├── LICENSE ├── README.md ├── examples ├── silica_Q3_amorph_4_7OH_18pct_ion.gro ├── silica_Q3_amorph_4_7OH_18pct_ion.itp └── system.top ├── forcefield └── charmm27_interface_v1_5.prm ├── interfaceff2gro.py └── msi2lmp ├── README ├── frc_files ├── README ├── cff91.frc ├── clayff.frc ├── compass_published.frc ├── cvff.frc ├── cvff_aug.frc ├── oplsaa.frc ├── pcff.frc ├── pcff.rlb ├── pcff_interface.frc ├── pcff_interface_templates.dat └── pcff_templates.dat ├── src ├── CheckLists.c ├── Forcefield.h ├── GetParameters.c ├── InitializeItems.c ├── MakeLists.c ├── Makefile ├── ReadCarFile.c ├── ReadFrcFile.c ├── ReadMdfFile.c ├── SearchAndFill.c ├── WriteDataFile.c ├── msi2lmp.c └── msi2lmp.h └── test ├── PyAC_bulk-clayff.car ├── PyAC_bulk-clayff.mdf ├── benzene-class1.car ├── benzene-class1.mdf ├── benzene-class2a.car ├── benzene-class2a.mdf ├── benzene-class2b.car ├── benzene-class2b.mdf ├── cnt-hexagonal-class1.car ├── cnt-hexagonal-class1.mdf ├── cnt-hexagonal-class2a.car ├── cnt-hexagonal-class2a.mdf ├── cnt-hexagonal-class2b.car ├── cnt-hexagonal-class2b.mdf ├── crambin-class1.car ├── crambin-class1.mdf ├── data-compare.pl ├── decane-oplsaa.car ├── decane-oplsaa.mdf ├── ethane-class1.car ├── ethane-class1.mdf ├── ethane-class2a.car ├── ethane-class2a.mdf ├── ethane-class2b.car ├── ethane-class2b.mdf ├── ethane-oplsaa.car ├── ethane-oplsaa.mdf ├── h2-h2o-class1.car ├── h2-h2o-class1.mdf ├── h2-h2o-class2b.car ├── h2-h2o-class2b.mdf ├── hap_crystal-class1.car ├── hap_crystal-class1.mdf ├── hap_crystal-class2b.car ├── hap_crystal-class2b.mdf ├── hydrogen-class1.car ├── hydrogen-class1.mdf ├── hydrogen-class2a.car ├── hydrogen-class2a.mdf ├── in.PyAC_bulk-clayff ├── in.benzene-class1 ├── in.benzene-class2a ├── in.benzene-class2b ├── in.cnt-hexagonal-class1 ├── in.cnt-hexagonal-class2a ├── in.cnt-hexagonal-class2b ├── in.crambin-class1 ├── in.decane-oplsaa ├── in.ethane-class1 ├── in.ethane-class2a ├── in.ethane-class2b ├── in.ethane-oplsaa ├── in.h2-h2o-class1 ├── in.h2-h2o-class2b ├── in.hap_crystal-class1 ├── in.hap_crystal-class2b ├── in.hydrogen-class1 ├── in.hydrogen-class2a ├── in.naphthalene-class1 ├── in.naphthalene-class2a ├── in.naphthalene-class2b ├── in.nylon-class1 ├── in.phen3_cff97-class1 ├── in.solv-poly-class2c ├── in.water-class1 ├── in.water-class2b ├── naphthalene-class1.car ├── naphthalene-class1.mdf ├── naphthalene-class2a.car ├── naphthalene-class2a.mdf ├── naphthalene-class2b.car ├── naphthalene-class2b.mdf ├── nylon-class1.car ├── nylon-class1.mdf ├── phen3_cff97-class1.car ├── phen3_cff97-class1.mdf ├── reference ├── PyAC_bulk-clayff.data ├── PyAC_bulk-clayff.data2 ├── benzene-class1.data ├── benzene-class1.data2 ├── benzene-class1.data3 ├── benzene-class2a.data ├── benzene-class2a.data2 ├── benzene-class2b.data ├── benzene-class2b.data2 ├── cnt-hexagonal-class1.data ├── cnt-hexagonal-class1.data2 ├── cnt-hexagonal-class2a.data ├── cnt-hexagonal-class2a.data2 ├── cnt-hexagonal-class2b.data ├── cnt-hexagonal-class2b.data2 ├── crambin-class1.data ├── crambin-class1.data2 ├── decane-oplsaa.data ├── decane-oplsaa.data2 ├── ethane-class1.data ├── ethane-class1.data2 ├── ethane-class2a.data ├── ethane-class2a.data2 ├── ethane-class2b.data ├── ethane-class2b.data2 ├── ethane-oplsaa.data ├── ethane-oplsaa.data2 ├── h2-h2o-class1.data ├── h2-h2o-class1.data2 ├── h2-h2o-class2b.data ├── h2-h2o-class2b.data2 ├── hap_crystal-class1.data ├── hap_crystal-class1.data2 ├── hap_crystal-class2b.data ├── hap_crystal-class2b.data2 ├── hydrogen-class1.data ├── hydrogen-class1.data2 ├── hydrogen-class2a.data ├── hydrogen-class2a.data2 ├── naphthalene-class1.data ├── naphthalene-class1.data2 ├── naphthalene-class2a.data ├── naphthalene-class2a.data2 ├── naphthalene-class2b.data ├── naphthalene-class2b.data2 ├── nylon-class1.data ├── nylon-class1.data2 ├── phen3_cff97-class1.data ├── phen3_cff97-class1.data2 ├── water-class1.data ├── water-class1.data2 ├── water-class2b.data └── water-class2b.data2 ├── runtests.sh ├── water-class1.car ├── water-class1.mdf ├── water-class2b.car └── water-class2b.mdf /README.md: -------------------------------------------------------------------------------- 1 | # interfaceff2gro 2 | 3 | interfaceff2gro is a Python script that creates input files for GROMACS using Hendrik Heinz research group Interface forcefield (doi:10.1021/la3038846, [Interface_ff](https://bionanostructures.com/interface-md/)) - so far it only works with CHARMM forcefield (for supported atomtypes please see prm file that is included [here](https://github.com/kolmank/interfaceff2gro/tree/master/forcefield)). It uses msi2lmp utility from [Lammps](https://github.com/lammps/lammps) software package to transform mdf and car files (Materials Studio files) to Lammps data file and [MDAnalysis](https://www.mdanalysis.org/) Python library. interfacesff2gro creates 3 files: a gro file having coordinates information of your structure, an itp file having topology information and system.top file being a master topology file. 4 | 5 | ## Getting Started 6 | 7 | The script was written in Python 3.6 (I have only tested it on Linux). The easiest way to build Python environment is by using [Conda](https://conda.io/docs/). The source file of msi2lmp are included in [msi2lmp folder](https://github.com/kolmank/interfaceff2gro/tree/master/msi2lmp) so you do not need to download them. 8 | 9 | ### Prerequisites 10 | 11 | Create Python 3.6 environment and install MDAnalysis. The easiest way is to use Conda. 12 | 13 | ``` 14 | conda config --add channels conda-forge 15 | conda create -n envname python=3.6 mdanalysis 16 | source activate envname 17 | ``` 18 | 19 | ### Installing 20 | 21 | Download the files to you computer: 22 | 23 | ``` 24 | git clone https://github.com/kolmank/interfaceff2gro.git 25 | ``` 26 | 27 | Enter msi2lmp directory and compile it. According to the authors of the code, the files have been prepared to be compiled using gcc so check if gcc is your default compiler. If you plan to use different compiler, you have to modify the files to make it work. Frc file having atomtypes, bondtypes and angletypes of Interface forcfield has been added to frc_files directory. To compile please use the commands below: 28 | 29 | ``` 30 | cd interfaceff2gro/msi2lmp/src/ 31 | make 32 | ``` 33 | 34 | Enter the main directory (/interfaceff2gro) and make interfaceff2gro.py executable: 35 | 36 | ``` 37 | cd .. 38 | cd .. 39 | chmod +x interfaceff2gro.py 40 | ``` 41 | 42 | The script is ready to go! 43 | 44 | ## Usage 45 | 46 | To use the script, copy car and mdf files to the main directory of the script (you can copy it directly from MODEL_DATABASE directory of Interface forcefield). IMPORTANT! Both files have to have the same name, otherwise the script wont work. Use the command below: 47 | 48 | ``` 49 | ./interfaceff2gro.py nameofyourcarfile.car 50 | ``` 51 | 52 | As a result, you should get three files: nameofyourcarfile.gro, nameofyourcarfile.itp and system.top. Examples can be found [here](https://github.com/kolmank/interfaceff2gro/tree/master/examples). 53 | 54 | ## Known limitations 55 | 56 | * It only works with rectangular simulation boxes. 57 | * Supports only atoms included in prm file, which is [here](https://github.com/kolmank/interfaceff2gro/tree/master/forcefield). According to my knowledge, it should work with silica, metal, cement (only c3a and c3s), clay and hydroxyapatite models that can be found in the database of Interface forcefield. 58 | 59 | ## Acknowledgments 60 | 61 | * Hendrik Heinz research group that created Interface forcefield (doi:10.1021/la3038846, [Interface_ff](https://bionanostructures.com/interface-md/)). 62 | * [Lammps](https://github.com/lammps/lammps) software package - msi2lmp used in this project is part of it. 63 | * [MDAnalysis](https://www.mdanalysis.org/) Python library. 64 | -------------------------------------------------------------------------------- /examples/system.top: -------------------------------------------------------------------------------- 1 | #include "charmm27.ff/forcefield.itp" 2 | #include "silica_Q3_amorph_4_7OH_18pct_ion.itp" 3 | #include "charmm27.ff/ions.itp" 4 | #include "charmm27.ff/tip4p.itp" 5 | 6 | [ system ] 7 | Surface 8 | 9 | [ molecules ] 10 | SURF 1 ;1 periodic slab 11 | 12 | -------------------------------------------------------------------------------- /msi2lmp/frc_files/README: -------------------------------------------------------------------------------- 1 | Set the environment variable MSI2LMP_LIBRARY or copy cvff.frc and cff9*.frc 2 | or any other *.frc files (which you have license to use) to this directory 3 | for use with msi2lmp. 4 | 5 | Note that LAMMPS does not distribute Accelrys (or old BioSym) 6 | force field files, since they are proprietary. All the 7 | files in this directory that are part of the LAMMPS distribution 8 | are openly available files that are in the public domain. 9 | 10 | 11 | -------------------------------------------------------------------------------- /msi2lmp/frc_files/clayff.frc: -------------------------------------------------------------------------------- 1 | !CLAYFF forcefield 2 | 3 | #atom_types cvff 4 | 5 | !Ver Ref Type Mass Element Connections Description and charge 6 | !---- --- ---- ---------- ------- ----------------------------------------- 7 | 1.0 1 st 28.08550 Si 4 tetrahedral silicon 2.1 8 | 1.0 1 ao 26.98154 Al 6 octahedral aluminum 1.575 9 | 1.0 1 at 26.98154 Al 4 tetrahedral aluminum 1.575 10 | 1.0 1 mgo 24.30500 Mg 6 octahedral magnesium 1.36 11 | 1.0 1 mgh 24.30500 Mg 6 hydroxide magnesium 1.05 12 | 1.0 1 cao 40.08000 Ca 6 octahedral calcium 1.36 13 | 1.0 1 cah 40.08000 Ca 6 hydroxide calcium 1.05 14 | 1.0 1 feo 55.84700 Fe 6 octahedral iron 1.575 15 | 1.0 1 lio 6.941000 Li 6 octahedral lithium 0.525 16 | 1.0 1 ob 15.99940 O 2 bridging oxygen -1.05 17 | 1.0 1 obss 15.99940 O 3 oxygen double sub. -1.2996 18 | 1.0 1 obts 15.99940 O 2 oxygen tet. sub. -1.1688 19 | 1.0 1 obos 15.99940 O 2 oxygen oct. sub. -1.1808 20 | 1.0 1 ohs 15.99940 O 2 hydroxyl O sub. -1.0808 21 | 1.0 1 oh 15.99940 O 2 hydroxyl O -0.95 22 | 1.0 1 oh- 15.99940 O 1 hydroxide O 23 | 1.0 1 o* 15.99940 O 2 spc water O -0.82 24 | 1.0 1 ho 1.007970 H 1 hydroxyl H 0.425 25 | 1.0 1 h* 1.007970 H 1 spc water H 0.41 26 | 1.0 1 Na 22.99000 Na 0 sodium ion 1.0 27 | 1.0 1 K 39.10 K 0 potassium ion 1.0 28 | 1.0 1 Cs 132.9100 Cs 0 cesium ion 1.0 29 | 1.0 1 Ca 40.07980 Ca 0 calcium ion 2.0 30 | 1.0 1 Ba 137.3300 Ba 0 barium ion 2.0 31 | 1.0 1 Mg 24.3050 Mg 0 magnesium ion 2.0 32 | 1.0 1 Sr 87.6200 Sr 0 strontium ion 2.0 33 | 1.0 1 Pb 207.2000 Pb 0 lead ion 2.0 34 | 1.0 1 Cl 35.45300 Cl 0 chloride ion -1.0 35 | 36 | 37 | #equivalence cvff 38 | 39 | > Equivalence table for any variant of cvff 40 | 41 | ! Equivalences 42 | ! ----------------------------------------- 43 | !Ver Ref Type NonB Bond Angle Torsion OOP 44 | !---- --- ---- ---- ---- ----- ------- ---- 45 | 1.0 1 h h h h h h 46 | 47 | 48 | 49 | #auto_equivalence cvff_auto 50 | 51 | ! Equivalences 52 | ! ----------------------------------------- 53 | !Ver Ref Type NonB Bond Bond Angle Angle Torsion Torsion OOP OOP 54 | ! Inct End atom Apex atom End Atoms Center Atoms End Atom Center Atom 55 | !---- --- ---- ---- ------ ---- ---------- --------- --------- ----------- -------- ----------- 56 | 2.0 18 h h h h_ h_ h_ h_ h_ h_ h_ 57 | 58 | 59 | 60 | #hbond_definition cvff 61 | 62 | 63 | #morse_bond cvff 64 | 65 | > E = D * (1 - exp(-ALPHA*(R - R0)))^2 66 | 67 | !Ver Ref I J R0 D ALPHA 68 | !