q/e pot pars 6 | Ow Ow 15.999 -1.04844 lj 3.16435 0.680946 7 | Hw Hw 1.008 0.52422 lj 0.00000 0.000000 8 | 9 | BONDS 10 | # i j pot re/A ka/kJmol-1 11 | Ow Hw cons 0.9572 4331.53 12 | 13 | ANGLES 14 | # i j k pot th/deg ka/kjmol-1 15 | Hw Ow Hw harm 104.52 317.57 16 | -------------------------------------------------------------------------------- /tools/inprogress/parse_molatom.py: -------------------------------------------------------------------------------- 1 | atoms = [] 2 | 3 | f = open("mol.atom", "r") 4 | 5 | for i in f: 6 | if i.strip().startswith("#"): 7 | pass 8 | else: 9 | tokens = i.strip().split() 10 | if len(tokens) == 3: 11 | molname = tokens[1] 12 | id = int(tokens[0]) 13 | if molname == "N2": 14 | atoms.append(id) 15 | f.close() 16 | 17 | o = open("n2.atoms", "w") 18 | for i in atoms: 19 | o.write("%d\n"%i) 20 | o.close() 21 | -------------------------------------------------------------------------------- /tools/vasp/fix-atoms.py.1: -------------------------------------------------------------------------------- 1 | import shutil, sys 2 | 3 | n0 = 8 4 | n1 = n0 + 20 5 | 6 | f = open("POSCAR", "r") 7 | poscar = f.readlines() 8 | f.close() 9 | 10 | # the first line poscar[9] 11 | shutil.copy("POSCAR", "POSCAR.0") 12 | o = open("POSCAR_new", "w") 13 | for i in range(n0): 14 | o.write(poscar[i]) 15 | 16 | for i in range(n0, n1): 17 | line = poscar[i].replace("T", "F") 18 | o.write(line) 19 | 20 | for i in range(n1, len(poscar)): 21 | o.write(poscar[i]) 22 | o.close() 23 | 24 | -------------------------------------------------------------------------------- /test/glycine/qm_charge.dat: -------------------------------------------------------------------------------- 1 | glycine 1 1 -0.305423 # O 2 | glycine 1 2 -0.401504 # O 3 | glycine 1 3 -0.116845 # C 4 | glycine 1 4 0.161397 # H 5 | glycine 1 5 0.151989 # H 6 | glycine 1 6 0.286361 # C 7 | glycine 1 7 0.281261 # H 8 | glycine 1 8 -0.447280 # N 9 | glycine 1 9 0.193229 # H 10 | glycine 1 10 0.196814 # H 11 | -------------------------------------------------------------------------------- /tools/deepmd/sp/run.sh: -------------------------------------------------------------------------------- 1 | #covert vasp output to raw file 2 | echo "converting vasp output to raw file ..." 3 | cmdall "python ~/soft/simpy/tools/deepmd/vasp2raw.py" 4 | 5 | mkdir ../data 6 | 7 | cat ./*/box.raw > ../data/box.raw 8 | cat ./*/coord.raw > ../data/coord.raw 9 | cat ./*/virial.raw > ../data/virial.raw 10 | cat ./*/force.raw > ../data/force.raw 11 | cat ./*/energy.raw > ../data/energy.raw 12 | 13 | cp ./type.raw ../data/ 14 | cp ~/soft/simpy/tools/deepmd/raw_to_set.sh ../data/ 15 | 16 | 17 | 18 | -------------------------------------------------------------------------------- /tools/kmc/de: -------------------------------------------------------------------------------- 1 | -2.864 , -0.001965, 2 | -1.165 , -0.001836, 3 | 0.06 , 0.0002737, 4 | -0.85 , -0.0001336, 5 | 0.22 , 9.791e-05, 6 | -0.256 , -4.539e-07, 7 | 0.323 , 7.032e-05, 8 | -0.153 , 0.0002258, 9 | 0.572 , 0.001533, 10 | 0.656 , 0.0014021, 11 | -1.734 , -0.002954, 12 | -1.64 , -8.705e-05, 13 | 0.501 , 0.0001268, 14 | 0.599 , -7.899e-05, 15 | 0.449 , -0.000126, 16 | -1.133 , -0.0001625, 17 | 0.351 , 7.978e-05, 18 | -1.708 , -5.505e-05, 19 | -1.839 , -3.693e-05, 20 | 1.039 , 6.272e-05, 21 | 1.449 , 0.001932, 22 | -------------------------------------------------------------------------------- /tools/kmc/eact: -------------------------------------------------------------------------------- 1 | 0.045 , -0.0005133 2 | 0.0 , -0.0003776 3 | 0.66 , 8.264e-05 4 | 1.1456 , -0.0001107 5 | 1.0 , 8.137e-05 6 | 0.7136 , 4.401e-05 7 | 0.9312 , 8.583e-05 8 | 0.8424 , 8.48e-05 9 | 0.572 , 0.001063 10 | 0.656 , 0.0009301 11 | 0.0 , -0.001397 12 | 0.2136 , -6.158e-05 13 | 1.2968000000000002 , -2.03e-05 14 | 1.1936 , 3.36e-05 15 | 1.072 , 6.285e-05 16 | 0.5599999999999999 , -0.000168 17 | 0.584 , -0.000229 18 | 0.6000000000000001 , -5e-05 19 | 0.0 , 1e-08 20 | 1.2192 , 4.47e-05 21 | 1.449 , 0.001349 22 | -------------------------------------------------------------------------------- /tools/movies/merge.sh: -------------------------------------------------------------------------------- 1 | #mencoder -really-quiet -ovc lavc -lavcopts vcodec=mjpeg -mf fps=${FPS} -vf scale=${videoX}:${videoY} -o $output_video_file_name video_*.avi 2 | 3 | FPS=24 4 | videoX=640 5 | videoY=480 6 | output_video_file_name="ml.mp4" 7 | 8 | mencoder -really-quiet -ovc lavc -lavcopts vcodec=mjpeg -mf fps=${FPS} -vf scale=${videoX}:${videoY} -o $output_video_file_name 0*.mp4 1*.mp4 9 | 10 | mencoder -really-quiet -ovc lavc -lavcopts vcodec=mjpeg -mf fps=24 -vf scale=640:480 -o ml.mp4 0*.mp4 1*.mp4 11 | -------------------------------------------------------------------------------- /tools/sas/example-nlist/input.dat: -------------------------------------------------------------------------------- 1 | UFF.atoms 2 | out.music 3 | 1.400 4 | 5000 5 | 26.00000 26.00000 26.00000 6 | 0.59 7 | 0.03 8 | 0.1 9 | cn.dat 10 | nlist.dat 11 | 12 | 13 | 14 | ! file containing the atom types + diameters 15 | ! file containing the coordinates 16 | ! probe size in A 17 | ! number of insertions 18 | ! length of unitcell 19 | ! crystal density in g / cm3 20 | ! scale factor cut off 21 | ! surface atom cut-off 22 | ! coordination number file 23 | ! neighbour list file 24 | -------------------------------------------------------------------------------- /tools/lammps/xrd/lammps.data: -------------------------------------------------------------------------------- 1 | # 2 | 3 | 4 atoms 4 | 5 | 1 atom types 6 | 7 | 0.0 3.6150999 xlo xhi 8 | 0.0 3.6150999 ylo yhi 9 | 0.0 3.6150999 zlo zhi 10 | Masses 11 | 12 | 1 63.546 # Cu 13 | 14 | Atoms 15 | 16 | 1 1 0.000000 0.000000000 0.000000000 0.000000000 17 | 2 1 0.000000 0.000000000 1.807549953 1.807549953 18 | 3 1 0.000000 1.807549953 0.000000000 1.807549953 19 | 4 1 0.000000 1.807549953 1.807549953 0.000000000 20 | -------------------------------------------------------------------------------- /tools/vasp/gether_poscar: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os, shutil 4 | 5 | folders = [] 6 | for i in os.listdir("."): 7 | if os.path.isdir(i): 8 | folders.append(i) 9 | folders.sort() 10 | 11 | n = 0 12 | for i in folders: 13 | os.chdir(i) 14 | files = [] 15 | for j in os.listdir("."): 16 | files.append(j) 17 | files.sort() 18 | for j in files: 19 | fname = "POSCAR_%06d"%n 20 | shutil.copy(j, "../%s"%fname) 21 | n += 1 22 | os.chdir("..") 23 | -------------------------------------------------------------------------------- /tools/ase/estimate_nmol.py: -------------------------------------------------------------------------------- 1 | import sys 2 | from ase.io import read 3 | from scipy.constants import N_A 4 | 5 | if len(sys.argv) == 4: 6 | atoms = read(sys.argv[1]) 7 | rho = float(sys.argv[2]) 8 | l = float(sys.argv[3]) 9 | 10 | wt = 0.0 11 | for i in atoms.get_masses(): 12 | wt += i 13 | 14 | l = l*1e-10 15 | v = l*l*l*1e6 16 | 17 | nmol = int(round(v*rho*N_A/wt)) 18 | print(nmol) 19 | else: 20 | print('Usage: estimate_nmol.py pdbfile rho (in g/cm3) l (in A)') 21 | 22 | -------------------------------------------------------------------------------- /arc/linux_tools/cmdall2: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | import os 3 | import os.path 4 | import sys 5 | 6 | usage = """this 7 | """ 8 | 9 | cmd = "" 10 | try: 11 | len(sys.argv) < 2 12 | except: 13 | print usage 14 | 15 | cmd = " ".join([i for i in sys.argv[1:]]) 16 | allpath = [i for i in os.listdir(".")] 