---- --- ---- ---- ------- -------- ------- 69 | 2.3 23 no o- 1.2178 140.2486 2.0000 70 | 71 | 72 | 73 | #quadratic_bond cvff 74 | 75 | > E = K2 * (R - R0)^2 76 | 77 | !Ver Ref I J R0 K2 78 | !---- --- ---- ---- ------- -------- 79 | 2.1 28 o* h* 1.0000 553.9350 80 | 2.1 28 oh ho 1.0000 553.9350 81 | 2.1 28 ohs ho 1.0000 553.9350 82 | 83 | 84 | #quadratic_angle cvff 85 | 86 | > E = K2 * (Theta - Theta0)^2 87 | 88 | !Ver Ref I J K Theta0 K2 89 | !---- --- ---- ---- ---- -------- ------- 90 | 1.0 1 h* o* h* 109.4700 45.7530 91 | 92 | 93 | 94 | #torsion_1 cvff_auto 95 | 96 | > E = Kphi * [ 1 + cos(n*Phi - Phi0) ] 97 | 98 | !Ver Ref I J K L Kphi n Phi0 99 | !---- --- ---- ---- ---- ---- ------- ------ ------- 100 | 2.0 18 * c_ n3n_ * 0.0500 3 0. 101 | 102 | 103 | 104 | #out_of_plane cvff_auto 105 | 106 | > E = Kchi * [ 1 + cos(n*Chi - Chi0) ] 107 | 108 | !Ver Ref I J K L Kchi n Chi0 109 | !---- --- ---- ---- ---- ---- ------- ------ ------- 110 | 2.0 18 * c'_ * * 10.0000 2 180.0000 111 | 112 | 113 | #nonbond(12-6) cvff 114 | 115 | @type A-B 116 | @combination geometric 117 | 118 | > E = Aij/r^12 - Bij/r^6 119 | > where Aij = sqrt( Ai * Aj ) 120 | > Bij = sqrt( Bi * Bj ) 121 | 122 | !Ver Ref I A B 123 | !---- --- ---- ----------- ----------- 124 | 1.0 1 st 12.3645 0.00954 125 | 1.0 1 ao 196.1446 0.03230 126 | 1.0 1 at 12.3645 0.00954 127 | 1.0 1 mgo 1636.3265 0.07688 128 | 1.0 1 mgh 1636.3265 0.07688 129 | 1.0 1 cao 17814.73 0.5987 130 | 1.0 1 cah 17624.076 0.595 131 | 1.0 1 feo 702.54 0.0504 132 | 1.0 1 lio 112.01 0.0201 133 | 1.0 1 ob 629358.0000 625.50000 134 | 1.0 1 obss 629358.0000 625.50000 135 | 1.0 1 obts 629358.0000 625.50000 136 | 1.0 1 obos 629358.0000 625.50000 137 | 1.0 1 ohs 629358.0000 625.50000 138 | 1.0 1 oh 629358.0000 625.50000 139 | 1.0 1 oh- 629358.0000 625.50000 140 | 1.0 1 o* 629358.0000 625.50000 141 | 1.0 1 ho 0.00000001 0.00000 142 | 1.0 1 h* 0.00000001 0.00000 143 | 1.0 1 Na 14763.1719 87.65132 144 | 1.0 1 K 754506.86 549.37 145 | 1.0 1 Cs 3998193.96 1264.63 146 | 1.0 1 Ca 125966.6068 224.46969 147 | 1.0 1 Ba 1799606.56 582.25 148 | 1.0 1 Mg 1369.00 69.22 149 | 1.0 1 Sr 1185860.37 688.73 150 | 1.0 1 Pb 861150.71 638.08 151 | 1.0 1 Cl 21081006.97 2905.31 152 | 153 | 154 | #bond_increments cvff 155 | 156 | !Ver Ref I J DeltaIJ DeltaJI 157 | !---- --- ---- ---- ------- ------- 158 | 2.3 23 no o- 0.1684 -0.1684 159 | 160 | -------------------------------------------------------------------------------- /msi2lmp/frc_files/pcff.rlb: -------------------------------------------------------------------------------- 1 | VERSION 2 | elib 3 | -------------------------------------------------------------------------------- /msi2lmp/src/CheckLists.c: -------------------------------------------------------------------------------- 1 | #include "msi2lmp.h" 2 | 3 | void CheckLists() { 4 | int i; 5 | 6 | for (i=0; i < total_no_bonds; i++) { 7 | if ((atoms[bonds[i].members[0]].type != bondtypes[bonds[i].type].types[0]) 8 | || (atoms[bonds[i].members[1]].type != bondtypes[bonds[i].type].types[1])) { 9 | fprintf(stderr,"Warning atom types in bond %d are inconsistent with bond type %d\n",i,bonds[i].type); 10 | } 11 | } 12 | 13 | for (i=0; i < total_no_angles;i++) { 14 | if ((atoms[angles[i].members[0]].type != angletypes[angles[i].type].types[0]) 15 | || (atoms[angles[i].members[1]].type != angletypes[angles[i].type].types[1]) 16 | || (atoms[angles[i].members[2]].type != angletypes[angles[i].type].types[2])) { 17 | fprintf(stderr,"Warning atom types in angle %d are inconsistent with angle type %d\n", i,angles[i].type); 18 | } 19 | } 20 | 21 | for (i=0; i < total_no_dihedrals; i++) { 22 | if ((atoms[dihedrals[i].members[0]].type != dihedraltypes[dihedrals[i].type].types[0]) 23 | || (atoms[dihedrals[i].members[1]].type != dihedraltypes[dihedrals[i].type].types[1]) 24 | || (atoms[dihedrals[i].members[2]].type != dihedraltypes[dihedrals[i].type].types[2]) 25 | || (atoms[dihedrals[i].members[3]].type != dihedraltypes[dihedrals[i].type].types[3])) { 26 | fprintf(stderr,"Warning atom types in dihedral %d are inconsistent with dihedral type %d\n",i,dihedrals[i].type); 27 | } 28 | } 29 | 30 | for (i=0; i < total_no_oops; i++) { 31 | 32 | if ((atoms[oops[i].members[0]].type != ooptypes[oops[i].type].types[0]) 33 | || (atoms[oops[i].members[1]].type != ooptypes[oops[i].type].types[1]) 34 | || (atoms[oops[i].members[2]].type != ooptypes[oops[i].type].types[2]) 35 | || (atoms[oops[i].members[3]].type != ooptypes[oops[i].type].types[3])) { 36 | fprintf(stderr,"Warning atom types in oop %d are inconsistent with oop type %d\n",i,oops[i].type); 37 | } 38 | } 39 | } 40 | -------------------------------------------------------------------------------- /msi2lmp/src/Forcefield.h: -------------------------------------------------------------------------------- 1 | /****************************** 2 | * 3 | * This is the header file for the routine that reads the forcefield file 4 | * into memory in order to speed up searching. 5 | * 6 | * It defines the data structures used to store the force field in memory 7 | */ 8 | 9 | #define MAX_NO_MEMS 6 10 | #define MAX_NO_PARAMS 8 11 | 12 | struct FrcFieldData { 13 | float ver; /* Version number of forcefield entry */ 14 | int ref; /* Reference within forcefield */ 15 | char ff_types[MAX_NO_MEMS][5]; 16 | double ff_param[MAX_NO_PARAMS]; 17 | }; 18 | 19 | struct FrcFieldItem { 20 | char keyword[25]; 21 | int number_of_members; /* number of members of item */ 22 | int number_of_parameters; /* number of parameters of item */ 23 | int entries; /* number of entries in item list */ 24 | struct FrcFieldData *data; /* contains all eqiuv and param data */ 25 | }; 26 | 27 | extern struct FrcFieldItem ff_atomtypes, equivalence, ff_vdw, ff_bond, ff_morse, ff_ang, ff_tor, ff_oop, 28 | ff_bonbon, ff_bonang, ff_angtor, ff_angangtor, ff_endbontor, ff_midbontor, ff_angang, ff_bonbon13; 29 | 30 | /* prototypes */ 31 | extern void InitializeItems(void); 32 | extern void ClearFrcItem(struct FrcFieldItem *item); 33 | extern void SearchAndFill(struct FrcFieldItem *item); 34 | extern const char *SearchAndCheck(const char *); 35 | 36 | -------------------------------------------------------------------------------- /msi2lmp/src/InitializeItems.c: -------------------------------------------------------------------------------- 1 | /* 2 | * This function fills in the keyword field, the number of members for each 3 | * item and the number of parameters for each item 4 | * 5 | */ 6 | 7 | #include "msi2lmp.h" 8 | #include "Forcefield.h" 9 | 10 | #include 11 | 12 | void InitializeItems(void) 13 | { 14 | /* ATOM TYPES */ 15 | strcpy(ff_atomtypes.keyword,"#atom_types"); 16 | ff_atomtypes.number_of_members = 1; 17 | ff_atomtypes.number_of_parameters = 1; 18 | 19 | /* EQUIVALENCE */ 20 | 21 | strcpy(equivalence.keyword,"#equivalence"); 22 | equivalence.number_of_members = 6; 23 | equivalence.number_of_parameters = 0; 24 | 25 | /* NON-BOND */ 26 | 27 | strcpy(ff_vdw.keyword,"#nonbond"); 28 | ff_vdw.number_of_members = 1; 29 | ff_vdw.number_of_parameters = 2; 30 | 31 | /* BOND */ 32 | 33 | ff_bond.number_of_members = 2; 34 | if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) { 35 | strcpy(ff_bond.keyword,"#quadratic_bond"); 36 | ff_bond.number_of_parameters = 2; 37 | } 38 | 39 | if (forcefield & FF_TYPE_CLASS2) { 40 | strcpy(ff_bond.keyword,"#quartic_bond"); 41 | ff_bond.number_of_parameters = 4; 42 | } 43 | 44 | /* MORSE */ 45 | 46 | if (forcefield & FF_TYPE_CLASS1) { 47 | ff_morse.number_of_members = 2; 48 | strcpy(ff_morse.keyword,"#morse_bond"); 49 | ff_morse.number_of_parameters = 3; 50 | } 51 | 52 | /* ANGLE */ 53 | 54 | ff_ang.number_of_members = 3; 55 | if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) { 56 | strcpy(ff_ang.keyword,"#quadratic_angle"); 57 | ff_ang.number_of_parameters = 2; 58 | } 59 | 60 | if (forcefield & FF_TYPE_CLASS2) { 61 | strcpy(ff_ang.keyword,"#quartic_angle"); 62 | ff_ang.number_of_parameters = 4; 63 | } 64 | 65 | /* TORSION */ 66 | 67 | ff_tor.number_of_members = 4; 68 | if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) { 69 | strcpy(ff_tor.keyword,"#torsion_1"); 70 | ff_tor.number_of_parameters = 3; 71 | } 72 | 73 | if (forcefield & FF_TYPE_CLASS2) { 74 | strcpy(ff_tor.keyword,"#torsion_3"); 75 | ff_tor.number_of_parameters = 6; 76 | } 77 | 78 | /* OOP */ 79 | 80 | ff_oop.number_of_members = 4; 81 | if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) { 82 | strcpy(ff_oop.keyword,"#out_of_plane"); 83 | ff_oop.number_of_parameters = 3; 84 | } 85 | 86 | if (forcefield & FF_TYPE_CLASS2) { 87 | strcpy(ff_oop.keyword,"#wilson_out_of_plane"); 88 | ff_oop.number_of_parameters = 2; 89 | } 90 | 91 | if (forcefield & FF_TYPE_CLASS2) { 92 | /* BOND-BOND */ 93 | 94 | strcpy(ff_bonbon.keyword,"#bond-bond"); 95 | ff_bonbon.number_of_members = 3; 96 | ff_bonbon.number_of_parameters = 1; 97 | 98 | /* BOND-ANGLE */ 99 | 100 | strcpy(ff_bonang.keyword,"#bond-angle"); 101 | ff_bonang.number_of_members = 3; 102 | ff_bonang.number_of_parameters = 2; 103 | 104 | /* ANGLE-TORSION */ 105 | 106 | strcpy(ff_angtor.keyword,"#angle-torsion_3"); 107 | ff_angtor.number_of_members = 4; 108 | ff_angtor.number_of_parameters = 6; 109 | 110 | /* ANGLE-ANGLE-TORSION */ 111 | 112 | strcpy(ff_angangtor.keyword,"#angle-angle-torsion_1"); 113 | ff_angangtor.number_of_members = 4; 114 | ff_angangtor.number_of_parameters = 1; 115 | 116 | /* END-BOND-TORSION */ 117 | 118 | strcpy(ff_endbontor.keyword,"#end_bond-torsion_3"); 119 | ff_endbontor.number_of_members = 4; 120 | ff_endbontor.number_of_parameters = 6; 121 | 122 | /* MID-BOND-TORSION */ 123 | 124 | strcpy(ff_midbontor.keyword,"#middle_bond-torsion_3"); 125 | ff_midbontor.number_of_members = 4; 126 | ff_midbontor.number_of_parameters = 3; 127 | 128 | /* ANGLE-ANGLE */ 129 | 130 | strcpy(ff_angang.keyword,"#angle-angle"); 131 | ff_angang.number_of_members = 4; 132 | ff_angang.number_of_parameters = 1; 133 | 134 | /* BOND-BOND-1-3 */ 135 | 136 | strcpy(ff_bonbon13.keyword,"#bond-bond_1_3"); 137 | ff_bonbon13.number_of_members = 4; 138 | ff_bonbon13.number_of_parameters = 1; 139 | } 140 | } 141 | -------------------------------------------------------------------------------- /msi2lmp/src/Makefile: -------------------------------------------------------------------------------- 1 | 2 | TARGET = msi2lmp.exe 3 | 4 | SRCS = msi2lmp.c \ 5 | ReadCarFile.c \ 6 | ReadMdfFile.c \ 7 | MakeLists.c \ 8 | ReadFrcFile.c \ 9 | InitializeItems.c \ 10 | SearchAndFill.c \ 11 | GetParameters.c \ 12 | CheckLists.c \ 13 | WriteDataFile.c 14 | 15 | OBJS = $(SRCS:.c=.o) 16 | 17 | HEADERS = msi2lmp.h Forcefield.h 18 | 19 | CC = gcc 20 | CFLAGS = -O -Wall -W -g 21 | LDFLAGS = 22 | FRCFILE = cvff.frc 23 | FRCFILE2 = cff91.frc 24 | README = README 25 | MKFILE = Makefile 26 | 27 | $(TARGET) : $(OBJS) 28 | $(CC) $(LDFLAGS) $(CFLAGS) -o $(TARGET) $(OBJS) -lm 29 | 30 | .c.o: 31 | $(CC) $(CFLAGS) -c $< 32 | clean: 33 | rm -f $(OBJS) $(TARGET) 34 | 35 | # dependencies 36 | CheckLists.o: CheckLists.c msi2lmp.h 37 | GetParameters.o: GetParameters.c msi2lmp.h Forcefield.h 38 | InitializeItems.o: InitializeItems.c msi2lmp.h Forcefield.h 39 | MakeLists.o: MakeLists.c msi2lmp.h 40 | msi2lmp.o: msi2lmp.c msi2lmp.h 41 | ReadCarFile.o: ReadCarFile.c msi2lmp.h 42 | ReadFrcFile.o: ReadFrcFile.c msi2lmp.h Forcefield.h 43 | ReadMdfFile.o: ReadMdfFile.c msi2lmp.h 44 | SearchAndFill.o: SearchAndFill.c msi2lmp.h Forcefield.h 45 | WriteDataFile.o: WriteDataFile.c msi2lmp.h Forcefield.h 46 | -------------------------------------------------------------------------------- /msi2lmp/src/ReadFrcFile.c: -------------------------------------------------------------------------------- 1 | /* 2 | * This routine reads the data from a .frc forcefield file and stores it in 3 | * dynamically allocated memory. This allows for fast searches of the 4 | * file. 5 | * 6 | */ 7 | 8 | #include "msi2lmp.h" 9 | #include "Forcefield.h" 10 | 11 | #include 12 | #include 13 | 14 | struct FrcFieldItem ff_atomtypes, equivalence, ff_vdw, ff_bond, ff_morse, ff_ang, ff_tor, ff_oop, 15 | ff_bonbon, ff_bonang, ff_angtor, ff_angangtor, ff_endbontor, ff_midbontor, ff_angang, ff_bonbon13; 16 | 17 | 18 | void ClearFrcData(void) 19 | { 20 | ClearFrcItem(&ff_atomtypes); 21 | ClearFrcItem(&equivalence); 22 | ClearFrcItem(&ff_vdw); 23 | ClearFrcItem(&ff_bond); 24 | if (forcefield & FF_TYPE_CLASS1) { /* Morse bond terms for class I */ 25 | ClearFrcItem(&ff_morse); 26 | } 27 | ClearFrcItem(&ff_ang); 28 | ClearFrcItem(&ff_tor); 29 | ClearFrcItem(&ff_oop); 30 | 31 | if (forcefield & FF_TYPE_CLASS2) { /* Cross terms for class II */ 32 | ClearFrcItem(&ff_bonbon); 33 | ClearFrcItem(&ff_bonang); 34 | ClearFrcItem(&ff_angtor); 35 | ClearFrcItem(&ff_angangtor); 36 | ClearFrcItem(&ff_endbontor); 37 | ClearFrcItem(&ff_midbontor); 38 | ClearFrcItem(&ff_bonbon13); 39 | ClearFrcItem(&ff_angang); 40 | } 41 | } 42 | 43 | void ReadFrcFile(void) 44 | { 45 | const char *val; 46 | 47 | /* Open Forcefield File */ 48 | if ( (FrcF = fopen(FrcFileName,"r")) == NULL ) { 49 | fprintf(stderr,"Cannot open %s\n", FrcFileName); 50 | exit(72); 51 | } 52 | InitializeItems(); /* sets keywords, number of members and number of 53 | parameters for each structure */ 54 | /* allocate memory to and search and fill each structure */ 55 | 56 | val = SearchAndCheck("type"); 57 | 58 | if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) { 59 | if (strcmp(val,"A-B") == 0) { 60 | ljtypeflag = 0; 61 | } else { 62 | fprintf(stderr," Inconsistent data in force field file.\n" 63 | " Expected: 'A-B' type non-bonded data, found: %s\n",val); 64 | exit(73); 65 | } 66 | } else if (forcefield & FF_TYPE_CLASS2) { 67 | if (strcmp(val,"r-eps") == 0) { 68 | ljtypeflag = 1; 69 | } else { 70 | fprintf(stderr,"Inconsistent parameter file.\n" 71 | " Expected: 'r-eps' type non-bonded data, found: %s\n",val); 72 | exit(74); 73 | } 74 | } 75 | free((void *)val); 76 | 77 | SearchAndFill(&ff_atomtypes); 78 | SearchAndFill(&equivalence); 79 | SearchAndFill(&ff_vdw); 80 | SearchAndFill(&ff_bond); 81 | if (forcefield & FF_TYPE_CLASS1) { /* Morse bond terms for class I */ 82 | SearchAndFill(&ff_morse); 83 | } 84 | SearchAndFill(&ff_ang); 85 | SearchAndFill(&ff_tor); 86 | SearchAndFill(&ff_oop); 87 | 88 | if (forcefield & FF_TYPE_CLASS2) { /* Cross terms for class II */ 89 | SearchAndFill(&ff_bonbon); 90 | SearchAndFill(&ff_bonang); 91 | SearchAndFill(&ff_angtor); 92 | SearchAndFill(&ff_angangtor); 93 | SearchAndFill(&ff_endbontor); 94 | SearchAndFill(&ff_midbontor); 95 | SearchAndFill(&ff_bonbon13); 96 | SearchAndFill(&ff_angang); 97 | } 98 | if (pflag > 1) { 99 | 100 | fprintf(stderr,"\n Item %s has %d entries\n", 101 | ff_atomtypes.keyword,ff_atomtypes.entries); 102 | fprintf(stderr," Item %s has %d entries\n", 103 | equivalence.keyword,equivalence.entries); 104 | fprintf(stderr," Item %s has %d entries\n", 105 | ff_vdw.keyword,ff_vdw.entries); 106 | fprintf(stderr," Item %s has %d entries\n", 107 | ff_bond.keyword,ff_bond.entries); 108 | if (forcefield & FF_TYPE_CLASS1) 109 | fprintf(stderr," Item %s has %d entries\n", 110 | ff_morse.keyword,ff_morse.entries); 111 | fprintf(stderr," Item %s has %d entries\n", 112 | ff_ang.keyword,ff_ang.entries); 113 | if (forcefield & FF_TYPE_CLASS2) { 114 | fprintf(stderr," Item %s has %d entries\n", 115 | ff_bonbon.keyword,ff_bonbon.entries); 116 | fprintf(stderr," Item %s has %d entries\n", 117 | ff_bonang.keyword,ff_bonang.entries); 118 | } 119 | fprintf(stderr," Item %s has %d entries\n", 120 | ff_tor.keyword,ff_tor.entries); 121 | if (forcefield & FF_TYPE_CLASS2) { 122 | fprintf(stderr," Item %s has %d entries\n", 123 | ff_angtor.keyword,ff_angtor.entries); 124 | fprintf(stderr," Item %s has %d entries\n", 125 | ff_angangtor.keyword,ff_angangtor.entries); 126 | fprintf(stderr," Item %s has %d entries\n", 127 | ff_endbontor.keyword,ff_endbontor.entries); 128 | fprintf(stderr," Item %s has %d entries\n", 129 | ff_midbontor.keyword,ff_midbontor.entries); 130 | fprintf(stderr," Item %s has %d entries\n", 131 | ff_bonbon13.keyword,ff_bonbon13.entries); 132 | } 133 | fprintf(stderr," Item %s has %d entries\n", 134 | ff_oop.keyword,ff_oop.entries); 135 | if (forcefield & FF_TYPE_CLASS2) { 136 | fprintf(stderr," Item %s has %d entries\n", 137 | ff_angang.keyword,ff_angang.entries); 138 | } 139 | fprintf(stderr,"\n"); 140 | } 141 | fclose(FrcF); 142 | } 143 | 144 | -------------------------------------------------------------------------------- /msi2lmp/src/msi2lmp.h: -------------------------------------------------------------------------------- 1 | /******************************** 2 | * 3 | * Header file for msi2lmp conversion program. 4 | * 5 | * This is the header file for the third version of a program 6 | * that generates a LAMMPS data file based on the information 7 | * in an MSI car file (atom coordinates) and mdf file (molecular 8 | * topology). A key part of the program looks up forcefield parameters 9 | * from an MSI frc file. 10 | * 11 | * The first version was written by Steve Lustig at Dupont, but 12 | * required using Discover to derive internal coordinates and 13 | * forcefield parameters 14 | * 15 | * The second version was written by Michael Peachey while an 16 | * intern in the Cray Chemistry Applications Group managed 17 | * by John Carpenter. This version derived internal coordinates 18 | * from the mdf file and looked up parameters in the frc file 19 | * thus eliminating the need for Discover. 20 | * 21 | * The third version was written by John Carpenter to optimize 22 | * the performance of the program for large molecular systems 23 | * (the original code for derving atom numbers was quadratic in time) 24 | * and to make the program fully dynamic. The second version used 25 | * fixed dimension arrays for the internal coordinates. 26 | * 27 | * The third version was revised in Fall 2011 by 28 | * Stephanie Teich-McGoldrick to add support non-orthogonal cells. 29 | * 30 | * The next revision was started in Summer/Fall 2013 by 31 | * Axel Kohlmeyer to improve portability to Windows compilers, 32 | * clean up command line parsing and improve compatibility with 33 | * the then current LAMMPS versions. This revision removes 34 | * compatibility with the obsolete LAMMPS version written in Fortran 90. 35 | */ 36 | 37 | # include 38 | 39 | #define MSI2LMP_VERSION "v3.9.8 / 06 Oct 2016" 40 | 41 | #define PI_180 0.01745329251994329576 42 | 43 | #define MAX_LINE_LENGTH 256 44 | #define MAX_CONNECTIONS 8 45 | #define MAX_STRING 64 46 | #define MAX_NAME 16 47 | 48 | #define WHITESPACE " \t\r\n\f" 49 | 50 | #define MAX_ATOM_TYPES 100 51 | #define MAX_BOND_TYPES 200 52 | #define MAX_ANGLE_TYPES 300 53 | #define MAX_DIHEDRAL_TYPES 400 54 | #define MAX_OOP_TYPES 400 55 | #define MAX_ANGLEANGLE_TYPES 400 56 | #define MAX_TYPES 12000 57 | 58 | #define FF_TYPE_COMMON 1<<0 59 | #define FF_TYPE_CLASS1 1<<1 60 | #define FF_TYPE_CLASS2 1<<2 61 | #define FF_TYPE_OPLSAA 1<<3 62 | 63 | struct ResidueList { 64 | int start; 65 | int end; 66 | char name[MAX_NAME]; 67 | }; 68 | 69 | struct MoleculeList { 70 | int start; 71 | int end; 72 | int no_residues; 73 | struct ResidueList *residue; 74 | }; 75 | 76 | /* Internal coodinate Lists */ 77 | 78 | struct BondList { 79 | int type; 80 | int members[2]; 81 | }; 82 | 83 | struct AngleList { 84 | int type; 85 | int members[3]; 86 | }; 87 | 88 | struct DihedralList { 89 | int type; 90 | int members[4]; 91 | }; 92 | 93 | struct OOPList { 94 | int type; 95 | int members[4]; 96 | }; 97 | 98 | struct AngleAngleList { 99 | int type; 100 | int members[4]; 101 | }; 102 | 103 | /* Internal coodinate Types Lists */ 104 | 105 | 106 | struct AtomTypeList 107 | { 108 | char potential[5]; 109 | double mass; 110 | double params[2]; 111 | int no_connect; 112 | }; 113 | 114 | struct BondTypeList { 115 | int types[2]; 116 | double params[4]; 117 | }; 118 | 119 | struct AngleTypeList { 120 | int types[3]; 121 | double params[4]; 122 | double bondangle_cross_term[4]; 123 | double bondbond_cross_term[3]; 124 | }; 125 | 126 | struct DihedralTypeList { 127 | int types[4]; 128 | double params[6]; 129 | double endbonddihedral_cross_term[8]; 130 | double midbonddihedral_cross_term[4]; 131 | double angledihedral_cross_term[8]; 132 | double angleangledihedral_cross_term[3]; 133 | double bond13_cross_term[3]; 134 | }; 135 | 136 | struct OOPTypeList { 137 | int types[4]; 138 | double params[3]; 139 | double angleangle_params[6]; 140 | }; 141 | 142 | struct AngleAngleTypeList { 143 | int types[4]; 144 | double params[6]; 145 | }; 146 | 147 | /* ---------------------------------------------- */ 148 | 149 | struct Atom { 150 | int molecule; /* molecule id */ 151 | int no; /* atom id */ 152 | char name[MAX_NAME]; /* atom name */ 153 | double x[3]; /* position vector */ 154 | int image[3]; /* image flag */ 155 | char potential[6]; /* atom potential type */ 156 | char element[4]; /* atom element */ 157 | double q; /* charge */ 158 | char residue_string[MAX_NAME]; /* residue string */ 159 | int no_connect; /* number of connections to atom */ 160 | char connections[MAX_CONNECTIONS][MAX_STRING]; /* long form, connection name*/ 161 | double bond_order[MAX_CONNECTIONS]; 162 | int conn_no[MAX_CONNECTIONS]; /* Atom number to which atom is connected */ 163 | int type; 164 | }; 165 | 166 | extern char *rootname; 167 | extern char *FrcFileName; 168 | extern double pbc[6]; /* A, B, C, alpha, beta, gamma */ 169 | extern double box[3][3]; /* hi/lo for x/y/z and xy, xz, yz for triclinic */ 170 | extern double shift[3]; /* shift vector for all coordinates and box positions */ 171 | extern int periodic; /* 0= nonperiodic 1= 3-D periodic */ 172 | extern int TriclinicFlag; /* 0= Orthogonal 1= Triclinic */ 173 | extern int forcefield; /* BitMask: the value FF_TYPE_COMMON is set for common components of the options below, 174 | * FF_TYPE_CLASS1 = ClassI, FF_TYPE_CLASS2 = ClassII, FF_TYPE_OPLSAA = OPLS-AA*/ 175 | extern int ljtypeflag; /* how LJ parameters are stored: 0 = A-B, 1 = r-eps */ 176 | extern int centerflag; /* 1= center box 0= keep box */ 177 | extern int hintflag; /* 1= print style hint comments 0= no hints */ 178 | extern int pflag; /* print level: 0, 1, 2, 3 */ 179 | extern int iflag; /* 0 stop at errors 1 = ignore errors */ 180 | extern int *no_atoms; 181 | extern int no_molecules; 182 | extern int replicate[3]; 183 | extern int total_no_atoms; 184 | extern int total_no_bonds; 185 | extern int total_no_angles; 186 | extern int total_no_dihedrals; 187 | extern int total_no_angle_angles; 188 | extern int total_no_oops; 189 | extern int no_atom_types; 190 | extern int no_bond_types; 191 | extern int no_angle_types; 192 | extern int no_dihedral_types; 193 | extern int no_oop_types; 194 | extern int no_angleangle_types; 195 | extern FILE *CarF; 196 | extern FILE *FrcF; 197 | extern FILE *PrmF; 198 | extern FILE *MdfF; 199 | extern FILE *RptF; 200 | extern struct Atom *atoms; 201 | extern struct MoleculeList *molecule; 202 | extern struct BondList *bonds; 203 | extern struct AngleList *angles; 204 | extern struct DihedralList *dihedrals; 205 | extern struct OOPList *oops; 206 | extern struct AngleAngleList *angleangles; 207 | extern struct AtomTypeList *atomtypes; 208 | extern struct BondTypeList *bondtypes; 209 | extern struct AngleTypeList *angletypes; 210 | extern struct DihedralTypeList *dihedraltypes; 211 | extern struct OOPTypeList *ooptypes; 212 | extern struct AngleAngleTypeList *angleangletypes; 213 | 214 | extern void FrcMenu(); 215 | extern void ReadCarFile(); 216 | extern void ReadMdfFile(); 217 | extern void ReadFrcFile(); 218 | extern void ClearFrcData(); 219 | extern void MakeLists(); 220 | extern void GetParameters(); 221 | extern void CheckLists(); 222 | extern void WriteDataFile(char *); 223 | 224 | extern void set_box(double box[3][3], double *h, double *h_inv); 225 | extern void lamda2x(double *lamda, double *x, double *h, double *boxlo); 226 | extern void x2lamda(double *x, double *lamda, double *h_inv, double *boxlo); 227 | 228 | extern void condexit(int); 229 | -------------------------------------------------------------------------------- /msi2lmp/test/benzene-class1.