17 | allpath.sort() 18 | 19 | print allpath 20 | 21 | for i in allpath: 22 | if os.path.isdir(i): 23 | os.chdir(i) 24 | print cmd 25 | os.system(cmd) 26 | os.chdir("../") 27 | 28 | -------------------------------------------------------------------------------- /test/glycine/freq.gjf: -------------------------------------------------------------------------------- 1 | %mem=800MB 2 | # freq b3lyp/6-311g(d,p) 3 | 4 | glycine 5 | 6 | 0 1 7 | O 0.57461 1.25556 0.00005 8 | O 1.67674 -0.70368 -0.00006 9 | C -0.74310 -0.75608 0.00009 10 | H -0.76118 -1.41926 0.87036 11 | H -0.76120 -1.41996 -0.86963 12 | C 0.63602 -0.09910 -0.00007 13 | H 1.49214 1.56794 0.00009 14 | N -1.92698 0.08533 -0.00010 15 | H -1.92468 0.69502 0.81084 16 | H -1.92453 0.69496 -0.81108 17 | 18 | 19 | 20 | 21 | 22 | -------------------------------------------------------------------------------- /tools/ase/ase-translate.py: -------------------------------------------------------------------------------- 1 | from math import pi 2 | import numpy as np 3 | from ase import Atoms 4 | from ase.io import read, write 5 | from ase.optimize import BFGS 6 | from ase.vibrations import Vibrations 7 | #from deepmd.calculator import DP 8 | from ase.build import molecule 9 | from ase.constraints import FixInternals 10 | 11 | atoms = read('input.vasp') 12 | for i in atoms: 13 | for n in range(3): 14 | i.position[n] = i.position[n] + 5 15 | atoms.wrap() 16 | 17 | write('POSCAR', atoms, vasp5=True) 18 | 19 | -------------------------------------------------------------------------------- /tools/kmc/species.template: -------------------------------------------------------------------------------- 1 | HNO2 0.0000 2 | NO* 0.0000 3 | OH* 0.0000 4 | H2 0.0000 5 | H* 0.0000 6 | H2O* 0.0000 7 | N* 0.0000 8 | O* 0.0000 9 | NH* 0.0000 10 | NH2* 0.0000 11 | NH3* 0.0000 12 | NH3 0.0000 13 | H2O 0.0000 14 | NO2* 0.0000 15 | NOH* 0.0000 16 | HNO* 0.0000 17 | HNOH* 0.0000 18 | N2H4* 0.0000 19 | N2H4 0.0000 20 | -------------------------------------------------------------------------------- /tools/reax/mo.py: -------------------------------------------------------------------------------- 1 | """modify the description section 2 | """ 3 | 4 | import shutil 5 | 6 | lines = [] 7 | f = open("geo", "r") 8 | 9 | for i in f: 10 | if i.strip().startswith("DESCR"): 11 | tokens = i.strip().split() 12 | tokens[1] = "r_hdn_" + tokens[1] 13 | line = " ".join(tokens) + "\n" 14 | else: 15 | line = i 16 | lines.append(line) 17 | f.close() 18 | shutil.copy("geo", "geo.bak") 19 | 20 | o = open("geo", "w") 21 | for i in lines: 22 | o.write(i) 23 | o.close() 24 | 25 | -------------------------------------------------------------------------------- /arc/linux_tools/readpdb.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | import os 3 | import os.path 4 | 5 | nstart = 90 6 | nend = 108 7 | ninterval = 2 8 | 9 | for a in range( nstart, nend, ninterval ): 10 | for b in range( nstart, nend, ninterval ): 11 | os.chdir("./a%03d_%03d"%(a,b)) 12 | if os.path.getsize("md0.log") > 100000 : 13 | os.system("editconf_mpi -f confout.gro -o aa%03d_%03d.pdb"%(a,b)) 14 | os.system("cp aa%03d_%03d.pdb ../pdb/"%(a,b)) 15 | os.chdir("../") 16 | 17 | -------------------------------------------------------------------------------- /tools/dftb/scan.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import matplotlib.pyplot as plt 3 | 4 | f = open("geo_start.gen", "r") 5 | lines = f.readlines() 6 | tokens = lines[0].strip().split() 7 | natoms = int(tokens[0]) 8 | 9 | 10 | cells = [] 11 | 12 | for i in range(natoms+3, natoms+6): 13 | tokens = lines[i].strip().split() 14 | cells.append([float(j) for j in tokens]) 15 | 16 | 17 | data = np.linspace(0.8, 1.2, 11) 18 | data = np.power(data, 1/3.0) 19 | for i in range(len(data)): 20 | print data 21 | 22 | 23 | 24 | -------------------------------------------------------------------------------- /tools/kmc/01-acs/species.template: -------------------------------------------------------------------------------- 1 | HNO2 0.0000 2 | NO* 0.0000 3 | OH* 0.0000 4 | H2 0.0000 5 | H* 0.0000 6 | H2O* 0.0000 7 | N* 0.0000 8 | O* 0.0000 9 | NH* 0.0000 10 | NH2* 0.0000 11 | NH3* 0.0000 12 | NH3 0.0000 13 | H2O 0.0000 14 | NO2* 0.0000 15 | NOH* 0.0000 16 | HNO* 0.0000 17 | HNOH* 0.0000 18 | N2H4* 0.0000 19 | N2H4 0.0000 20 | -------------------------------------------------------------------------------- /tools/math/shapely-point-in-polygon.py: -------------------------------------------------------------------------------- 1 | # point in polygon 2 | import numpy as np 3 | from math import sqrt 4 | 5 | from shapely.geometry import Point 6 | from shapely.geometry.polygon import Polygon 7 | 8 | point = Point(13.0, 0.0) 9 | pt = np.array([[-1, 0], [-0.24*sqrt(3), 0.9], [0.24*sqrt(3), 0.9], 10 | [1, 0], [0.24*sqrt(3), -0.9], [-0.24*sqrt(3), -0.9],]) 11 | ns = 0 12 | for ns in range(1,20,2): 13 | polygon = Polygon(ns*pt) 14 | if polygon.contains(point) == True: 15 | break 16 | print(ns) 17 | -------------------------------------------------------------------------------- /tools/nanocut/decahedron/decahedron.py: -------------------------------------------------------------------------------- 1 | from ase.cluster.decahedron import Decahedron 2 | from ase.io import write 3 | 4 | p = 15 # natoms on 100 face normal to 5-fold axis 5 | q = 1 # natoms 0n 100 parallel to 5-fold axis 6 | r = 0 # depth of the Marks re-entrance? 7 | atoms = Decahedron('Cu', p, q, r) 8 | print('#atoms = {}'.format(len(atoms))) 9 | #write('images/decahedron.png', atoms) 10 | write('decahedron-%03d.xyz'%p, atoms) 11 | 12 | """ 13 | p = 15 6 nm 2815 14 | p = 45 20 nm 75945 15 | p = 80 32 nm 426680 16 | """ 17 | -------------------------------------------------------------------------------- /tools/plot/hist.py: -------------------------------------------------------------------------------- 1 | import sys 2 | import numpy as np 3 | import matplotlib.pyplot as plt 4 | 5 | infile = "data.dat" 6 | if len(sys.argv) > 1: 7 | infile = sys.argv[1] 8 | 9 | data = np.loadtxt(infile) 10 | hist, edge = np.histogram(data, bins=51) 11 | dx = edge[1] - edge[0] 12 | x = edge[:-1] + 0.5*dx 13 | 14 | plt.bar(x, hist, width=dx*0.8) 15 | #plt.show() 16 | plt.savefig("hist.png") 17 | 18 | o = open("hist.dat", "w") 19 | for i in range(len(x)): 20 | o.write("%12.4f%12.4f\n"%(x[i], hist[i])) 21 | o.close() 22 | -------------------------------------------------------------------------------- /lib/e_2_csv.py: -------------------------------------------------------------------------------- 1 | """ 2 | Csv tools 3 | 4 | @log: 5 | 2013_10_12: initiation 6 | 7 | """ 8 | import os 9 | import argparse 10 | from utilities import parseBlock 11 | from mytype import System, Molecule, Atom 12 | from geo import Geo 13 | from output_conf import toGeo, toXyz, toReaxLammps, toPdb, toGjf 14 | 15 | def main(): 16 | parser = argparse.ArgumentParser() 17 | parser.add_argument("fname", default="csv", nargs="?", help="csv file name") 18 | args = parser.parse_args() 19 | 20 | if __name__ == "__main__": 21 | main() 22 | -------------------------------------------------------------------------------- /tools/lammps/xrd/log.cite: -------------------------------------------------------------------------------- 1 | This LAMMPS simulation made specific use of work described in the 2 | following references. See http://lammps.sandia.gov/cite.html 3 | for details. 4 | 5 | compute_xrd command: 6 | 7 | @Article{Coleman13, 8 | author = {S. P. Coleman, D. E. Spearot, L. Capolungo}, 9 | title = {Virtual diffraction analysis of Ni [010] symmetric tilt grain boundaries}, 10 | journal = {Modelling and Simulation in Materials Science and Engineering}, 11 | year = 2013, 12 | volume = 21, 13 | pages = {055020} 14 | } 15 | 16 | -------------------------------------------------------------------------------- /tools/dftb/dftb-uv.