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Tue Jul 02 12:34:43 2013 5 | PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1) 6 | H1 2.500000000 5.000000000 -5.000000000 BENZ 1 h H 0.102 7 | C2 3.594720000 5.000000000 -5.000000000 BENZ 1 cp C -0.102 8 | C3 4.290270000 6.204730000 -5.000000000 BENZ 1 cp C -0.102 9 | C4 5.681370000 6.204730000 -5.000000000 BENZ 1 cp C -0.102 10 | C5 6.376920000 5.000000000 -5.000000000 BENZ 1 cp C -0.102 11 | C6 5.681370000 3.795270000 -5.000000000 BENZ 1 cp C -0.102 12 | C7 4.290270000 3.795270000 -5.000000000 BENZ 1 cp C -0.102 13 | H8 7.471640000 5.000000000 -5.000000000 BENZ 1 h H 0.102 14 | H9 3.742910000 7.152785000 -5.000000000 BENZ 1 h H 0.102 15 | H10 6.228730000 7.152785000 -5.000000000 BENZ 1 h H 0.102 16 | H11 6.228730000 2.847215000 -5.000000000 BENZ 1 h H 0.102 17 | H12 3.742910000 2.847215000 -5.000000000 BENZ 1 h H 0.102 18 | end 19 | end 20 | -------------------------------------------------------------------------------- /msi2lmp/test/benzene-class1.mdf: -------------------------------------------------------------------------------- 1 | !BIOSYM molecular_data 4 2 | 3 | !Date: Tue Jul 02 12:34:43 2013 Materials Studio Generated MDF file 4 | 5 | #topology 6 | 7 | @column 1 element 8 | @column 2 atom_type 9 | @column 3 charge_group 10 | @column 4 isotope 11 | @column 5 formal_charge 12 | @column 6 charge 13 | @column 7 switching_atom 14 | @column 8 oop_flag 15 | @column 9 chirality_flag 16 | @column 10 occupancy 17 | @column 11 xray_temp_factor 18 | @column 12 connections 19 | 20 | @molecule benzene 21 | 22 | XXXX_1:H1 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C2 23 | XXXX_1:C2 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 H1 C3/1.5 C7/1.5 24 | XXXX_1:C3 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C2/1.5 C4/1.5 H9 25 | XXXX_1:C4 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C3/1.5 C5/1.5 H10 26 | XXXX_1:C5 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C4/1.5 H8 C6/1.5 27 | XXXX_1:C6 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C5/1.5 C7/1.5 H11 28 | XXXX_1:C7 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C2/1.5 C6/1.5 H12 29 | XXXX_1:H8 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C5 30 | XXXX_1:H9 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C3 31 | XXXX_1:H10 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C4 32 | XXXX_1:H11 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C6 33 | XXXX_1:H12 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C7 34 | 35 | ! 36 | #symmetry 37 | @periodicity 3 xyz 38 | @group (P1) 39 | 40 | #end 41 | -------------------------------------------------------------------------------- /msi2lmp/test/benzene-class2a.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Tue Jul 02 12:34:43 2013 5 | PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1) 6 | H1 2.500000000 5.000000000 -5.000000000 XXXX 1 h1 H 0.102 7 | C2 3.594720000 5.000000000 -5.000000000 XXXX 1 c3a C -0.102 8 | C3 4.290270000 6.204730000 -5.000000000 XXXX 1 c3a C -0.102 9 | C4 5.681370000 6.204730000 -5.000000000 XXXX 1 c3a C -0.102 10 | C5 6.376920000 5.000000000 -5.000000000 XXXX 1 c3a C -0.102 11 | C6 5.681370000 3.795270000 -5.000000000 XXXX 1 c3a C -0.102 12 | C7 4.290270000 3.795270000 -5.000000000 XXXX 1 c3a C -0.102 13 | H8 7.471640000 5.000000000 -5.000000000 XXXX 1 h1 H 0.102 14 | H9 3.742910000 7.152785000 -5.000000000 XXXX 1 h1 H 0.102 15 | H10 6.228730000 7.152785000 -5.000000000 XXXX 1 h1 H 0.102 16 | H11 6.228730000 2.847215000 -5.000000000 XXXX 1 h1 H 0.102 17 | H12 3.742910000 2.847215000 -5.000000000 XXXX 1 h1 H 0.102 18 | end 19 | end 20 | -------------------------------------------------------------------------------- /msi2lmp/test/benzene-class2a.mdf: -------------------------------------------------------------------------------- 1 | !BIOSYM molecular_data 4 2 | 3 | !Date: Tue Jul 02 12:34:43 2013 Materials Studio Generated MDF file 4 | 5 | #topology 6 | 7 | @column 1 element 8 | @column 2 atom_type 9 | @column 3 charge_group 10 | @column 4 isotope 11 | @column 5 formal_charge 12 | @column 6 charge 13 | @column 7 switching_atom 14 | @column 8 oop_flag 15 | @column 9 chirality_flag 16 | @column 10 occupancy 17 | @column 11 xray_temp_factor 18 | @column 12 connections 19 | 20 | @molecule benzene 21 | 22 | XXXX_1:H1 H h1 ? 0 0 0.1020 0 0 8 1.0000 0.0000 C2 23 | XXXX_1:C2 C c3a ? 0 0 -0.1020 0 0 8 1.0000 0.0000 H1 C3/1.5 C7/1.5 24 | XXXX_1:C3 C c3a ? 0 0 -0.1020 0 0 8 1.0000 0.0000 C2/1.5 C4/1.5 H9 25 | XXXX_1:C4 C c3a ? 0 0 -0.1020 0 0 8 1.0000 0.0000 C3/1.5 C5/1.5 H10 26 | XXXX_1:C5 C c3a ? 0 0 -0.1020 0 0 8 1.0000 0.0000 C4/1.5 H8 C6/1.5 27 | XXXX_1:C6 C c3a ? 0 0 -0.1020 0 0 8 1.0000 0.0000 C5/1.5 C7/1.5 H11 28 | XXXX_1:C7 C c3a ? 0 0 -0.1020 0 0 8 1.0000 0.0000 C2/1.5 C6/1.5 H12 29 | XXXX_1:H8 H h1 ? 0 0 0.1020 0 0 8 1.0000 0.0000 C5 30 | XXXX_1:H9 H h1 ? 0 0 0.1020 0 0 8 1.0000 0.0000 C3 31 | XXXX_1:H10 H h1 ? 0 0 0.1020 0 0 8 1.0000 0.0000 C4 32 | XXXX_1:H11 H h1 ? 0 0 0.1020 0 0 8 1.0000 0.0000 C6 33 | XXXX_1:H12 H h1 ? 0 0 0.1020 0 0 8 1.0000 0.0000 C7 34 | 35 | ! 36 | #symmetry 37 | @periodicity 3 xyz 38 | @group (P1) 39 | 40 | #end 41 | -------------------------------------------------------------------------------- /msi2lmp/test/benzene-class2b.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Tue Jul 02 12:34:43 2013 5 | PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1) 6 | H1 2.500000000 5.000000000 -5.000000000 XXXX 1 h H 0.102 7 | C2 3.594720000 5.000000000 -5.000000000 XXXX 1 cp C -0.102 8 | C3 4.290270000 6.204730000 -5.000000000 XXXX 1 cp C -0.102 9 | C4 5.681370000 6.204730000 -5.000000000 XXXX 1 cp C -0.102 10 | C5 6.376920000 5.000000000 -5.000000000 XXXX 1 cp C -0.102 11 | C6 5.681370000 3.795270000 -5.000000000 XXXX 1 cp C -0.102 12 | C7 4.290270000 3.795270000 -5.000000000 XXXX 1 cp C -0.102 13 | H8 7.471640000 5.000000000 -5.000000000 XXXX 1 h H 0.102 14 | H9 3.742910000 7.152785000 -5.000000000 XXXX 1 h H 0.102 15 | H10 6.228730000 7.152785000 -5.000000000 XXXX 1 h H 0.102 16 | H11 6.228730000 2.847215000 -5.000000000 XXXX 1 h H 0.102 17 | H12 3.742910000 2.847215000 -5.000000000 XXXX 1 h H 0.102 18 | end 19 | end 20 | -------------------------------------------------------------------------------- /msi2lmp/test/benzene-class2b.mdf: -------------------------------------------------------------------------------- 1 | !BIOSYM molecular_data 4 2 | 3 | !Date: Tue Jul 02 12:34:43 2013 Materials Studio Generated MDF file 4 | 5 | #topology 6 | 7 | @column 1 element 8 | @column 2 atom_type 9 | @column 3 charge_group 10 | @column 4 isotope 11 | @column 5 formal_charge 12 | @column 6 charge 13 | @column 7 switching_atom 14 | @column 8 oop_flag 15 | @column 9 chirality_flag 16 | @column 10 occupancy 17 | @column 11 xray_temp_factor 18 | @column 12 connections 19 | 20 | @molecule benzene 21 | 22 | XXXX_1:H1 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C2 23 | XXXX_1:C2 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 H1 C3/1.5 C7/1.5 24 | XXXX_1:C3 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C2/1.5 C4/1.5 H9 25 | XXXX_1:C4 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C3/1.5 C5/1.5 H10 26 | XXXX_1:C5 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C4/1.5 H8 C6/1.5 27 | XXXX_1:C6 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C5/1.5 C7/1.5 H11 28 | XXXX_1:C7 C cp 1 0 0 -0.1020 0 0 8 1.0000 0.0000 C2/1.5 C6/1.5 H12 29 | XXXX_1:H8 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C5 30 | XXXX_1:H9 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C3 31 | XXXX_1:H10 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C4 32 | XXXX_1:H11 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C6 33 | XXXX_1:H12 H h 1 0 0 0.1020 0 0 8 1.0000 0.0000 C7 34 | 35 | ! 36 | #symmetry 37 | @periodicity 3 xyz 38 | @group (P1) 39 | 40 | #end 41 | -------------------------------------------------------------------------------- /msi2lmp/test/ethane-class1.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Tue Jul 02 12:42:22 2013 5 | PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1) 6 | C1 4.462910000 5.148330000 -5.000410000 XXXX 1 c C -0.080 7 | C2 5.965490000 5.079930000 -4.999750000 XXXX 1 c C -0.080 8 | H3 4.099550000 6.054480000 -5.502500000 XXXX 1 h H 0.027 9 | H4 4.020330000 4.288350000 -5.519840000 XXXX 1 h H 0.027 10 | H5 4.057610000 5.156680000 -3.980190000 XXXX 1 h H 0.027 11 | H6 6.409980000 5.944880000 -4.490510000 XXXX 1 h H 0.027 12 | H7 6.329880000 4.179410000 -4.488110000 XXXX 1 h H 0.027 13 | H8 6.370610000 5.061380000 -6.019850000 XXXX 1 h H 0.027 14 | end 15 | end 16 | -------------------------------------------------------------------------------- /msi2lmp/test/ethane-class1.mdf: -------------------------------------------------------------------------------- 1 | !BIOSYM molecular_data 4 2 | 3 | !Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file 4 | 5 | #topology 6 | 7 | @column 1 element 8 | @column 2 atom_type 9 | @column 3 charge_group 10 | @column 4 isotope 11 | @column 5 formal_charge 12 | @column 6 charge 13 | @column 7 switching_atom 14 | @column 8 oop_flag 15 | @column 9 chirality_flag 16 | @column 10 occupancy 17 | @column 11 xray_temp_factor 18 | @column 12 connections 19 | 20 | @molecule ethane 21 | 22 | XXXX_1:C1 C c 1 0 0 -0.0800 0 0 8 1.0000 0.0000 C2 H3 H4 H5 23 | XXXX_1:C2 C c 1 0 0 -0.0800 0 0 8 1.0000 0.0000 C1 H6 H7 H8 24 | XXXX_1:H3 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1 25 | XXXX_1:H4 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1 26 | XXXX_1:H5 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1 27 | XXXX_1:H6 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2 28 | XXXX_1:H7 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2 29 | XXXX_1:H8 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2 30 | 31 | ! 