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import sys, os 4 | import shutil 5 | 6 | dpath = '/home/tcheng/soft/simpy/tools/dftb' 7 | 8 | fname = sys.argv[1] 9 | os.system('python %s %s'%(os.path.join(dpath, 'any2gen'), fname)) 10 | os.system('python %s %s'%(os.path.join(dpath, 'get_input.py'), 'opt')) 11 | os.system('dftb+') 12 | shutil.copy('geo_end.gen', 'geo_start.gen') 13 | os.system('python %s %s'%(os.path.join(dpath, 'get_input.py'), 'tddft')) 14 | os.system('dftb+') 15 | os.system('python %s'%(os.path.join(dpath, 'uv.py'))) 16 | -------------------------------------------------------------------------------- /tools/gromacs/mols/ifpsc-de/pbs: -------------------------------------------------------------------------------- 1 | #PBS -N vasp 2 | #PBS -l nodes=1:ppn=24 3 | #PBS -l walltime=12:00:00 4 | #PBS -q batch 5 | #PBS -V 6 | #PBS -j oe 7 | #PBS -S /bin/bash 8 | # 9 | ### Set intel environment### 10 | source /opt/intel/compilers_and_libraries_2018/linux/bin/compilervars.sh intel64 11 | source /opt/intel/mkl/bin/mklvars.sh intel64 12 | source /opt/intel/impi/2018.1.163/bin64/mpivars.sh 13 | source /opt/software/gromacs/gromacs2019/bin/GMXRC 14 | 15 | cd $PBS_O_WORKDIR 16 | 17 | # Run LAMMPS 18 | gmx_mpi grompp 19 | gmx_mpi mdrun 20 | -------------------------------------------------------------------------------- /tools/nanocut/pt_to/run.sh: -------------------------------------------------------------------------------- 1 | nanocut to_05_01.ini a05.xyz && cp a05.xyz ~/Dropbox/ 2 | nanocut to_07_02.ini a07.xyz && cp a07.xyz ~/Dropbox/ 3 | nanocut to_10_03.ini a10.xyz && cp a10.xyz ~/Dropbox/ 4 | nanocut to_13_04.ini a13.xyz && cp a13.xyz ~/Dropbox/ 5 | nanocut to_16_05.ini a16.xyz && cp a16.xyz ~/Dropbox/ 6 | nanocut to_19_06.ini a19.xyz && cp a19.xyz ~/Dropbox/ 7 | python get_d.py a05.xyz 8 | python get_d.py a07.xyz 9 | python get_d.py a10.xyz 10 | python get_d.py a13.xyz 11 | python get_d.py a16.xyz 12 | python get_d.py a19.xyz 13 | -------------------------------------------------------------------------------- /tools/pygen/p2c: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import sys 4 | from pymatgen.symmetry.analyzer import SpacegroupAnalyzer 5 | from pymatgen.core.surface import Slab, SlabGenerator, generate_all_slabs, Structure, Lattice, ReconstructionGenerator 6 | from pymatgen.io.vasp.inputs import Poscar 7 | 8 | if len(sys.argv) > 1: 9 | fname = sys.argv[1] 10 | struct = Structure.from_file(fname) 11 | struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure() 12 | open('conventional.vasp', 'w').write(str(Poscar(struct))) 13 | 14 | -------------------------------------------------------------------------------- /examples/03_xyz2cfg/lammps_input: -------------------------------------------------------------------------------- 1 | 2 | units real 3 | atom_style charge 4 | boundary p p p 5 | 6 | read_data lammps.data 7 | 8 | dump 1 all custom 1 dump.lammpstrj id type x y z vx vy vz 9 | dump_modify 1 sort id 10 | dump 101 all cfg 1 dump.*.cfg mass type xs ys zs vx vy vz fx fy fz 11 | dump_modify 101 element Li Cl S O P 12 | 13 | log rerun.log 14 | 15 | #--------Simulation-------- 16 | rerun movie.xyz dump x y z box no format xyz 17 | 18 | -------------------------------------------------------------------------------- /tools/cif/any2cif: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env /exec/python/pythonEPD-6.3-2-rh3-x86/bin/python 2 | 3 | """ 4 | Convert any file format (with correct ext) to .cif. 5 | @Note: need ase. 6 | any2gen infile 7 | """ 8 | 9 | import sys 10 | from ase.io import read, write 11 | 12 | if len(sys.argv) > 1: 13 | infile = sys.argv[1] 14 | atoms = read(infile) 15 | if "." in infile: 16 | outfile = infile.split(".")[0] + ".cif" 17 | else: 18 | outfile = infile + ".cif" 19 | write(outfile, atoms) 20 | else: 21 | print __doc__ 22 | 23 | -------------------------------------------------------------------------------- /test/glycine/fort.91: -------------------------------------------------------------------------------- 1 | I glycine 2 | 1 O 3 | 1 2 O 2.47460 4 | 1 2 3 C 56.30164 2.49999 5 | 1 2 3 4 H -127.48746 95.91605 1.13372 6 | 2 4 3 5 H 97.59673 104.16891 1.13372 7 | 3 4 2 6 C 32.78130 47.94107 1.27436 8 | 3 5 1 7 H 122.74760 135.70904 0.99964 9 | 2 6 3 8 N -179.92950 115.99873 1.49335 10 | 1 7 8 9 H -67.64693 70.09151 1.02403 11 | 1 9 8 10 H -46.06400 124.15343 1.02403 12 | -------------------------------------------------------------------------------- /tools/jdft/inp_jdft/cu/common: -------------------------------------------------------------------------------- 1 | ion-species GBRV/$ID_pbe_v1.2.uspp 2 | ion-species GBRV/$ID_pbe_v1.uspp 3 | elec-ex-corr gga-PBE # Why not mix in exact exchange? (gga-PBE by default) 4 | elec-cutoff 20.0 # Plane-wave cutoff in Hartrees (20 by default) 5 | electronic-minimize \ 6 | nIterations 1000 \ 7 | energyDiffThreshold 1e-5 # who needs 16 digits? 8 | 9 | elec-fermi-fillings 0 0.003675 # Fillings are a fermi function with T = 0.1 eV 10 | 11 | fluid SaLSA 12 | fluid-solvent H2O 13 | fluid-cation K+ 0.1 14 | fluid-anion F- 0.1 15 | 16 | -------------------------------------------------------------------------------- /tools/jdft/inp_jdft/pt/common: -------------------------------------------------------------------------------- 1 | ion-species GBRV/$ID_pbe_v1.2.uspp 2 | ion-species GBRV/$ID_pbe_v1.uspp 3 | elec-ex-corr gga-PBE # Why not mix in exact exchange? (gga-PBE by default) 4 | elec-cutoff 20.0 # Plane-wave cutoff in Hartrees (20 by default) 5 | electronic-minimize \ 6 | nIterations 1000 \ 7 | energyDiffThreshold 1e-5 # who needs 16 digits? 8 | 9 | elec-fermi-fillings 0 0.003675 # Fillings are a fermi function with T = 0.1 eV 10 | 11 | fluid SaLSA 12 | fluid-solvent H2O 13 | fluid-cation K+ 0.1 14 | fluid-anion F- 0.1 15 | 16 | -------------------------------------------------------------------------------- /tools/linux/pwdu: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | """ 4 | convert linux path to windows format 5 | """ 6 | 7 | import os 8 | 9 | cmd = os.getcwd() 10 | wcmd = cmd 11 | if "PMD" in cmd: 12 | wcmd = wcmd.replace("/net/hulk/PMD/tcheng/", "/home/tao/Disk/pmd/") 13 | elif "temp1" in cmd: 14 | wcmd = wcmd.replace("/temp1/jobs/", "/home/tao/Disk/giant12/") 15 | elif "/net/hulk/home6/chengtao/" in cmd: 16 | wcmd = wcmd.replace("/net/hulk/home6/chengtao/", "/home/tao/Disk/atom/") 17 | 18 | #wcmd = wcmd.replace("/", "\\") 19 | print(wcmd) 20 | 21 | -------------------------------------------------------------------------------- /arc/linux_tools/subfolder: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os 4 | o = open('all.sh', 'w') 5 | o.write("""#!/bin/bash 6 | #PBS -l nodes=1:ppn=8 7 | cd $PBS_O_WORKDIR 8 | """) 9 | 10 | folderList = [] 11 | 12 | for i in os.listdir('.'): 13 | if os.path.isdir(i): 14 | folderList.append(i) 15 | 16 | folderList.sort() 17 | 18 | for i in folderList: 19 | o.write('cd %s\n'%i) 20 | o.write('grompp -f equil -c em -p *.top -o equil -maxwarn 2\n') 21 | o.write('mdrun -s equil -c equil\n') 22 | o.write('cd ..\n') 23 | 24 | o.close() 25 | -------------------------------------------------------------------------------- /tools/caltech/dat/WAT/F3C.bgf: -------------------------------------------------------------------------------- 1 | BIOGRF 200 2 | DESCRP F3C 3 | REMARK BGF file created by Cerius2 4 | FORCEFIELD DREIDING 5 | FORMAT ATOM (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5,f10.5) 6 | ATOM 1 O1 WAT 1 1 0.38770 0.02814 0.02554 O_3F 0 2 -0.82000 7 | ATOM 2 H2 WAT 1 1 -0.12379 -0.45986 -0.97101 H_F 0 0 0.41000 8 | ATOM 3 H3 WAT 1 1 -0.27316 0.42100 0.95199 H_F 0 0 0.41000 9 | FORMAT CONECT (a6,12i6) 10 | CONECT 1 11 | CONECT 2 12 | CONECT 3 13 | END 14 | -------------------------------------------------------------------------------- /tools/fftool-git/fftool-master/examples/dmf.zmat: -------------------------------------------------------------------------------- 1 | DMF 2 | 3 | 1 CTN 4 | 2 NCO 1 1.448 5 | 3 CTN 2 1.448 1 120.2 6 | 4 CO 2 1.380 1 120.5 3 180.0 7 | 5 OC 4 1.223 2 125.6 1 180.0 8 | 6 H 1 1.090 2 111.4 3 0.0 9 | 7 H 1 1.090 2 108.7 3 240.0 10 | 8 H 1 1.090 2 108.7 3 120.0 11 | 9 H 3 1.090 2 111.2 1 0.0 12 | 10 H 3 1.090 2 108.9 1 240.0 13 | 11 H 3 1.090 2 108.9 1 120.0 14 | 12 HCO 4 1.100 2 112.6 1 0.0 15 | 16 | oplsaa.ff 17 | 18 | -------------------------------------------------------------------------------- /arc/linux_tools/node.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | import os 3 | 4 | os.system("pbsnodes > all_nodes.log") 5 | 6 | f = open("all_nodes.log" , 'r') 7 | 8 | cpu_remain = 1 9 | for i in f: 10 | if i[:7] == "compute": 11 | print i[:-1] 12 | if i[13:-1] == "job-exclusive": 13 | print "no cpu" 14 | if i[5:9] == "jobs": 15 | if len(i.split(",")): 16 | no_re = 8 - len(i.split(",")) 17 | else: 18 | no_re = 8 19 | print no_re 20 | 21 | f.close() 22 | 23 | os.system("rm all_nodes.log") 24 | -------------------------------------------------------------------------------- /tools/caltech/dat/WAT/F3C_OPT.bgf: -------------------------------------------------------------------------------- 1 | BIOGRF 200 2 | DESCRP F3C 3 | REMARK BGF file created by Cerius2 4 | FORCEFIELD DREIDING 5 | FORMAT ATOM (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5,f10.5) 6 | ATOM 1 O1 WAT 1 1 0.38770 0.02814 0.02554 O_3F 0 2 -0.81026 7 | ATOM 2 H2 WAT 1 1 -0.12379 -0.45986 -0.97101 H_F 0 0 0.40513 8 | ATOM 3 H3 WAT 1 1 -0.27316 0.42100 0.95199 H_F 0 0 0.40513 9 | FORMAT CONECT (a6,12i6) 10 | CONECT 1 11 | CONECT 2 12 | CONECT 3 13 | END 14 | -------------------------------------------------------------------------------- /tools/linux/ave.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import sys 4 | import numpy as np 5 | import matplotlib.pyplot as plt 6 | 7 | def main(): 8 | if len(sys.argv) > 2: 9 | fname = sys.argv[1] 10 | nr = sys.argv[2] 11 | 12 | data = np.loadtxt(fname) 13 | data = data.transpose() 14 | 15 | f = 0.1 16 | nstart = int(f*len(data)) 17 | 18 | plt.plot(data[0], data[1]) 19 | ave = np.average(data[1][nstart:]) 20 | print ave 21 | plt.show() 22 | 23 | 24 | if __name__ == "__main__": 25 | main() 26 | -------------------------------------------------------------------------------- /tools/caltech/dat/WAT/dreiding3Wat.bgf: -------------------------------------------------------------------------------- 1 | BIOGRF 200 2 | DESCRP F3C 3 | REMARK BGF file created by Cerius2 4 | FORCEFIELD DREIDING 5 | FORMAT ATOM (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5,f10.5) 6 | ATOM 1 O1 WAT 1 1 0.38770 0.02814 0.02554 O_3W 0 2 -0.61000 7 | ATOM 2 H2 WAT 1 1 -0.12379 -0.45986 -0.97101 H___A 0 0 0.30500 8 | ATOM 3 H3 WAT 1 1 -0.27316 0.42100 0.95199 H___A 0 0 0.30500 9 | FORMAT CONECT (a6,12i6) 10 | CONECT 1 11 | CONECT 2 12 | CONECT 3 13 | END 14 | -------------------------------------------------------------------------------- /lib/e_2_multi_geo.py: -------------------------------------------------------------------------------- 1 | """ parse the geo file with multi configuration into 2 | seperated files 3 | """ 4 | import os 5 | from utilities import parseBlock 6 | from mytype import System, Molecule, Atom 7 | from geo import Geo 8 | from output_conf import toGeo 9 | from output_conf import toXyz 10 | 11 | os.chdir("/home/tao/Documents/debug/geofile") 12 | parseBlock("geo", 1) 13 | for i in range(204): 14 | fname = "out%03d"%i 15 | a = Geo(fname) 16 | b = a.parser() 17 | b.assignAtomTypes() 18 | toGeo(b, b.name+'.geo') 19 | toXyz(b, b.name+'.xyz') 20 | 21 | -------------------------------------------------------------------------------- /tools/vasp/select_frame.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python2 2 | 3 | import sys 4 | import os 5 | import shutil 6 | import numpy as np 7 | 8 | if len(sys.argv) < 3: 9 | print("Need three parameters!") 10 | print("t0 t1 nt!") 11 | else: 12 | t0 = int(sys.argv[1]) 13 | t1 = int(sys.argv[2]) 14 | nt = int(sys.argv[3]) 15 | if not os.path.exists("wf"): 16 | os.mkdir("wf") 17 | 18 | data = np.linspace(t0, t1, nt) 19 | print(t0, t1, data) 20 | for i in data: 21 | fname = "POSCAR_%06d"%int(i) 22 | shutil.copy(fname, "wf") 23 | 24 | -------------------------------------------------------------------------------- /arc/linux_tools/rm_m: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | import os 3 | 4 | def parsefolder(folder, filetype): 5 | for i in os.listdir(folder): 6 | fullname = os.path.join(folder, i) 7 | if os.path.isdir(fullname): 8 | parsefolder(fullname, filetype) 9 | else: 10 | if filetype in fullname: 11 | os.remove(fullname) 12 | 13 | if __name__ == "__main__": 14 | parsefolder('.',".edr") 15 | parsefolder('.',".tpr") 16 | parsefolder('.',".trr") 17 | parsefolder('.',".sh.") 18 | parsefolder('.',"test.pdb") 19 | -------------------------------------------------------------------------------- /tools/lammps/neb/get_coords.py: -------------------------------------------------------------------------------- 1 | coords = { 2 | 2059:[], 3 | 2245:[], 4 | 3699:[], 5 | 3997:[], 6 | 3998:[], 7 | } 8 | 9 | f = open("dump.lammpstrj", "r") 10 | 11 | for i in f: 12 | tokens = i.strip().split() 13 | if len(tokens) == 8: 14 | id = int(tokens[0]) 15 | x = float(tokens[2]) 16 | y = float(tokens[3]) 17 | z = float(tokens[4]) 18 | if id in coords.keys(): 19 | coords[id] = [x, y, z] 20 | f.close() 21 | 22 | for i in coords.keys().sort(): 23 | print i, coords[i][0], coords[i][1], coords[i][2] 24 | 25 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/pre/parser/eth.gro: -------------------------------------------------------------------------------- 1 | MolecularModel coordinate for GROMACS generated by WEBDFF 2 | 9 3 | 1UNK C 1 0.412 0.509 0.449 4 | 1UNK C 2 0.528 0.485 0.537 5 | 1UNK O 3 0.630 0.570 0.499 6 | 1UNK H 4 0.375 0.616 0.467 7 | 1UNK H 5 0.432 0.492 0.349 8 | 1UNK H 6 0.360 0.409 0.469 9 | 1UNK H 7 0.567 0.383 0.520 10 | 1UNK H 8 0.496 0.500 0.642 11 | 1UNK H 9 0.701 0.540 0.566 12 | 1.00000 1.00000 1.00000 13 | -------------------------------------------------------------------------------- /tools/vasp/vasp2.zwicky: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os 4 | import shutil 5 | 6 | folder = 'inp' 7 | if not os.path.exists(folder): 8 | os.mkdir(folder) 9 | 10 | flist = ["POSCAR", "POTCAR", "KPOINTS", "INCAR", 11 | "runVASP_12.in"] 12 | 13 | for i in flist: 14 | inputfile = i 15 | outputfile = os.path.join(folder, inputfile) 16 | shutil.copy(inputfile, outputfile) 17 | 18 | if os.path.exists("CONTCAR"): 19 | inputfile = "CONTCAR" 20 | outputfile = os.path.join(folder, "POSCAR") 21 | shutil.copy(inputfile, outputfile) 22 | 23 | 24 | -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | # Auto detect text files and perform LF normalization 2 | * text=auto 3 | 4 | # Custom for Visual Studio 5 | *.cs diff=csharp 6 | *.sln merge=union 7 | *.csproj merge=union 8 | *.vbproj merge=union 9 | *.fsproj merge=union 10 | *.dbproj merge=union 11 | 12 | # Standard to msysgit 13 | *.doc diff=astextplain 14 | *.DOC diff=astextplain 15 | *.docx diff=astextplain 16 | *.DOCX diff=astextplain 17 | *.dot diff=astextplain 18 | *.DOT diff=astextplain 19 | *.pdf diff=astextplain 20 | *.PDF diff=astextplain 21 | *.rtf diff=astextplain 22 | *.RTF diff=astextplain 23 | -------------------------------------------------------------------------------- /tools/deepmd/reaxff-ml/pbs.gpu: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | #SBATCH -A wag 4 | #SBATCH --time=2:00:00 # walltime 5 | #SBATCH --ntasks=1 # number of processor cores (i.e. tasks) 6 | #SBATCH --nodes=1 # number of nodes 7 | #SBATCH --mem-per-cpu=8G # memory per CPU core 8 | #SBATCH --gres=gpu:1 9 | 10 | # LOAD MODULES, INSERT CODE, AND RUN YOUR PROGRAMS HERE 11 | module load intel/18.1 mkl/18.1 cuda/9.1 12 | export LD_LIBRARY_PATH=/central/software/CUDA/9.1/lib64:$LD_LIBRARY_PATH 13 | 14 | cd $SLURM_SUBMIT_DIR 15 | /central/home/tcheng/soft/vasp.5.4.4/vasp.5.4.4/bin/vasp_gpu > log 16 | 17 | -------------------------------------------------------------------------------- /tools/rdkit/mol2xyz.py: -------------------------------------------------------------------------------- 1 | import sys 2 | 3 | f = open('%s.mol'%sys.argv[1], 