32 | #symmetry 33 | @periodicity 3 xyz 34 | @group (P1) 35 | 36 | #end 37 | -------------------------------------------------------------------------------- /msi2lmp/test/ethane-class2a.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Tue Jul 02 12:42:22 2013 5 | PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1) 6 | C1 4.462910000 5.148330000 -5.000410000 XXXX 1 c4 C -0.080 7 | C2 5.965490000 5.079930000 -4.999750000 XXXX 1 c4 C -0.080 8 | H3 4.099550000 6.054480000 -5.502500000 XXXX 1 h1 H 0.027 9 | H4 4.020330000 4.288350000 -5.519840000 XXXX 1 h1 H 0.027 10 | H5 4.057610000 5.156680000 -3.980190000 XXXX 1 h1 H 0.027 11 | H6 6.409980000 5.944880000 -4.490510000 XXXX 1 h1 H 0.027 12 | H7 6.329880000 4.179410000 -4.488110000 XXXX 1 h1 H 0.027 13 | H8 6.370610000 5.061380000 -6.019850000 XXXX 1 h1 H 0.027 14 | end 15 | end 16 | -------------------------------------------------------------------------------- /msi2lmp/test/ethane-class2a.mdf: -------------------------------------------------------------------------------- 1 | !BIOSYM molecular_data 4 2 | 3 | !Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file 4 | 5 | #topology 6 | 7 | @column 1 element 8 | @column 2 atom_type 9 | @column 3 charge_group 10 | @column 4 isotope 11 | @column 5 formal_charge 12 | @column 6 charge 13 | @column 7 switching_atom 14 | @column 8 oop_flag 15 | @column 9 chirality_flag 16 | @column 10 occupancy 17 | @column 11 xray_temp_factor 18 | @column 12 connections 19 | 20 | @molecule ethane 21 | 22 | XXXX_1:C1 C c4 1 0 0 -0.0800 0 0 8 1.0000 0.0000 C2 H3 H4 H5 23 | XXXX_1:C2 C c4 1 0 0 -0.0800 0 0 8 1.0000 0.0000 C1 H6 H7 H8 24 | XXXX_1:H3 H h1 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1 25 | XXXX_1:H4 H h1 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1 26 | XXXX_1:H5 H h1 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1 27 | XXXX_1:H6 H h1 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2 28 | XXXX_1:H7 H h1 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2 29 | XXXX_1:H8 H h1 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2 30 | 31 | ! 32 | #symmetry 33 | @periodicity 3 xyz 34 | @group (P1) 35 | 36 | #end 37 | -------------------------------------------------------------------------------- /msi2lmp/test/ethane-class2b.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Tue Jul 02 12:42:22 2013 5 | PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1) 6 | C1 4.462910000 5.148330000 -5.000410000 XXXX 1 c C -0.080 7 | C2 5.965490000 5.079930000 -4.999750000 XXXX 1 c C -0.080 8 | H3 4.099550000 6.054480000 -5.502500000 XXXX 1 h H 0.027 9 | H4 4.020330000 4.288350000 -5.519840000 XXXX 1 h H 0.027 10 | H5 4.057610000 5.156680000 -3.980190000 XXXX 1 h H 0.027 11 | H6 6.409980000 5.944880000 -4.490510000 XXXX 1 h H 0.027 12 | H7 6.329880000 4.179410000 -4.488110000 XXXX 1 h H 0.027 13 | H8 6.370610000 5.061380000 -6.019850000 XXXX 1 h H 0.027 14 | end 15 | end 16 | -------------------------------------------------------------------------------- /msi2lmp/test/ethane-class2b.mdf: -------------------------------------------------------------------------------- 1 | !BIOSYM molecular_data 4 2 | 3 | !Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file 4 | 5 | #topology 6 | 7 | @column 1 element 8 | @column 2 atom_type 9 | @column 3 charge_group 10 | @column 4 isotope 11 | @column 5 formal_charge 12 | @column 6 charge 13 | @column 7 switching_atom 14 | @column 8 oop_flag 15 | @column 9 chirality_flag 16 | @column 10 occupancy 17 | @column 11 xray_temp_factor 18 | @column 12 connections 19 | 20 | @molecule ethane 21 | 22 | XXXX_1:C1 C c 1 0 0 -0.0800 0 0 8 1.0000 0.0000 C2 H3 H4 H5 23 | XXXX_1:C2 C c 1 0 0 -0.0800 0 0 8 1.0000 0.0000 C1 H6 H7 H8 24 | XXXX_1:H3 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1 25 | XXXX_1:H4 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1 26 | XXXX_1:H5 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C1 27 | XXXX_1:H6 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2 28 | XXXX_1:H7 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2 29 | XXXX_1:H8 H h 1 0 0 0.0270 0 0 8 1.0000 0.0000 C2 30 | 31 | ! 32 | #symmetry 33 | @periodicity 3 xyz 34 | @group (P1) 35 | 36 | #end 37 | -------------------------------------------------------------------------------- /msi2lmp/test/ethane-oplsaa.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Tue Jul 02 12:42:22 2013 5 | PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1) 6 | C1 4.462910000 5.148330000 -5.000410000 XXXX 1 CT C -0.180 7 | C2 5.965490000 5.079930000 -4.999750000 XXXX 1 CT C -0.180 8 | H3 4.099550000 6.054480000 -5.502500000 XXXX 1 HC H 0.060 9 | H4 4.020330000 4.288350000 -5.519840000 XXXX 1 HC H 0.060 10 | H5 4.057610000 5.156680000 -3.980190000 XXXX 1 HC H 0.060 11 | H6 6.409980000 5.944880000 -4.490510000 XXXX 1 HC H 0.060 12 | H7 6.329880000 4.179410000 -4.488110000 XXXX 1 HC H 0.060 13 | H8 6.370610000 5.061380000 -6.019850000 XXXX 1 HC H 0.060 14 | end 15 | end 16 | -------------------------------------------------------------------------------- /msi2lmp/test/ethane-oplsaa.mdf: -------------------------------------------------------------------------------- 1 | !BIOSYM molecular_data 4 2 | 3 | !Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file 4 | 5 | #topology 6 | 7 | @column 1 element 8 | @column 2 atom_type 9 | @column 3 charge_group 10 | @column 4 isotope 11 | @column 5 formal_charge 12 | @column 6 charge 13 | @column 7 switching_atom 14 | @column 8 oop_flag 15 | @column 9 chirality_flag 16 | @column 10 occupancy 17 | @column 11 xray_temp_factor 18 | @column 12 connections 19 | 20 | @molecule ethane 21 | 22 | XXXX_1:C1 C CT 1 0 0 -0.1800 0 0 8 1.0000 0.0000 C2 H3 H4 H5 23 | XXXX_1:C2 C CT 1 0 0 -0.1800 0 0 8 1.0000 0.0000 C1 H6 H7 H8 24 | XXXX_1:H3 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C1 25 | XXXX_1:H4 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C1 26 | XXXX_1:H5 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C1 27 | XXXX_1:H6 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C2 28 | XXXX_1:H7 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C2 29 | XXXX_1:H8 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C2 30 | 31 | ! 32 | #symmetry 33 | @periodicity 3 xyz 34 | @group (P1) 35 | 36 | #end 37 | -------------------------------------------------------------------------------- /msi2lmp/test/h2-h2o-class1.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Tue Jul 02 12:42:22 2013 5 | PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1) 6 | H1 4.600000000 5.000000000 2.500000000 HYDR 1 h H 0.000 7 | H2 5.400000000 5.000000000 2.500000000 HYDR 1 h H 0.000 8 | end 9 | O1 5.000000000 5.000000000 7.500000000 TIP3 2 otip O -0.834 10 | H2 4.000000000 5.000000000 7.500000000 TIP3 2 htip H 0.417 11 | H3 5.000000000 4.000000000 7.500000000 TIP3 2 htip H 0.417 12 | end 13 | end 14 | -------------------------------------------------------------------------------- /msi2lmp/test/h2-h2o-class1.mdf: -------------------------------------------------------------------------------- 1 | !BIOSYM molecular_data 4 2 | 3 | !Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file 4 | 5 | #topology 6 | 7 | @column 1 element 8 | @column 2 atom_type 9 | @column 3 charge_group 10 | @column 4 isotope 11 | @column 5 formal_charge 12 | @column 6 charge 13 | @column 7 switching_atom 14 | @column 8 oop_flag 15 | @column 9 chirality_flag 16 | @column 10 occupancy 17 | @column 11 xray_temp_factor 18 | @column 12 connections 19 | 20 | @molecule hydrogen 21 | 22 | HYDR_1:H1 H h 1 0 0 0.0000 0 0 8 1.0000 0.0000 H2 23 | HYDR_1:H2 H h 1 0 0 0.0000 0 0 8 1.0000 0.0000 H1 24 | TIP3_1:O1 O otip 2 0 0 -0.8340 0 0 8 1.0000 0.0000 H2 H3 25 | TIP3_1:H2 H htip 2 0 0 0.4170 0 0 8 1.0000 0.0000 O1 26 | TIP3_1:H3 H htip 2 0 0 0.4170 0 0 8 1.0000 0.0000 O1 27 | 28 | ! 29 | #symmetry 30 | @periodicity 3 xyz 31 | @group (P1) 32 | 33 | #end 34 | -------------------------------------------------------------------------------- /msi2lmp/test/h2-h2o-class2b.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Tue Jul 02 12:42:22 2013 5 | PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1) 6 | O1 5.000000000 5.000000000 2.500000000 TIP3 2 o* O -0.834 7 | H2 4.000000000 5.000000000 2.500000000 TIP3 2 h* H 0.417 8 | H3 5.000000000 4.000000000 2.500000000 TIP3 2 h* H 0.417 9 | end 10 | H1 4.600000000 5.000000000 7.500000000 HYDR 1 h H 0.000 11 | H2 5.400000000 5.000000000 7.500000000 HYDR 1 h H 0.000 12 | end 13 | end 14 | -------------------------------------------------------------------------------- /msi2lmp/test/h2-h2o-class2b.mdf: -------------------------------------------------------------------------------- 1 | !BIOSYM molecular_data 4 2 | 3 | !Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file 4 | 5 | #topology 6 | 7 | @column 1 element 8 | @column 2 atom_type 9 | @column 3 charge_group 10 | @column 4 isotope 11 | @column 5 formal_charge 12 | @column 6 charge 13 | @column 7 switching_atom 14 | @column 8 oop_flag 15 | @column 9 chirality_flag 16 | @column 10 occupancy 17 | @column 11 xray_temp_factor 18 | @column 12 connections 19 | 20 | @molecule hydrogen 21 | 22 | TIP3_1:O1 O o* 1 0 0 -0.8340 0 0 8 1.0000 0.0000 H2 H3 23 | TIP3_1:H2 H h* 1 0 0 0.4170 0 0 8 1.0000 0.0000 O1 24 | TIP3_1:H3 H h* 1 0 0 0.4170 0 0 8 1.0000 0.0000 O1 25 | HYDR_1:H1 H h 2 0 0 0.0000 0 0 8 1.0000 0.0000 H2 26 | HYDR_1:H2 H h 2 0 0 0.0000 0 0 8 1.0000 0.0000 H1 27 | 28 | ! 29 | #symmetry 30 | @periodicity 3 xyz 31 | @group (P1) 32 | 33 | #end 34 | -------------------------------------------------------------------------------- /msi2lmp/test/hap_crystal-class1.