'r') 4 | lines = f.readlines() 5 | f.close() 6 | 7 | tokens = lines[3].strip().split() 8 | n_atoms = int(tokens[0]) 9 | 10 | coords = [] 11 | for i in range(len(lines)): 12 | tokens = lines[i].strip().split() 13 | if len(tokens) == 16: 14 | line = '%s %s %s %s\n'%(tokens[3], tokens[0], tokens[1], tokens[2]) 15 | coords.append(line) 16 | 17 | o = open('%s.xyz'%sys.argv[1], 'w') 18 | o.write('%d\n\n'%len(coords)) 19 | for i in coords: 20 | o.write(i) 21 | o.close() 22 | 23 | 24 | 25 | -------------------------------------------------------------------------------- /arc/linux_tools/dos2unix_all: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os 4 | import os.path 5 | 6 | root_folder = os.getcwd() 7 | 8 | def dos2unix(folder): 9 | listall = os.listdir(folder) 10 | for i in listall: 11 | current_dir = os.path.join(folder, i) 12 | if os.path.isdir(current_dir): 13 | dos2unix(current_dir) 14 | else: 15 | if os.path.getsize(current_dir): 16 | os.system("dos2unix %s"%current_dir) 17 | else : 18 | pass 19 | 20 | if __name__ == "__main__": 21 | dos2unix(root_folder) 22 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/pre/parser/hist.py: -------------------------------------------------------------------------------- 1 | f = open('po.log' , 'r') 2 | 3 | min = 500 4 | max = 0 5 | ener_list = [] 6 | sum = 0 7 | 8 | for i in f: 9 | ener = float(i.strip()) 10 | if min > ener: 11 | min = ener 12 | if max < ener: 13 | max = ener 14 | ener_list.append(ener) 15 | 16 | step = (max-min)/50.0 17 | 18 | hist = [0]*101 19 | 20 | for i in ener_list: 21 | sum += i 22 | hist[int((i-min)/step)] +=1 23 | 24 | for i in hist: 25 | print i 26 | 27 | print '------------average--------------' 28 | print sum / len(ener_list) 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/CONTCAR: -------------------------------------------------------------------------------- 1 | OUTCAR.0006.+1.out 1.0e-02 2 | 1.00000000000000 3 | 2.4819487690084672 0.0000000000000000 0.0000000000000000 4 | -1.2409743845546799 2.1494306848475140 0.0000000000000000 5 | 0.0000000000000010 0.0000000000000010 12.0000000000000000 6 | C 7 | 2 8 | Direct 9 | 0.0032833820485862 0.0017657267232494 0.1416700386583329 10 | 0.3300402381476815 0.6648993472899036 0.1416702350416656 11 | 12 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 13 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 14 | -------------------------------------------------------------------------------- /tools/caltech/dat/WAT/tip3.bgf: -------------------------------------------------------------------------------- 1 | BIOGRF 200 2 | DESCRP tip3 3 | REMARK BGF file created by Cerius2 4 | REMARK BGF file created by Cerius2 5 | FORCEFIELD DREIDING 6 | FORMAT ATOM (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5,f10.5) 7 | HETATM 1 O1 WAT A 444 -0.23900 -0.30900 0.00000 OW 0 2 -0.83400 8 | HETATM 2 H2 WAT A 444 0.71800 -0.30900 0.00000 HW 0 0 0.41700 9 | HETATM 3 H3 WAT A 444 -0.47900 0.61800 0.00000 HW 0 0 0.41700 10 | FORMAT CONECT (a6,12i6) 11 | CONECT 1 12 | CONECT 2 13 | CONECT 3 14 | END 15 | -------------------------------------------------------------------------------- /arc/linux_tools/gulp/change.py: -------------------------------------------------------------------------------- 1 | import os 2 | import os.path 3 | import shutil 4 | 5 | for i in os.listdir("./"): 6 | if os.path.isdir(i): 7 | shutil.copyfile("%s/tatb.gin"%i, "%s/tatb_back.gin"%i) 8 | f = open("%s/tatb_back.gin"%i, 'r') 9 | o = open("%s/tatb.gin"%i, 'w') 10 | 11 | for j in f: 12 | if j.startswith("C1 O4 0.2020 3.5600"): 13 | o.write("C1 O4 0.260903 2.90043 0.0 8.0 0.0 0.0\n") 14 | else: 15 | o.write(j) 16 | o.close() 17 | f.close() 18 | -------------------------------------------------------------------------------- /examples/05_vasp_raman/results/phonon/CONTCAR: -------------------------------------------------------------------------------- 1 | graphite 2 | 1.00000000000000 3 | 2.4819487690084672 0.0000000000000000 0.0000000000000000 4 | -1.2409743845546799 2.1494306848475140 0.0000000000000000 5 | 0.0000000000000010 0.0000000000000010 12.0000000000000000 6 | C 7 | 2 8 | Direct 9 | 0.0000000000000000 0.0000000000000000 0.1416700039999981 10 | 0.3333300050000005 0.6666700239999983 0.1408366706666647 11 | 12 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 13 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 14 | -------------------------------------------------------------------------------- /tools/caltech/dat/WAT/tip3_charmm.bgf: -------------------------------------------------------------------------------- 1 | BIOGRF 200 2 | DESCRP tip3 3 | REMARK BGF file created by Cerius2 4 | REMARK BGF file created by Cerius2 5 | FORCEFIELD DREIDING 6 | FORMAT ATOM (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5,f10.5) 7 | HETATM 1 O1 WAT A 444 -0.23900 -0.30900 0.00000 OT 0 2 -0.83400 8 | HETATM 2 H2 WAT A 444 0.71800 -0.30900 0.00000 HT 0 0 0.41700 9 | HETATM 3 H3 WAT A 444 -0.47900 0.61800 0.00000 HT 0 0 0.41700 10 | FORMAT CONECT (a6,12i6) 11 | CONECT 1 12 | CONECT 2 13 | CONECT 3 14 | END 15 | -------------------------------------------------------------------------------- /tools/deepmd/merge-lammps.py: -------------------------------------------------------------------------------- 1 | import shutil, os 2 | 3 | folders = [] 4 | f = open("flist", "r") 5 | for i in f: 6 | folders.append(i.strip()) 7 | f.close() 8 | 9 | raw_files = ["energy.raw", "force.raw", "virial.raw"] 10 | for i in raw_files: 11 | lines = [] 12 | print(folders) 13 | for j in folders: 14 | print(j) 15 | f = open("./%s/lammps_raw/%s"%(j, i), "r") 16 | for k in f: 17 | lines.append(k) 18 | f.close() 19 | o = open(i, "w") 20 | for k in lines: 21 | print(k) 22 | o.write(k) 23 | o.close() 24 | 25 | 26 | -------------------------------------------------------------------------------- /tools/nanocut/nw/to_13_4.ini: -------------------------------------------------------------------------------- 1 | [geometry] 2 | lattice_vectors: 3 | 3.94400000 0.00000000 0.00000000 4 | 0.00000000 3.94400000 0.00000000 5 | 0.00000000 0.00000000 3.94400000 6 | 7 | basis: 8 | Pt 0.000000000 0.000000000 0.000000000 9 | Pt 0.000000000 0.500000000 0.500000000 10 | Pt 0.500000000 0.000000000 0.500000000 11 | Pt 0.500000000 0.500000000 0.000000000 12 | 13 | basis_coordsys: lattice 14 | 15 | [periodicity] 16 | period_type: 1D 17 | axis: 4 4 0 18 | 19 | [periodic_1D_cylinder:1] 20 | radius: 10 21 | -------------------------------------------------------------------------------- /tools/vasp/fix-atoms.py: -------------------------------------------------------------------------------- 1 | import shutil, sys 2 | 3 | n0 = 9 4 | fix_atoms = [] 5 | 6 | g1 = range(29) 7 | for i in g1: 8 | fix_atoms.append(i) 9 | 10 | """ 11 | g2 = [2, 10, 11, 19] 12 | for i in g2: 13 | fix_atoms.append(i) 14 | """ 15 | 16 | f = open("POSCAR", "r") 17 | poscar = f.readlines() 18 | f.close() 19 | 20 | # the first line poscar[9] 21 | shutil.copy("POSCAR", "POSCAR.0") 22 | 23 | for i in fix_atoms: 24 | nid = n0 + i 25 | poscar[nid] = poscar[nid].replace("T", "F") 26 | 27 | o = open("POSCAR_new", "w") 28 | for i in poscar: 29 | o.write(i) 30 | o.close() 31 | 32 | -------------------------------------------------------------------------------- /arc/linux_tools/parse_xvg.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | def parse_xvg(fname): 4 | x = [] 5 | y = [] 6 | f = open(fname, 'r') 7 | 8 | for i in f: 9 | if len(i.strip()) == 0: 10 | pass 11 | elif i.strip().startswith('@'): 12 | pass 13 | elif i.strip().startswith('#'): 14 | pass 15 | else: 16 | tokens = i.split() 17 | x.append(float(tokens[0])) 18 | y.append(float(tokens[-1])) 19 | 20 | f.close() 21 | return x, y 22 | 23 | if __name__ == "__main__": 24 | print "test" 25 | -------------------------------------------------------------------------------- /test/glycine/molfra.out: -------------------------------------------------------------------------------- 1 | Bond order cutoff:0.3000 2 | Iteration Freq. Molecular formula Molecular mass 3 | 0 1 x C2H5O2N 75.0380 4 | Total number of molecules: 1 5 | Total number of atoms: 10 6 | Total system mass: 75.037999999999997 7 | Bond order cutoff:0.3000 8 | Iteration Freq. Molecular formula Molecular mass 9 | 0 1 x C2H5O2N 75.0380 10 | Total number of molecules: 1 11 | Total number of atoms: 10 12 | Total system mass: 75.037999999999997 13 | -------------------------------------------------------------------------------- /tools/kmc/rxn: -------------------------------------------------------------------------------- 1 | HNO2 + * + * <--> NO* + OH* , 2 | H2 + * + * <--> H* + H* , 3 | OH* + H* <--> H2O* + * , 4 | NO* + * <--> N* + O* , 5 | O* + H* <--> OH* + * , 6 | N* + H* <--> NH* + * , 7 | NH* + H* <--> NH2* + * , 8 | NH2* + H* <--> NH3* + * , 9 | NH3* <--> NH3 + * , 10 | H2O* <--> H2O + * , 11 | HNO2 + * + * <--> NO2* + H* , 12 | NO2* + * <--> NO* + O* , 13 | NO* + H* <--> NOH* , 14 | NO* + H* <--> HNO* , 15 | NOH* + H* <--> HNOH* , 16 | NOH* + * <--> N* + OH* , 17 | HNO* + H* <--> HNOH* , 18 | HNO* + * <--> NH* + O* , 19 | HNOH* + * <--> NH* + OH* , 20 | 2NH2* <--> N2H4* + * , 21 | N2H4* <--> N2H4 + * , 22 | -------------------------------------------------------------------------------- /tools/lammps/xrd/log.lammps: -------------------------------------------------------------------------------- 1 | LAMMPS (16 Mar 2018) 2 | atom_style charge 3 | boundary p p p 4 | 5 | units metal 6 | timestep 0.001 7 | 8 | read_data lammps.data 9 | orthogonal box = (0 0 0) to (3.6151 3.6151 3.6151) 10 | 1 by 1 by 1 MPI processor grid 11 | reading atoms ... 12 | 4 atoms 13 | pair_style none 14 | atom_modify sort 0 0 15 | 16 | # synchrotron 17 | compute XRD all xrd 1.0 Cu 2Theta 20 110 c 1 1 1 LP 1 echo 18 | ERROR: Unknown compute style xrd (../modify.cpp:1195) 19 | Last command: compute XRD all xrd 1.0 Cu 2Theta 20 110 c 1 1 1 LP 1 echo 20 | -------------------------------------------------------------------------------- /tools/deepmd/get-sp.sh: -------------------------------------------------------------------------------- 1 | # generate vasp raw 2 | cmdall "cp CONTCAR POSCAR" 3 | cmdall "python ~/soft/simpy/tools/deepmd/vasp2raw.py" 4 | 5 | # generate lammps raw 6 | cmdall "python ~/soft/simpy/lib/e_2_contcar.py POSCAR" 7 | copyall ffield control.reaxc lammps_input 8 | cmdall '/central/home/tcheng/soft/lammps/lammps-16Mar18/src/lmp_intel_cpu_intelmpi -in lammps_input' 9 | cmdall "python ~/soft/simpy/tools/deepmd/reaxff-ml/lammps2raw.py" 10 | 11 | # generate lv raw 12 | cmdall "python ~/soft/simpy/tools/deepmd/reaxff-ml/lvdiff_real.py " 13 | 14 | # gether data 15 | python ~/soft/simpy/tools/deepmd/merge-sp.py 16 | -------------------------------------------------------------------------------- /tools/project/ldh/sintering_model.py: -------------------------------------------------------------------------------- 1 | """ A simple model to test the idea of surface reducation 2 | when two (or more) sphere merge into one large sphere 3 | """ 4 | 5 | import math 6 | def cal(n = 12): 7 | r1 = 4.0 8 | r2 = math.pow(0.2, 1/3.0) * r1 9 | r3 = math.pow(n, 1/3.0) * r1 10 | r4 = r3 - (r1 - r2) 11 | ratio1 = 1 - math.pow(r4/r3, 3.0) 12 | 13 | v = n * 4.0/3 * math.pi * r1**3 14 | a1 = math.pow(v, 1/3.0) 15 | a2 = a1 - (r1 - r2) 16 | ratio2 = 1 - math.pow(a2/a1, 3.0) 17 | print "%4d, %8.2f, %8.2f"%(n, ratio1, ratio2) 18 | 19 | for i in range(1, 100): 20 | cal(i) -------------------------------------------------------------------------------- /arc/linux_tools/old/generateCoordXvg.py: -------------------------------------------------------------------------------- 1 | def generateCoordXvg(n, N, ndxfile): 2 | import os 3 | import os.path 4 | for i in range(N/n): 5 | if os.path.exists("m%d"%i): 6 | pass 7 | else: 8 | os.system("mkdir m%d"%i) 9 | os.system("echo %d | g_traj_mpi -s equil.tpr -f traj.trr -n %s -ox"%((i + 2), ndxfile)) 10 | os.system("mv coord.xvg m%d"%i) 11 | os.system("cp equil.mdp template.gro *.top *.itp m%d"%i) 12 | 13 | if __name__ == "__main__": 14 | n = 502 15 | N = 2510 16 | ndxfile = "out.ndx" 17 | generateCoordXvg(n, N, ndxfile) 18 | -------------------------------------------------------------------------------- /tools/hun/frag.sh: -------------------------------------------------------------------------------- 1 | # get xyz from XDATCAR 2 | perl ~/soft/simpy/tools/vasp/xdat2xyz.pl 3 | # get Lammps data from POSCAR 4 | python ~/soft/simpy/lib/e_2_contcar.py 5 | # copy data 6 | cp lammps.data lammps 7 | cp movie.xyz lammps 8 | # cd folder 9 | cd lammps 10 | # run lammps 11 | lammps -in lammps_input 12 | # lmp to config.out 13 | dump2config.py rerun.lmp ./anal/config.out 14 | # lmp to reaxbonds.out 15 | trj2reaxbonds.py lammps.trj ./anal/reaxbonds.out 16 | # cd folder 17 | cd anal 18 | # if have H 19 | python ~/soft/simpy/tools/hun/refine_bonds.py 20 | # analysis the species 21 | ./molfrag.sh control.file 22 | 23 | 24 | -------------------------------------------------------------------------------- /tools/reax/addcharge.py: -------------------------------------------------------------------------------- 1 | """ 2 | convert qm charge to reaxFF charge training set 3 | """ 4 | 5 | import os 6 | 7 | def main(): 8 | if os.path.exists("qm_charge.dat"): 9 | o = open("add.charge", "w") 10 | f = open("qm_charge.dat", "r") 11 | for i in f: 12 | tokens = i.strip().split() 13 | if len(tokens) > 4: 14 | mol = tokens[0] 15 | n = int(tokens[2]) 16 | q = float(tokens[3]) 17 | o.write("%-20s%-8.4f%5d%12.4f\n"%(mol, 0.1, n, q)) 18 | o.close() 19 | 20 | if __name__ == "__main__": 21 | main() 22 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/pre/parser/dipole.py: -------------------------------------------------------------------------------- 1 | import math 2 | 3 | from parse_gro import parse_gro 4 | from parse_top import parse_top 5 | 6 | DEBYE = 160.2177/3.3564 7 | 8 | coords, box = parse_gro('run.gro') 9 | top = parse_top('out.top') 10 | 11 | dip_x = 0 12 | dip_y = 0 13 | dip_z = 0 14 | 15 | if len(top) == len(coords): 16 | for i in range(len(top)): 17 | dip_x += coords[i][-3] * float(top[i].split()[-2]) 18 | dip_y += coords[i][-2] * float(top[i].split()[-2]) 19 | dip_z += coords[i][-1] * float(top[i].split()[-2]) 20 | 21 | print math.sqrt(dip_x*dip_x + dip_y*dip_y + dip_z*dip_z)*DEBYE 22 | -------------------------------------------------------------------------------- /doc/config.conf: -------------------------------------------------------------------------------- 1 | [epydoc] # Epydoc section marker (required by ConfigParser) 2 | 3 | # Information about the project. 4 | #name: Tao Cheng 5 | #url: http://cool.project/ 6 | 7 | # The list of modules to document. Modules can be named using 8 | # dotted names, module filenames, or package directory names. 9 | # This option may be repeated. 10 | modules: ../lib/mytype.py 11 | 12 | # Write html output to the directory "apidocs" 13 | output: html 14 | target: ./html 15 | 16 | # Include all automatically generated graphs. These graphs are 17 | # generated using Graphviz dot. 18 | graph: all 19 | dotpath: /usr/local/bin/dot 20 | -------------------------------------------------------------------------------- /lib/config.conf: -------------------------------------------------------------------------------- 1 | [epydoc] # Epydoc section marker (required by ConfigParser) 2 | 3 | # Information about the project. 4 | #name: Tao Cheng 5 | #url: http://cool.project/ 6 | 7 | # The list of modules to document. Modules can be named using 8 | # dotted names, module filenames, or package directory names. 9 | # This option may be repeated. 