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Sat Sep 28 14:53:25 2013 5 | PBC 9.4214 18.8428 6.8814 90.0000 90.0000 90.0000 (P1) 6 | O1 -1.624219154 8.097696078 1.776747746 XXXX 1 o O -0.587 7 | O2 1.502039588 5.454548283 5.208548215 XXXX 1 o O -0.588 8 | O3 5.473135150 9.582203385 1.698707871 XXXX 1 o O -0.588 9 | O4 1.017177018 7.836457987 1.655336849 XXXX 1 o O -0.569 10 | O5 2.128465751 5.133975314 1.682995589 XXXX 1 o O -0.568 11 | O6 -3.906651937 8.881489521 5.078345256 XXXX 1 o O -0.569 12 | O7 -0.505405628 6.104981557 0.520103175 XXXX 1 o O -0.593 13 | O8 4.368060853 4.686240017 0.509230529 XXXX 1 o O -0.598 14 | O9 -3.159612633 6.680696169 3.970761259 XXXX 1 o O -0.593 15 | O10 -0.340215093 6.181566449 3.029805285 XXXX 1 o O -0.585 16 | O11 4.259096511 4.745758541 3.021092421 XXXX 1 o O -0.576 17 | O12 -3.202135223 6.888148742 6.479770697 XXXX 1 o O -0.586 18 | Ca1 -2.382573017 9.453046931 0.006968682 XXXX 1 ca+ Ca 1.255 19 | Ca2 -2.325796023 9.576218139 3.428878127 XXXX 1 ca+ Ca 1.254 20 | Ca3 -0.076380180 4.079881499 1.745044087 XXXX 1 ca+ Ca 1.217 21 | Ca4 -5.921566269 10.257604097 5.121788234 XXXX 1 ca+ Ca 1.216 22 | Ca5 -1.211278300 6.053987274 5.191326594 XXXX 1 ca+ Ca 1.216 23 | P1 -0.385120417 7.101979887 1.743525377 XXXX 1 p P 0.480 24 | P2 3.460425980 4.274945926 1.740130960 XXXX 1 p P 0.481 25 | P3 -3.986908229 7.300465906 5.169344339 XXXX 1 p P 0.479 26 | O13 7.064357124 4.080776384 2.022615052 XXXX 1 o O -0.865 27 | H1 7.062035079 4.085255630 2.987706372 XXXX 1 ho H 0.266 28 | O14 6.334919154 0.061475662 5.217447746 XXXX 1 o O -0.587 29 | O15 3.208660412 2.704623456 1.767848215 XXXX 1 o O -0.588 30 | O16 -10.183835150 14.895311833 5.139407871 XXXX 1 o O -0.588 31 | O17 3.693522982 0.322713752 5.096036849 XXXX 1 o O -0.569 32 | O18 2.582234249 3.025196425 5.123695589 XXXX 1 o O -0.568 33 | O19 8.617351937 -0.722317782 1.637645256 XXXX 1 o O -0.569 34 | O20 5.216105628 2.054190182 3.960803175 XXXX 1 o O -0.593 35 | O21 0.342639147 3.472931722 3.949930529 XXXX 1 o O -0.598 36 | O22 7.870312633 1.478475570 0.530061259 XXXX 1 o O -0.593 37 | O23 5.050915093 1.977605290 6.470505285 XXXX 1 o O -0.585 38 | O24 0.451603489 3.413413198 6.461792421 XXXX 1 o O -0.576 39 | O25 7.912835223 1.271022997 3.039070697 XXXX 1 o O -0.586 40 | Ca6 -2.328126983 15.024468286 3.447668682 XXXX 1 ca+ Ca 1.255 41 | Ca7 -2.384903977 14.901297078 6.869578127 XXXX 1 ca+ Ca 1.254 42 | Ca8 4.787080180 4.079290240 5.185744087 XXXX 1 ca+ Ca 1.217 43 | Ca9 1.210866269 14.219911120 1.681088234 XXXX 1 ca+ Ca 1.216 44 | Ca10 5.921978300 2.105184465 1.750626594 XXXX 1 ca+ Ca 1.216 45 | P4 5.095820417 1.057191852 5.184225377 XXXX 1 p P 0.480 46 | P5 1.250274020 3.884225813 5.180830960 XXXX 1 p P 0.481 47 | P6 8.697608229 0.858705833 1.728644339 XXXX 1 p P 0.479 48 | O26 -2.353657124 4.078395355 5.463315052 XXXX 1 o O -0.865 49 | H2 -2.351335079 4.073916109 6.428406372 XXXX 1 ho H 0.266 50 | O27 1.624219154 8.220647401 5.104652254 XXXX 1 o O -0.587 51 | O28 -1.502039588 10.863795195 1.672851785 XXXX 1 o O -0.588 52 | O29 -5.473135150 6.736140093 5.182692129 XXXX 1 o O -0.588 53 | O30 -1.017177018 8.481885491 5.226063151 XXXX 1 o O -0.569 54 | O31 -2.128465751 11.184368164 5.198404411 XXXX 1 o O -0.568 55 | O32 3.906651937 7.436853957 1.803054744 XXXX 1 o O -0.569 56 | O33 0.505405628 10.213361921 6.361296825 XXXX 1 o O -0.593 57 | O34 -4.368060853 11.632103462 6.372169471 XXXX 1 o O -0.598 58 | O35 3.159612633 9.637647309 2.910638741 XXXX 1 o O -0.593 59 | O36 0.340215093 10.136777029 3.851594715 XXXX 1 o O -0.585 60 | O37 -4.259096511 11.572584937 3.860307579 XXXX 1 o O -0.576 61 | O38 3.202135223 9.430194736 0.401629303 XXXX 1 o O -0.586 62 | Ca11 2.382573017 6.865296547 6.874431318 XXXX 1 ca+ Ca 1.255 63 | Ca12 2.325796023 6.742125339 3.452521873 XXXX 1 ca+ Ca 1.254 64 | Ca13 0.076380180 12.238461979 5.136355913 XXXX 1 ca+ Ca 1.217 65 | Ca14 5.921566269 6.060739381 1.759611766 XXXX 1 ca+ Ca 1.216 66 | Ca15 1.211278300 10.264356204 1.690073406 XXXX 1 ca+ Ca 1.216 67 | P7 0.385120417 9.216363591 5.137874623 XXXX 1 p P 0.480 68 | P8 -3.460425980 12.043397553 5.141269040 XXXX 1 p P 0.481 69 | P9 3.986908229 9.017877573 1.712055661 XXXX 1 p P 0.479 70 | O39 -7.064357124 12.237567095 4.858784948 XXXX 1 o O -0.865 71 | H3 -7.062035079 12.233087848 3.893693628 XXXX 1 ho H 0.266 72 | O40 -6.334919154 16.256867817 1.663952254 XXXX 1 o O -0.587 73 | O41 -3.208660412 13.613720023 5.113551785 XXXX 1 o O -0.588 74 | O42 10.183835150 1.423031646 1.741992129 XXXX 1 o O -0.588 75 | O43 -3.693522982 15.995629726 1.785363151 XXXX 1 o O -0.569 76 | O44 -2.582234249 13.293147054 1.757704411 XXXX 1 o O -0.568 77 | O45 -8.617351937 17.040661261 5.243754744 XXXX 1 o O -0.569 78 | O46 -5.216105628 14.264153297 2.920596825 XXXX 1 o O -0.593 79 | O47 -0.342639147 12.845411756 2.931469471 XXXX 1 o O -0.598 80 | O48 -7.870312633 14.839867909 6.351338741 XXXX 1 o O -0.593 81 | O49 -5.050915093 14.340738188 0.410894715 XXXX 1 o O -0.585 82 | O50 -0.451603489 12.904930280 0.419607579 XXXX 1 o O -0.576 83 | O51 -7.912835223 15.047320482 3.842329303 XXXX 1 o O -0.586 84 | Ca16 2.328126983 1.293875192 3.433731318 XXXX 1 ca+ Ca 1.255 85 | Ca17 2.384903977 1.417046400 0.011821873 XXXX 1 ca+ Ca 1.254 86 | Ca18 -4.787080180 12.239053239 1.695655913 XXXX 1 ca+ Ca 1.217 87 | Ca19 -1.210866269 2.098432358 5.200311766 XXXX 1 ca+ Ca 1.216 88 | Ca20 -5.921978300 14.213159014 5.130773406 XXXX 1 ca+ Ca 1.216 89 | P10 -5.095820417 15.261151626 1.697174623 XXXX 1 p P 0.480 90 | P11 -1.250274020 12.434117665 1.700569040 XXXX 1 p P 0.481 91 | P12 -8.697608229 15.459637645 5.152755661 XXXX 1 p P 0.479 92 | O52 2.353657124 12.239948123 1.418084948 XXXX 1 o O -0.865 93 | H4 2.351335079 12.244427370 0.452993628 XXXX 1 ho H 0.266 94 | end 95 | end 96 | -------------------------------------------------------------------------------- /msi2lmp/test/hap_crystal-class2b.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Sat Sep 28 14:53:25 2013 5 | PBC 9.4214 18.8428 6.8814 90.0000 90.0000 90.0000 (P1) 6 | O1 -1.624219154 8.097696078 1.776747746 XXXX 1 o O -0.587 7 | O2 1.502039588 5.454548283 5.208548215 XXXX 1 o O -0.588 8 | O3 5.473135150 9.582203385 1.698707871 XXXX 1 o O -0.588 9 | O4 1.017177018 7.836457987 1.655336849 XXXX 1 o O -0.569 10 | O5 2.128465751 5.133975314 1.682995589 XXXX 1 o O -0.568 11 | O6 -3.906651937 8.881489521 5.078345256 XXXX 1 o O -0.569 12 | O7 -0.505405628 6.104981557 0.520103175 XXXX 1 o O -0.593 13 | O8 4.368060853 4.686240017 0.509230529 XXXX 1 o O -0.598 14 | O9 -3.159612633 6.680696169 3.970761259 XXXX 1 o O -0.593 15 | O10 -0.340215093 6.181566449 3.029805285 XXXX 1 o O -0.585 16 | O11 4.259096511 4.745758541 3.021092421 XXXX 1 o O -0.576 17 | O12 -3.202135223 6.888148742 6.479770697 XXXX 1 o O -0.586 18 | Ca1 -2.382573017 9.453046931 0.006968682 XXXX 1 ca+ Ca 1.255 19 | Ca2 -2.325796023 9.576218139 3.428878127 XXXX 1 ca+ Ca 1.254 20 | Ca3 -0.076380180 4.079881499 1.745044087 XXXX 1 ca+ Ca 1.217 21 | Ca4 -5.921566269 10.257604097 5.121788234 XXXX 1 ca+ Ca 1.216 22 | Ca5 -1.211278300 6.053987274 5.191326594 XXXX 1 ca+ Ca 1.216 23 | P1 -0.385120417 7.101979887 1.743525377 XXXX 1 p P 0.480 24 | P2 3.460425980 4.274945926 1.740130960 XXXX 1 p P 0.481 25 | P3 -3.986908229 7.300465906 5.169344339 XXXX 1 p P 0.479 26 | O13 7.064357124 4.080776384 2.022615052 XXXX 1 o O -0.865 27 | H1 7.062035079 4.085255630 2.987706372 XXXX 1 ho H 0.266 28 | O14 6.334919154 0.061475662 5.217447746 XXXX 1 o O -0.587 29 | O15 3.208660412 2.704623456 1.767848215 XXXX 1 o O -0.588 30 | O16 -10.183835150 14.895311833 5.139407871 XXXX 1 o O -0.588 31 | O17 3.693522982 0.322713752 5.096036849 XXXX 1 o O -0.569 32 | O18 2.582234249 3.025196425 5.123695589 XXXX 1 o O -0.568 33 | O19 8.617351937 -0.722317782 1.637645256 XXXX 1 o O -0.569 34 | O20 5.216105628 2.054190182 3.960803175 XXXX 1 o O -0.593 35 | O21 0.342639147 3.472931722 3.949930529 XXXX 1 o O -0.598 36 | O22 7.870312633 1.478475570 0.530061259 XXXX 1 o O -0.593 37 | O23 5.050915093 1.977605290 6.470505285 XXXX 1 o O -0.585 38 | O24 0.451603489 3.413413198 6.461792421 XXXX 1 o O -0.576 39 | O25 7.912835223 1.271022997 3.039070697 XXXX 1 o O -0.586 40 | Ca6 -2.328126983 15.024468286 3.447668682 XXXX 1 ca+ Ca 1.255 41 | Ca7 -2.384903977 14.901297078 6.869578127 XXXX 1 ca+ Ca 1.254 42 | Ca8 4.787080180 4.079290240 5.185744087 XXXX 1 ca+ Ca 1.217 43 | Ca9 1.210866269 14.219911120 1.681088234 XXXX 1 ca+ Ca 1.216 44 | Ca10 5.921978300 2.105184465 1.750626594 XXXX 1 ca+ Ca 1.216 45 | P4 5.095820417 1.057191852 5.184225377 XXXX 1 p P 0.480 46 | P5 1.250274020 3.884225813 5.180830960 XXXX 1 p P 0.481 47 | P6 8.697608229 0.858705833 1.728644339 XXXX 1 p P 0.479 48 | O26 -2.353657124 4.078395355 5.463315052 XXXX 1 o O -0.865 49 | H2 -2.351335079 4.073916109 6.428406372 XXXX 1 ho H 0.266 50 | O27 1.624219154 8.220647401 5.104652254 XXXX 1 o O -0.587 51 | O28 -1.502039588 10.863795195 1.672851785 XXXX 1 o O -0.588 52 | O29 -5.473135150 6.736140093 5.182692129 XXXX 1 o O -0.588 53 | O30 -1.017177018 8.481885491 5.226063151 XXXX 1 o O -0.569 54 | O31 -2.128465751 11.184368164 5.198404411 XXXX 1 o O -0.568 55 | O32 3.906651937 7.436853957 1.803054744 XXXX 1 o O -0.569 56 | O33 0.505405628 10.213361921 6.361296825 XXXX 1 o O -0.593 57 | O34 -4.368060853 11.632103462 6.372169471 XXXX 1 o O -0.598 58 | O35 3.159612633 9.637647309 2.910638741 XXXX 1 o O -0.593 59 | O36 0.340215093 10.136777029 3.851594715 XXXX 1 o O -0.585 60 | O37 -4.259096511 11.572584937 3.860307579 XXXX 1 o O -0.576 61 | O38 3.202135223 9.430194736 0.401629303 XXXX 1 o O -0.586 62 | Ca11 2.382573017 6.865296547 6.874431318 XXXX 1 ca+ Ca 1.255 63 | Ca12 2.325796023 6.742125339 3.452521873 XXXX 1 ca+ Ca 1.254 64 | Ca13 0.076380180 12.238461979 5.136355913 XXXX 1 ca+ Ca 1.217 65 | Ca14 5.921566269 6.060739381 1.759611766 XXXX 1 ca+ Ca 1.216 66 | Ca15 1.211278300 10.264356204 1.690073406 XXXX 1 ca+ Ca 1.216 67 | P7 0.385120417 9.216363591 5.137874623 XXXX 1 p P 0.480 68 | P8 -3.460425980 12.043397553 5.141269040 XXXX 1 p P 0.481 69 | P9 3.986908229 9.017877573 1.712055661 XXXX 1 p P 0.479 70 | O39 -7.064357124 12.237567095 4.858784948 XXXX 1 o O -0.865 71 | H3 -7.062035079 12.233087848 3.893693628 XXXX 1 ho H 0.266 72 | O40 -6.334919154 16.256867817 1.663952254 XXXX 1 o O -0.587 73 | O41 -3.208660412 13.613720023 5.113551785 XXXX 1 o O -0.588 74 | O42 10.183835150 1.423031646 1.741992129 XXXX 1 o O -0.588 75 | O43 -3.693522982 15.995629726 1.785363151 XXXX 1 o O -0.569 76 | O44 -2.582234249 13.293147054 1.757704411 XXXX 1 o O -0.568 77 | O45 -8.617351937 17.040661261 5.243754744 XXXX 1 o O -0.569 78 | O46 -5.216105628 14.264153297 2.920596825 XXXX 1 o O -0.593 79 | O47 -0.342639147 12.845411756 2.931469471 XXXX 1 o O -0.598 80 | O48 -7.870312633 14.839867909 6.351338741 XXXX 1 o O -0.593 81 | O49 -5.050915093 14.340738188 0.410894715 XXXX 1 o O -0.585 82 | O50 -0.451603489 12.904930280 0.419607579 XXXX 1 o O -0.576 83 | O51 -7.912835223 15.047320482 3.842329303 XXXX 1 o O -0.586 84 | Ca16 2.328126983 1.293875192 3.433731318 XXXX 1 ca+ Ca 1.255 85 | Ca17 2.384903977 1.417046400 0.011821873 XXXX 1 ca+ Ca 1.254 86 | Ca18 -4.787080180 12.239053239 1.695655913 XXXX 1 ca+ Ca 1.217 87 | Ca19 -1.210866269 2.098432358 5.200311766 XXXX 1 ca+ Ca 1.216 88 | Ca20 -5.921978300 14.213159014 5.130773406 XXXX 1 ca+ Ca 1.216 89 | P10 -5.095820417 15.261151626 1.697174623 XXXX 1 p P 0.480 90 | P11 -1.250274020 12.434117665 1.700569040 XXXX 1 p P 0.481 91 | P12 -8.697608229 15.459637645 5.152755661 XXXX 1 p P 0.479 92 | O52 2.353657124 12.239948123 1.418084948 XXXX 1 o O -0.865 93 | H4 2.351335079 12.244427370 0.452993628 XXXX 1 ho H 0.266 94 | end 95 | end 96 | -------------------------------------------------------------------------------- /msi2lmp/test/hydrogen-class1.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Tue Jul 02 12:42:22 2013 5 | PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1) 6 | H1 4.600000000 5.000000000 5.000000000 HYDR 1 h H 0.000 7 | H2 5.400000000 5.000000000 5.000000000 HYDR 1 h H 0.000 8 | end 9 | end 10 | -------------------------------------------------------------------------------- /msi2lmp/test/hydrogen-class1.mdf: -------------------------------------------------------------------------------- 1 | !BIOSYM molecular_data 4 2 | 3 | !Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file 4 | 5 | #topology 6 | 7 | @column 1 element 8 | @column 2 atom_type 9 | @column 3 charge_group 10 | @column 4 isotope 11 | @column 5 formal_charge 12 | @column 6 charge 13 | @column 7 switching_atom 14 | @column 8 oop_flag 15 | @column 9 chirality_flag 16 | @column 10 occupancy 17 | @column 11 xray_temp_factor 18 | @column 12 connections 19 | 20 | @molecule hydrogen 21 | 22 | HYDR_1:H1 H h 1 0 0 0.0000 0 0 8 1.0000 0.0000 H2 23 | HYDR_1:H2 H h 1 0 0 0.0000 0 0 8 1.0000 0.0000 H1 24 | 25 | ! 26 | #symmetry 27 | @periodicity 3 xyz 28 | @group (P1) 29 | 30 | #end 31 | -------------------------------------------------------------------------------- /msi2lmp/test/hydrogen-class2a.