10 | modules: ./lib 11 | 12 | # Write html output to the directory "apidocs" 13 | output: html 14 | target: ./html_test 15 | 16 | # Include all automatically generated graphs. These graphs are 17 | # generated using Graphviz dot. 18 | graph: all 19 | dotpath: /usr/local/bin/dot 20 | 21 | -------------------------------------------------------------------------------- /lib/e_2_trainset.py: -------------------------------------------------------------------------------- 1 | 2 | import os 3 | import argparse 4 | #from utilities import parseBlock 5 | from mytype import System, Molecule, Atom 6 | from trainset import Trainset 7 | #from output_conf import toGeo, toXyz, toReaxLammps, toPdb, toGjf 8 | 9 | def large_than_10(): 10 | a = Trainset() 11 | for i in range(len(a.energy_lines)): 12 | md = a.energy[0][i] 13 | qm = a.energy[1][i] 14 | if abs(md - qm) > 10.0: 15 | print a.energy_lines[i].strip() 16 | else: 17 | print abs(md - qm) 18 | 19 | if __name__ == "__main__": 20 | large_than_10() 21 | 22 | 23 | 24 | -------------------------------------------------------------------------------- /tools/maestro/mae.py: -------------------------------------------------------------------------------- 1 | def get_charge(fname): 2 | o = open('q.dat', 'w') 3 | f = open(fname, 'r') 4 | for i in f: 5 | if i.strip().startswith('m_atom'): 6 | break 7 | for i in f: 8 | if i.strip().startswith(':::'): 9 | break 10 | for i in f: 11 | if i.strip().startswith(':::'): 12 | break 13 | else: 14 | tokens = i.strip().split() 15 | q = tokens[7] 16 | o.write(q+'\n') 17 | f.close() 18 | o.close() 19 | 20 | if __name__ == '__main__': 21 | fname = 'mmod_mini_7.mae' 22 | get_charge(fname) 23 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/pre/ifpsc/.svn/all-wcprops: -------------------------------------------------------------------------------- 1 | K 25 2 | svn:wc:ra_dav:version-url 3 | V 64 4 | /svn/ms-tools-python~source-code-repository/!svn/ver/3/pre/ifpsc 5 | END 6 | fe.py 7 | K 25 8 | svn:wc:ra_dav:version-url 9 | V 70 10 | /svn/ms-tools-python~source-code-repository/!svn/ver/3/pre/ifpsc/fe.py 11 | END 12 | fe_trpaz.py 13 | K 25 14 | svn:wc:ra_dav:version-url 15 | V 76 16 | /svn/ms-tools-python~source-code-repository/!svn/ver/3/pre/ifpsc/fe_trpaz.py 17 | END 18 | freeEnergy.log 19 | K 25 20 | svn:wc:ra_dav:version-url 21 | V 79 22 | /svn/ms-tools-python~source-code-repository/!svn/ver/3/pre/ifpsc/freeEnergy.log 23 | END 24 | -------------------------------------------------------------------------------- /tools/lammps/xrd/plot-xrd.py: -------------------------------------------------------------------------------- 1 | import os 2 | import matplotlib 3 | matplotlib.use('Agg') 4 | import matplotlib.pyplot as plt 5 | import numpy as np 6 | 7 | fname = 'xrd.dat' 8 | 9 | data = np.loadtxt(fname, skiprows=4) 10 | data = data.transpose() 11 | 12 | fig = plt.figure(figsize=(4, 3), dpi=300) 13 | ax = fig.add_subplot(111) 14 | 15 | ax.plot(data[1], data[2], color='black', lw=0.5) 16 | #ax.scatter(data[1], data[2], 8, color='black') 17 | 18 | ax.set_xlim([5.0, 50.0]) 19 | ax.set_xlabel(r'2$\theta$ (deg)', fontsize=14) 20 | ax.set_ylabel('Intensity', fontsize=14) 21 | 22 | plt.tight_layout() 23 | plt.savefig('xrd.svg') 24 | -------------------------------------------------------------------------------- /tools/sas/example/cn.log: -------------------------------------------------------------------------------- 1 | r_ref_0 = 2.7880 2 | r_ref_1 = 3.9440 3 | r_ref_2 = 4.8300 4 | 201 of atoms in the system 5 | cut_off_func = 1 6 | Using simple cut-off function. 7 | cut range = 1.8000 8 | Cut-off (3.9440) is larger than r_ref_1 (3.9440). 9 | Using r_ref_1 (3.9440) as cut-off. 10 | The max coordination number is 12 11 | 0 atoms with coordination of 4 12 | Hist: 13 | 1 0 14 | 2 0 15 | 3 0 16 | 4 0 17 | 5 0 18 | 6 24 19 | 7 36 20 | 8 6 21 | 9 56 22 | 10 0 23 | 11 0 24 | 12 79 25 | -------------------------------------------------------------------------------- /tools/vasp/dimer/readme: -------------------------------------------------------------------------------- 1 | 1. Frequency calculation to determine the imaginary frequency. 2 | VASP frequency calculation 3 | ENCUT = 200 4 | EDIFF = 1E-06 5 | IBRION = 5 6 | NFREE = 1 7 | 2. Check the vibration mode of the i-frequency. 8 | imagefreq.py 9 | freqmov.pl POSCAR freq23 freq24 30 0.6 10 | 3. Prepare Modecar file 11 | modemake.py freq24 12 | 4. Do the dimer calculation 13 | IBRION = 3 14 | POTIM = 0 15 | ICHAIN = 2 16 | DdR = 0.005 17 | DRotMax = 10 18 | DFNMin = 0.01 19 | DFNMax = 1.0 20 | 5. Check the DIMCAR file 21 | 22 | ref: https://zhuanlan.zhihu.com/p/31732134 23 | -------------------------------------------------------------------------------- /tools/sas/example-nlist/cn.log: -------------------------------------------------------------------------------- 1 | r_ref_0 = 2.7880 2 | r_ref_1 = 3.9440 3 | r_ref_2 = 4.8300 4 | 201 of atoms in the system 5 | cut_off_func = 1 6 | Using simple cut-off function. 7 | cut range = 1.8000 8 | Cut-off (3.9440) is larger than r_ref_1 (3.9440). 9 | Using r_ref_1 (3.9440) as cut-off. 10 | The max coordination number is 12 11 | 0 atoms with coordination of 4 12 | Hist: 13 | 1 0 14 | 2 0 15 | 3 0 16 | 4 0 17 | 5 0 18 | 6 24 19 | 7 36 20 | 8 6 21 | 9 56 22 | 10 0 23 | 11 0 24 | 12 79 25 | -------------------------------------------------------------------------------- /arc/linux_tools/qsgrompp: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import time 4 | import os 5 | core = 8 6 | o = open('subjob.sh', 'w') 7 | o.write("#!/bin/bash\n") 8 | o.write("#PBS -l nodes=1:ppn=%d\n"%core) 9 | o.write("cd $PBS_O_WORKDIR\n") 10 | current = os.getcwd() 11 | node_folder = os.path.join("/state/partition1", "gromacs_chengtao_%d"%int(time.time())) 12 | o.write("mkdir %s\n"%node_folder) 13 | o.write("cp * %s\n"%node_folder) 14 | o.write("cd %s\n"%node_folder) 15 | o.write("mpirun -np %d mdrun -s run -c run\n"%core) 16 | o.write("cp * %s\n"%current) 17 | o.write("cd %s\n"%current) 18 | o.write("rm -rf %s\n"%node_folder) 19 | o.close() 20 | 21 | 22 | -------------------------------------------------------------------------------- /tools/linux/html2docx: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python2 2 | """ 3 | Usage: html2docx[link] 4 | Log: 5 | 2017-12-01: output the log info 6 | """ 7 | 8 | import os 9 | import sys 10 | import time 11 | DEBUG = 0 12 | 13 | if len(sys.argv) > 1: 14 | link = sys.argv[1] 15 | fname = "k%d"%(int(time.time())) 16 | 17 | o = open(fname+".log", "w") 18 | o.write("%s\n"%link) 19 | o.write("convert html to docx\n") 20 | cmd = "pandoc -s -r html %s -t docx -s -o %s.docx"%(link, fname) 21 | o.write("done\n") 22 | if DEBUG: 23 | print cmd 24 | os.system(cmd) 25 | o.close() 26 | else: 27 | print __doc__ 28 | 29 | 30 | 31 | -------------------------------------------------------------------------------- /tools/fftool/convert_gromacs.py: -------------------------------------------------------------------------------- 1 | # convert gromacs format to normal format 2 | 3 | params = [] 4 | f = open('dihedral.itp', 'r') 5 | for i in f: 6 | tokens = i.strip().split() 7 | if len(tokens) > 11: 8 | params.append(tokens) 9 | f.close() 10 | 11 | o = open('opls-dihedral.dat', 'w') 12 | for i in params: 13 | a1, a2, a3, a4 = i[0:4] 14 | c0, c1, c2, c3, c4, c5 = [float(j) for j in i[5:11]] 15 | f4 = -0.25 * c4 16 | f3 = -0.5 * c3 17 | f2 = -c2 - c4 18 | f1 = -2*c1 - 1.5*c3 19 | o.write("%-4s%-4s%-4s%-4s opls"%(a1, a2, a3, a4)) 20 | o.write("%10.4f%10.4f%10.4f%10.4f\n"%(f1, f2, f3, f4)) 21 | o.close() 22 | -------------------------------------------------------------------------------- /tools/garffield/check_geo.py: -------------------------------------------------------------------------------- 1 | """ 2 | Check the element parts of geo. 3 | """ 4 | import shutil 5 | f = open("geo", "r") 6 | 7 | lines = [] 8 | 9 | n = 0 10 | 11 | for i in f: 12 | line = i 13 | if "HETATM" in i: 14 | ele = i[64:66] 15 | if len(ele.strip()) == 0: 16 | n += 1 17 | ele = i[13:15] 18 | line = i[:64] + ele + i[66:] 19 | lines.append(line) 20 | f.close() 21 | 22 | if n > 0: 23 | shutil.copy("geo", "geo.bak") 24 | print("Warning: The elements parts are missing in the GEO file" 25 | 26 | o = open("geo", "w") 27 | for i in lines: 28 | o.write(i) 29 | o.close() 30 | 31 | -------------------------------------------------------------------------------- /tools/vasp/vasp2: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os 4 | import sys 5 | import shutil 6 | 7 | if not os.path.exists("inp"): 8 | os.mkdir("inp") 9 | 10 | if os.path.exists("POSCAR"): 11 | shutil.copy("POSCAR", "inp") 12 | if os.path.exists("POTCAR"): 13 | shutil.copy("POTCAR", "inp") 14 | if os.path.exists("KPOINTS"): 15 | shutil.copy("KPOINTS", "inp") 16 | if os.path.exists("INCAR"): 17 | shutil.copy("INCAR", "inp") 18 | if os.path.exists("run.in"): 19 | shutil.copy("run.in", "inp") 20 | if os.path.exists("ICONST"): 21 | shutil.copy("ICONST", "inp") 22 | if os.path.exists("pbs"): 23 | shutil.copy("pbs", "inp") 24 | 25 | -------------------------------------------------------------------------------- /doc/html/frames.