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Tue Jul 02 12:42:22 2013 5 | PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1) 6 | H1 4.600000000 5.000000000 5.000000000 HYDR 1 h1h H 0.000 7 | H2 5.400000000 5.000000000 5.000000000 HYDR 1 h1h H 0.000 8 | end 9 | end 10 | -------------------------------------------------------------------------------- /msi2lmp/test/hydrogen-class2a.mdf: -------------------------------------------------------------------------------- 1 | !BIOSYM molecular_data 4 2 | 3 | !Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file 4 | 5 | #topology 6 | 7 | @column 1 element 8 | @column 2 atom_type 9 | @column 3 charge_group 10 | @column 4 isotope 11 | @column 5 formal_charge 12 | @column 6 charge 13 | @column 7 switching_atom 14 | @column 8 oop_flag 15 | @column 9 chirality_flag 16 | @column 10 occupancy 17 | @column 11 xray_temp_factor 18 | @column 12 connections 19 | 20 | @molecule hydrogen 21 | 22 | HYDR_1:H1 H h1h 1 0 0 0.0000 0 0 8 1.0000 0.0000 H2 23 | HYDR_1:H2 H h1h 1 0 0 0.0000 0 0 8 1.0000 0.0000 H1 24 | 25 | ! 26 | #symmetry 27 | @periodicity 3 xyz 28 | @group (P1) 29 | 30 | #end 31 | -------------------------------------------------------------------------------- /msi2lmp/test/in.PyAC_bulk-clayff: -------------------------------------------------------------------------------- 1 | log log.PyAC_bulk-clayff 2 | units real 3 | boundary p p p 4 | atom_style full 5 | pair_style lj/cut/coul/long 15.0 6 | pair_modify mix geometric 7 | bond_style harmonic 8 | kspace_style pppm 1.0e-5 9 | 10 | read_data PyAC_bulk-clayff.data 11 | 12 | thermo_style multi 13 | minimize 0.0 0.0 100 1000 14 | 15 | write_data PyAC_bulk-clayff.data2 16 | -------------------------------------------------------------------------------- /msi2lmp/test/in.benzene-class1: -------------------------------------------------------------------------------- 1 | log log.benzene-class1 2 | units real 3 | atom_style full 4 | pair_style lj/cut/coul/cut 15.0 5 | bond_style harmonic 6 | angle_style harmonic 7 | dihedral_style harmonic 8 | improper_style cvff 9 | 10 | read_data benzene-class1.data 11 | 12 | thermo_style multi 13 | minimize 0.0 0.0 100 1000 14 | 15 | write_data benzene-class1.data2 16 | -------------------------------------------------------------------------------- /msi2lmp/test/in.benzene-class2a: -------------------------------------------------------------------------------- 1 | log log.benzene-class2a 2 | units real 3 | atom_style full 4 | pair_style lj/class2/coul/cut 15.0 5 | bond_style class2 6 | angle_style class2 7 | dihedral_style class2 8 | improper_style class2 9 | 10 | read_data benzene-class2a.data 11 | 12 | thermo_style multi 13 | minimize 0.0 0.0 100 1000 14 | 15 | write_data benzene-class2a.data2 16 | -------------------------------------------------------------------------------- /msi2lmp/test/in.benzene-class2b: -------------------------------------------------------------------------------- 1 | log log.benzene-class2b 2 | units real 3 | atom_style full 4 | pair_style lj/class2/coul/cut 15.0 5 | bond_style class2 6 | angle_style class2 7 | dihedral_style class2 8 | improper_style class2 9 | 10 | read_data benzene-class2b.data 11 | 12 | thermo_style multi 13 | minimize 0.0 0.0 100 1000 14 | 15 | write_data benzene-class2b.data2 16 | -------------------------------------------------------------------------------- /msi2lmp/test/in.cnt-hexagonal-class1: -------------------------------------------------------------------------------- 1 | log log.cnt-hexagonal-class1 2 | units real 3 | atom_style full 4 | pair_style lj/cut/coul/cut 15.0 5 | bond_style harmonic 6 | angle_style harmonic 7 | dihedral_style harmonic 8 | improper_style cvff 9 | 10 | read_data cnt-hexagonal-class1.data 11 | 12 | thermo_style multi 13 | minimize 0.0 0.0 100 1000 14 | 15 | write_data cnt-hexagonal-class1.data2 16 | -------------------------------------------------------------------------------- /msi2lmp/test/in.cnt-hexagonal-class2a: -------------------------------------------------------------------------------- 1 | log log.cnt-hexagonal-class2a 2 | units real 3 | atom_style full 4 | pair_style lj/class2/coul/cut 15.0 5 | bond_style class2 6 | angle_style class2 7 | dihedral_style class2 8 | improper_style class2 9 | 10 | read_data cnt-hexagonal-class2a.data 11 | 12 | thermo_style multi 13 | minimize 0.0 0.0 100 1000 14 | 15 | write_data cnt-hexagonal-class2a.data2 16 | -------------------------------------------------------------------------------- /msi2lmp/test/in.cnt-hexagonal-class2b: -------------------------------------------------------------------------------- 1 | log log.cnt-hexagonal-class2b 2 | units real 3 | atom_style full 4 | pair_style lj/class2/coul/cut 15.0 5 | bond_style class2 6 | angle_style class2 7 | dihedral_style class2 8 | improper_style class2 9 | 10 | read_data cnt-hexagonal-class2b.data 11 | 12 | thermo_style multi 13 | minimize 0.0 0.0 100 1000 14 | 15 | write_data cnt-hexagonal-class2b.data2 16 | -------------------------------------------------------------------------------- /msi2lmp/test/in.crambin-class1: -------------------------------------------------------------------------------- 1 | log log.crambin-class1 2 | units real 3 | boundary m m m 4 | atom_style full 5 | pair_style lj/cut/coul/cut 15.0 6 | bond_style harmonic 7 | angle_style harmonic 8 | dihedral_style harmonic 9 | improper_style cvff 10 | 11 | read_data crambin-class1.data 12 | 13 | thermo_style multi 14 | minimize 0.0 0.0 100 1000 15 | 16 | write_data crambin-class1.data2 17 | -------------------------------------------------------------------------------- /msi2lmp/test/in.decane-oplsaa: -------------------------------------------------------------------------------- 1 | log log.decane-oplsaa 2 | units real 3 | atom_style full 4 | pair_style lj/cut/coul/cut 15.0 5 | bond_style harmonic 6 | angle_style harmonic 7 | dihedral_style opls 8 | 9 | read_data decane-oplsaa.data 10 | 11 | thermo_style multi 12 | minimize 0.0 0.0 100 1000 13 | 14 | write_data decane-oplsaa.data2 15 | -------------------------------------------------------------------------------- /msi2lmp/test/in.ethane-class1: -------------------------------------------------------------------------------- 1 | log log.ethane-class1 2 | units real 3 | atom_style full 4 | pair_style lj/cut/coul/cut 15.0 5 | bond_style harmonic 6 | angle_style harmonic 7 | dihedral_style harmonic 8 | 9 | read_data ethane-class1.data 10 | 11 | thermo_style multi 12 | minimize 0.0 0.0 100 1000 13 | 14 | write_data ethane-class1.data2 15 | -------------------------------------------------------------------------------- /msi2lmp/test/in.ethane-class2a: -------------------------------------------------------------------------------- 1 | log log.ethane-class2a 2 | units real 3 | atom_style full 4 | pair_style lj/class2/coul/cut 15.0 5 | bond_style class2 6 | angle_style class2 7 | dihedral_style class2 8 | improper_style class2 9 | 10 | read_data ethane-class2a.data 11 | 12 | thermo_style multi 13 | minimize 0.0 0.0 100 1000 14 | 15 | write_data ethane-class2a.data2 16 | -------------------------------------------------------------------------------- /msi2lmp/test/in.ethane-class2b: -------------------------------------------------------------------------------- 1 | log log.ethane-class2b 2 | units real 3 | atom_style full 4 | pair_style lj/class2/coul/cut 15.0 5 | bond_style class2 6 | angle_style class2 7 | dihedral_style class2 8 | improper_style class2 9 | 10 | read_data ethane-class2b.data 11 | 12 | thermo_style multi 13 | minimize 0.0 0.0 100 1000 14 | 15 | write_data ethane-class2b.data2 16 | -------------------------------------------------------------------------------- /msi2lmp/test/in.ethane-oplsaa: -------------------------------------------------------------------------------- 1 | log log.ethane-oplsaa 2 | units real 3 | atom_style full 4 | pair_style lj/cut/coul/cut 15.0 5 | bond_style harmonic 6 | angle_style harmonic 7 | dihedral_style opls 8 | 9 | read_data ethane-oplsaa.data 10 | 11 | thermo_style multi 12 | minimize 0.0 0.0 100 1000 13 | 14 | write_data ethane-oplsaa.data2 15 | -------------------------------------------------------------------------------- /msi2lmp/test/in.h2-h2o-class1: -------------------------------------------------------------------------------- 1 | log log.h2-h2o-class1 2 | units real 3 | atom_style full 4 | pair_style lj/cut/coul/cut 15.0 5 | bond_style harmonic 6 | angle_style harmonic 7 | 8 | read_data h2-h2o-class1.data 9 | 10 | thermo_style multi 11 | minimize 0.0 0.0 100 1000 12 | 13 | write_data h2-h2o-class1.data2 14 | -------------------------------------------------------------------------------- /msi2lmp/test/in.h2-h2o-class2b: -------------------------------------------------------------------------------- 1 | log log.h2-h2o-class2b 2 | units real 3 | atom_style full 4 | pair_style lj/class2/coul/cut 15.0 5 | bond_style class2 6 | angle_style class2 7 | 8 | read_data h2-h2o-class2b.data 9 | 10 | thermo_style multi 11 | minimize 0.0 0.0 100 1000 12 | 13 | write_data h2-h2o-class2b.data2 14 | -------------------------------------------------------------------------------- /msi2lmp/test/in.hap_crystal-class1: -------------------------------------------------------------------------------- 1 | log log.hap_crystal-class1 2 | units real 3 | atom_style full 4 | pair_style lj/cut/coul/cut 15.0 5 | bond_style harmonic 6 | angle_style harmonic 7 | 8 | read_data hap_crystal-class1.data 9 | 10 | thermo_style multi 11 | minimize 0.0 0.0 100 1000 12 | 13 | write_data hap_crystal-class1.data2 14 | -------------------------------------------------------------------------------- /msi2lmp/test/in.hap_crystal-class2b: -------------------------------------------------------------------------------- 1 | log log.hap_crystal-class2b 2 | units real 3 | atom_style full 4 | pair_style lj/class2/coul/cut 15.0 5 | bond_style class2 6 | angle_style class2 7 | improper_style class2 8 | 9 | read_data hap_crystal-class2b.data 10 | 11 | thermo_style multi 12 | minimize 0.0 0.0 100 1000 13 | 14 | write_data hap_crystal-class2b.data2 15 | -------------------------------------------------------------------------------- /msi2lmp/test/in.hydrogen-class1: -------------------------------------------------------------------------------- 1 | log log.hydrogen-class1 2 | units real 3 | atom_style full 4 | pair_style lj/cut/coul/cut 15.0 5 | bond_style harmonic 6 | 7 | read_data hydrogen-class1.data 8 | 9 | thermo_style multi 10 | minimize 0.0 0.0 100 1000 11 | 12 | write_data hydrogen-class1.data2 13 | -------------------------------------------------------------------------------- /msi2lmp/test/in.hydrogen-class2a: -------------------------------------------------------------------------------- 1 | log log.hydrogen-class2a 2 | units real 3 | atom_style full 4 | pair_style lj/class2/coul/cut 15.0 5 | bond_style class2 6 | 7 | read_data hydrogen-class2a.data 8 | 9 | thermo_style multi 10 | minimize 0.0 0.0 100 1000 11 | 12 | write_data hydrogen-class2a.data2 13 | -------------------------------------------------------------------------------- /msi2lmp/test/in.naphthalene-class1: -------------------------------------------------------------------------------- 1 | log log.naphthalene-class1 2 | units real 3 | atom_style full 4 | pair_style