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | API Documentation 7 | 8 | 9 | 10 | 12 | 14 | 15 | 16 | 17 | 18 | -------------------------------------------------------------------------------- /doc/html/index.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | API Documentation 7 | 8 | 9 | 10 | 12 | 14 | 15 | 16 | 17 | 18 | -------------------------------------------------------------------------------- /doc/tools/frames.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | API Documentation 7 | 8 | 9 | 10 | 12 | 14 | 15 | 16 | 17 | 18 | -------------------------------------------------------------------------------- /doc/tools/index.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | API Documentation 7 | 8 | 9 | 10 | 12 | 14 | 15 | 16 | 17 | 18 | -------------------------------------------------------------------------------- /tools/intermol/gmx2lmp: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env /opt/anaconda3/bin/python3 2 | 3 | exe = '/opt/anaconda3/bin/python3' 4 | 5 | import os, sys 6 | 7 | test_energy = 0 8 | 9 | gro = sys.argv[1] 10 | top = sys.argv[2] 11 | lmp = sys.argv[3] 12 | 13 | cwd = os.getcwd() 14 | os.makedirs(lmp, exist_ok=True) 15 | 16 | #os.chdir('../InterMol/intermol') 17 | os.chdir('/Users/tao/soft/InterMol/intermol') 18 | if test_energy: 19 | os.system('%s convert.py --gro_in %s/%s %s/%s --lammps --odir %s/%s -e'%(exe, cwd, gro, cwd, top, cwd, lmp)) 20 | else: 21 | os.system('%s convert.py --gro_in %s/%s %s/%s --lammps --odir %s/%s'%(exe, cwd, gro, cwd, top, cwd, lmp)) 22 | os.chdir(cwd) 23 | -------------------------------------------------------------------------------- /tools/vasp/get_homo_lumo_gap.py: -------------------------------------------------------------------------------- 1 | f = open("OUTCAR", "r") 2 | 3 | flag = 1 4 | while(flag): 5 | flag = 0 6 | for i in f: 7 | flag = 1 8 | if i.strip().startswith("E-fermi"): 9 | break 10 | for i in f: 11 | if i.strip().startswith("band"): 12 | break 13 | for i in f: 14 | tokens = i.strip().split() 15 | if len(tokens) == 3: 16 | if float(tokens[2]) > 0: 17 | e_homo = float(tokens[1]) 18 | else: 19 | e_lumo = float(tokens[1]) 20 | print(e_lumo - e_homo) 21 | break 22 | else: 23 | break 24 | -------------------------------------------------------------------------------- /arc/linux_tools/lammps/read_lmplog.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | #-*- coding: utf-8 -*- 3 | 4 | def read_lmplog(lmplog): 5 | ''' 6 | Read the log.lammps and dump all the data to the list of [result] 7 | Structure of [result]: [[column 1], [column 2], ..., [column n]] 8 | Structure of [column n]: ['Name', 'Value 1', ..., 'Value n'] 9 | ''' 10 | block = None 11 | for i in lmplog: 12 | if i.startswith("Loop"): 13 | block = None 14 | elif block is not None: 15 | for ncol in range(len(result)): 16 | result[ncol].append(i.split()[ncol]) 17 | elif i.startswith("Step"): 18 | block = [] 19 | result = [[j] for j in i.split()] 20 | return result 21 | 22 | -------------------------------------------------------------------------------- /tools/caltech/dat/LAMMPS/in.lammps.solv.2pt: -------------------------------------------------------------------------------- 1 | log ${sname}.2pt.eng 2 | timestep 2.0 3 | 4 | shakeOpts 5 | 6 | print "================================================" 7 | print "NVT dynamics for 20ps dumping velocities" 8 | print "================================================" 9 | thermo 2 10 | thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol 11 | thermo_modify line multi 12 | fix thermostat all nvt temp ${temp} ${temp} 100.0 13 | dump traj all custom 2 ${sname}.2pt.lammps id type xu yu zu vx vy vz 14 | run 10000 15 | unfix thermostat 16 | undump traj 17 | -------------------------------------------------------------------------------- /tools/hun/toVmd.py: -------------------------------------------------------------------------------- 1 | f = open("molid.out", "r") 2 | o = open("molid.vmd", "w") 3 | 4 | na = 240 5 | nb = 8 6 | 7 | """ 8 | 1 18 O6C4N8 2 106 6 41 77 42 5 109 110 105 78 114 113 1 161 165 162 166 9 | """ 10 | 11 | for i in f: 12 | if i.strip().startswith("#"): 13 | pass 14 | else: 15 | tokens = i.strip().split() 16 | n = 0 17 | for j in tokens: 18 | if n < 3: 19 | o.write(j+" ") 20 | else: 21 | id = int(j) - 1 22 | for k in range(nb): 23 | o.write("%d "%(id + k*na)) 24 | n += 1 25 | o.write("\n") 26 | o.close() 27 | f.close() 28 | -------------------------------------------------------------------------------- /tools/onyx/tocheng: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os 4 | import sys 5 | import argparse 6 | 7 | def main(): 8 | parser = argparse.ArgumentParser() 9 | parser.add_argument("fname", nargs="+", help="geo file name") 10 | parser.add_argument("-o", default="/home/tao/Dropbox", help="convert the file to other formats (geo, xyz, gjf, lammps)") 11 | args = parser.parse_args() 12 | files = args.fname 13 | folder = args.o 14 | ip = "131.215.26.220" 15 | usr = "tao" 16 | cmd = "scp -r " 17 | cmd += " ".join(files) 18 | cmd += " "+usr+"@"+ip+":"+folder 19 | os.system(cmd) 20 | 21 | if __name__ == "__main__": 22 | main() 23 | 24 | -------------------------------------------------------------------------------- /tools/sas/html/index.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | API Documentation 7 | 8 | 9 | 10 | 12 | 14 | 15 | 16 | 17 | 18 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/docs/frames.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | scipy 7 | 8 | 9 | 10 | 12 | 14 | 15 | 16 | 17 | 18 | -------------------------------------------------------------------------------- /arc/simulation_tools_py/docs/index.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | scipy 7 | 8 | 9 | 10 | 12 | 14 | 15 | 16 | 17 | 18 | -------------------------------------------------------------------------------- /tools/sas/html/frames.html: -------------------------------------------------------------------------------- 1 | 2 | 4 | 5 | 6 | API Documentation 7 | 8 | 9 | 10 | 12 | 14 | 15 | 16 | 17 | 18 | -------------------------------------------------------------------------------- /tools/deepmd/reaxff-ml/merge.py: -------------------------------------------------------------------------------- 1 | import shutil, os 2 | 3 | folders = [] 4 | f = open("flist", "r") 5 | for i in f: 6 | folders.append(i.strip()) 7 | f.close() 8 | 9 | shutil.copy("./%s/lv_raw/type.raw"%folders[0], ".") 10 | 11 | raw_files = ["box.raw", "coord.raw", "energy.raw", "force.raw", "virial.raw"] 12 | for i in raw_files: 13 | lines = [] 14 | print(folders) 15 | for j in folders: 16 | print(j) 17 | f = open("./%s/lv_raw/%s"%(j, i), "r") 18 | for k in f: 19 | lines.append(k) 20 | f.close() 21 | o = open(i, "w") 22 | for k in lines: 23 | print(k) 24 | o.write(k) 25 | o.close() 26 | 27 | 28 | --------------------------------------------------------------------------------