lj/cut/coul/cut 15.0 5 | bond_style harmonic 6 | angle_style harmonic 7 | dihedral_style harmonic 8 | improper_style cvff 9 | 10 | read_data naphthalene-class1.data 11 | 12 | thermo_style multi 13 | minimize 0.0 0.0 100 1000 14 | 15 | write_data naphthalene-class1.data2 16 | -------------------------------------------------------------------------------- /msi2lmp/test/in.naphthalene-class2a: -------------------------------------------------------------------------------- 1 | log log.naphthalene-class2a 2 | units real 3 | atom_style full 4 | pair_style lj/class2/coul/cut 15.0 5 | bond_style class2 6 | angle_style class2 7 | dihedral_style class2 8 | improper_style class2 9 | 10 | read_data naphthalene-class2a.data 11 | 12 | thermo_style multi 13 | minimize 0.0 0.0 100 1000 14 | 15 | write_data naphthalene-class2a.data2 16 | -------------------------------------------------------------------------------- /msi2lmp/test/in.naphthalene-class2b: -------------------------------------------------------------------------------- 1 | log log.naphthalene-class2b 2 | units real 3 | atom_style full 4 | pair_style lj/class2/coul/cut 15.0 5 | bond_style class2 6 | angle_style class2 7 | dihedral_style class2 8 | improper_style class2 9 | 10 | read_data naphthalene-class2b.data 11 | 12 | thermo_style multi 13 | minimize 0.0 0.0 100 1000 14 | 15 | write_data naphthalene-class2b.data2 16 | -------------------------------------------------------------------------------- /msi2lmp/test/in.nylon-class1: -------------------------------------------------------------------------------- 1 | log log.nylon-class1 2 | units real 3 | boundary m m m 4 | atom_style full 5 | pair_style lj/cut/coul/cut 15.0 6 | bond_style harmonic 7 | angle_style harmonic 8 | dihedral_style harmonic 9 | improper_style cvff 10 | 11 | read_data nylon-class1.data 12 | 13 | thermo_style multi 14 | minimize 0.0 0.0 100 1000 15 | 16 | write_data nylon-class1.data2 17 | -------------------------------------------------------------------------------- /msi2lmp/test/in.phen3_cff97-class1: -------------------------------------------------------------------------------- 1 | log log.phen3_cff97-class1 2 | boundary m m m 3 | units real 4 | atom_style full 5 | pair_style lj/cut/coul/cut 15.0 6 | bond_style harmonic 7 | angle_style harmonic 8 | dihedral_style harmonic 9 | improper_style cvff 10 | 11 | read_data phen3_cff97-class1.data 12 | 13 | thermo_style multi 14 | minimize 0.0 0.0 100 1000 15 | 16 | write_data phen3_cff97-class1.data2 17 | -------------------------------------------------------------------------------- /msi2lmp/test/in.solv-poly-class2c: -------------------------------------------------------------------------------- 1 | log log.solv-poly-class2c 2 | units real 3 | atom_style full 4 | pair_style lj/class2/coul/long 10.0 5 | bond_style class2 6 | angle_style class2 7 | dihedral_style class2 8 | improper_style class2 9 | kspace_style pppm 1.0e-4 10 | read_data solv-poly-class2c.data 11 | 12 | thermo_style multi 13 | minimize 0.0 0.0 100 1000 14 | 15 | write_data solv-poly-class2c.data2 16 | -------------------------------------------------------------------------------- /msi2lmp/test/in.water-class1: -------------------------------------------------------------------------------- 1 | log log.water-class1 2 | units real 3 | atom_style full 4 | pair_style lj/cut/coul/cut 15.0 5 | bond_style harmonic 6 | angle_style harmonic 7 | 8 | read_data water-class1.data 9 | 10 | thermo_style multi 11 | minimize 0.0 0.0 100 1000 12 | 13 | write_data water-class1.data2 14 | -------------------------------------------------------------------------------- /msi2lmp/test/in.water-class2b: -------------------------------------------------------------------------------- 1 | log log.water-class2b 2 | units real 3 | atom_style full 4 | pair_style lj/class2/coul/cut 15.0 5 | bond_style class2 6 | angle_style class2 7 | 8 | read_data water-class2b.data 9 | 10 | thermo_style multi 11 | minimize 0.0 0.0 100 1000 12 | 13 | write_data water-class2b.data2 14 | -------------------------------------------------------------------------------- /msi2lmp/test/naphthalene-class1.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Tue Jul 02 12:43:30 2013 5 | PBC 20.0000 20.0000 20.0000 90.0000 90.0000 90.0000 (P1) 6 | H1 6.500000000 -9.500000000 -10.000000000 NAPH 1 h H 0.132 7 | C2 7.599900000 -9.500000000 -10.000000000 NAPH 1 cp C -0.128 8 | C3 8.288980000 -8.262840000 -10.000000000 NAPH 1 cp C -0.127 9 | C4 9.661860000 -8.228710000 -10.001500000 NAPH 1 cp C -0.117 10 | C5 10.406020000 -9.440000000 -10.006040000 NAPH 1 cp C -0.037 11 | C6 9.719960000 -10.680950000 -10.004000000 NAPH 1 cp C -0.036 12 | C7 8.297670000 -10.682850000 -10.001160000 NAPH 1 cp C -0.117 13 | H8 7.705780000 -7.329930000 -9.996380000 NAPH 1 h H 0.131 14 | H9 10.206130000 -7.272850000 -10.002830000 NAPH 1 h H 0.133 15 | H10 7.770540000 -11.648530000 -10.000400000 NAPH 1 h H 0.132 16 | C11 11.828680000 -9.441740000 -10.010130000 NAPH 1 cp C -0.119 17 | C12 12.527620000 -10.622850000 -10.015250000 NAPH 1 cp C -0.127 18 | C13 11.844840000 -11.863540000 -10.015940000 NAPH 1 cp C -0.127 19 | C14 10.470950000 -11.888220000 -10.009030000 NAPH 1 cp C -0.118 20 | H15 12.355170000 -8.475370000 -10.009670000 NAPH 1 h H 0.132 21 | H16 13.627550000 -10.611020000 -10.018380000 NAPH 1 h H 0.131 22 | H17 12.414260000 -12.804680000 -10.020060000 NAPH 1 h H 0.133 23 | H18 9.938140000 -12.850570000 -10.009550000 NAPH 1 h H 0.131 24 | end 25 | end 26 | -------------------------------------------------------------------------------- /msi2lmp/test/naphthalene-class1.mdf: -------------------------------------------------------------------------------- 1 | !BIOSYM molecular_data 4 2 | 3 | !Date: Tue Jul 02 12:43:30 2013 Materials Studio Generated MDF file 4 | 5 | #topology 6 | 7 | @column 1 element 8 | @column 2 atom_type 9 | @column 3 charge_group 10 | @column 4 isotope 11 | @column 5 formal_charge 12 | @column 6 charge 13 | @column 7 switching_atom 14 | @column 8 oop_flag 15 | @column 9 chirality_flag 16 | @column 10 occupancy 17 | @column 11 xray_temp_factor 18 | @column 12 connections 19 | 20 | @molecule naphthalene 21 | 22 | NAPH_1:H1 H h 1 0 0 0.1320 0 0 8 1.0000 0.0000 C2 23 | NAPH_1:C2 C cp 1 0 0 -0.1280 0 0 8 1.0000 0.0000 H1 C3/1.5 C7/1.5 24 | NAPH_1:C3 C cp 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C2/1.5 C4/1.5 H8 25 | NAPH_1:C4 C cp 1 0 0 -0.1170 0 0 8 1.0000 0.0000 C3/1.5 C5/1.5 H9 26 | NAPH_1:C5 C cp 1 0 0 -0.0370 0 0 8 1.0000 0.0000 C4/1.5 C6/1.5 C11/1.5 27 | NAPH_1:C6 C cp 1 0 0 -0.0360 0 0 8 1.0000 0.0000 C5/1.5 C7/1.5 C14/1.5 28 | NAPH_1:C7 C cp 1 0 0 -0.1170 0 0 8 1.0000 0.0000 C2/1.5 C6/1.5 H10 29 | NAPH_1:H8 H h 1 0 0 0.1310 0 0 8 1.0000 0.0000 C3 30 | NAPH_1:H9 H h 1 0 0 0.1330 0 0 8 1.0000 0.0000 C4 31 | NAPH_1:H10 H h 1 0 0 0.1320 0 0 8 1.0000 0.0000 C7 32 | NAPH_1:C11 C cp 1 0 0 -0.1190 0 0 8 1.0000 0.0000 C5/1.5 C12/1.5 H15 33 | NAPH_1:C12 C cp 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C11/1.5 C13/1.5 H16 34 | NAPH_1:C13 C cp 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C12/1.5 C14/1.5 H17 35 | NAPH_1:C14 C cp 1 0 0 -0.1180 0 0 8 1.0000 0.0000 C6/1.5 C13/1.5 H18 36 | NAPH_1:H15 H h 1 0 0 0.1320 0 0 8 1.0000 0.0000 C11 37 | NAPH_1:H16 H h 1 0 0 0.1310 0 0 8 1.0000 0.0000 C12 38 | NAPH_1:H17 H h 1 0 0 0.1330 0 0 8 1.0000 0.0000 C13 39 | NAPH_1:H18 H h 1 0 0 0.1310 0 0 8 1.0000 0.0000 C14 40 | 41 | ! 42 | #symmetry 43 | @periodicity 3 xyz 44 | @group (P1) 45 | 46 | #end 47 | -------------------------------------------------------------------------------- /msi2lmp/test/naphthalene-class2a.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Tue Jul 02 12:43:30 2013 5 | PBC 20.0000 20.0000 20.0000 90.0000 90.0000 90.0000 (P1) 6 | H1 6.500000000 -9.500000000 -10.000000000 NAPH 1 h1 H 0.132 7 | C2 7.599900000 -9.500000000 -10.000000000 NAPH 1 c3a C -0.128 8 | C3 8.288980000 -8.262840000 -10.000000000 NAPH 1 c3a C -0.127 9 | C4 9.661860000 -8.228710000 -10.001500000 NAPH 1 c3a C -0.117 10 | C5 10.406020000 -9.440000000 -10.006040000 NAPH 1 c3a C -0.037 11 | C6 9.719960000 -10.680950000 -10.004000000 NAPH 1 c3a C -0.036 12 | C7 8.297670000 -10.682850000 -10.001160000 NAPH 1 c3a C -0.117 13 | H8 7.705780000 -7.329930000 -9.996380000 NAPH 1 h1 H 0.131 14 | H9 10.206130000 -7.272850000 -10.002830000 NAPH 1 h1 H 0.133 15 | H10 7.770540000 -11.648530000 -10.000400000 NAPH 1 h1 H 0.132 16 | C11 11.828680000 -9.441740000 -10.010130000 NAPH 1 c3a C -0.119 17 | C12 12.527620000 -10.622850000 -10.015250000 NAPH 1 c3a C -0.127 18 | C13 11.844840000 -11.863540000 -10.015940000 NAPH 1 c3a C -0.127 19 | C14 10.470950000 -11.888220000 -10.009030000 NAPH 1 c3a C -0.118 20 | H15 12.355170000 -8.475370000 -10.009670000 NAPH 1 h1 H 0.132 21 | H16 13.627550000 -10.611020000 -10.018380000 NAPH 1 h1 H 0.131 22 | H17 12.414260000 -12.804680000 -10.020060000 NAPH 1 h1 H 0.133 23 | H18 9.938140000 -12.850570000 -10.009550000 NAPH 1 h1 H 0.131 24 | end 25 | end 26 | -------------------------------------------------------------------------------- /msi2lmp/test/naphthalene-class2a.mdf: -------------------------------------------------------------------------------- 1 | !BIOSYM molecular_data 4 2 | 3 | !Date: Tue Jul 02 12:43:30 2013 Materials Studio Generated MDF file 4 | 5 | #topology 6 | 7 | @column 1 element 8 | @column 2 atom_type 9 | @column 3 charge_group 10 | @column 4 isotope 11 | @column 5 formal_charge 12 | @column 6 charge 13 | @column 7 switching_atom 14 | @column 8 oop_flag 15 | @column 9 chirality_flag 16 | @column 10 occupancy 17 | @column 11 xray_temp_factor 18 | @column 12 connections 19 | 20 | @molecule naphthalene 21 | 22 | NAPH_1:H1 H h1 1 0 0 0.1320 0 0 8 1.0000 0.0000 C2 23 | NAPH_1:C2 C c3a 1 0 0 -0.1280 0 0 8 1.0000 0.0000 H1 C3/1.5 C7/1.5 24 | NAPH_1:C3 C c3a 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C2/1.5 C4/1.5 H8 25 | NAPH_1:C4 C c3a 1 0 0 -0.1170 0 0 8 1.0000 0.0000 C3/1.5 C5/1.5 H9 26 | NAPH_1:C5 C c3a 1 0 0 -0.0370 0 0 8 1.0000 0.0000 C4/1.5 C6/1.5 C11/1.5 27 | NAPH_1:C6 C c3a 1 0 0 -0.0360 0 0 8 1.0000 0.0000 C5/1.5 C7/1.5 C14/1.5 28 | NAPH_1:C7 C c3a 1 0 0 -0.1170 0 0 8 1.0000 0.0000 C2/1.5 C6/1.5 H10 29 | NAPH_1:H8 H h1 1 0 0 0.1310 0 0 8 1.0000 0.0000 C3 30 | NAPH_1:H9 H h1 1 0 0 0.1330 0 0 8 1.0000 0.0000 C4 31 | NAPH_1:H10 H h1 1 0 0 0.1320 0 0 8 1.0000 0.0000 C7 32 | NAPH_1:C11 C c3a 1 0 0 -0.1190 0 0 8 1.0000 0.0000 C5/1.5 C12/1.5 H15 33 | NAPH_1:C12 C c3a 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C11/1.5 C13/1.5 H16 34 | NAPH_1:C13 C c3a 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C12/1.5 C14/1.5 H17 35 | NAPH_1:C14 C c3a 1 0 0 -0.1180 0 0 8 1.0000 0.0000 C6/1.5 C13/1.5 H18 36 | NAPH_1:H15 H h1 1 0 0 0.1320 0 0 8 1.0000 0.0000 C11 37 | NAPH_1:H16 H h1 1 0 0 0.1310 0 0 8 1.0000 0.0000 C12 38 | NAPH_1:H17 H h1 1 0 0 0.1330 0 0 8 1.0000 0.0000 C13 39 | NAPH_1:H18 H h1 1 0 0 0.1310 0 0 8 1.0000 0.0000 C14 40 | 41 | ! 42 | #symmetry 43 | @periodicity 3 xyz 44 | @group (P1) 45 | 46 | #end 47 | -------------------------------------------------------------------------------- /msi2lmp/test/naphthalene-class2b.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Tue Jul 02 12:43:30 2013 5 | PBC 20.0000 20.0000 20.0000 90.0000 90.0000 90.0000 (P1) 6 | H1 6.500000000 -9.500000000 -10.000000000 NAPH 1 h H 0.132 7 | C2 7.599900000 -9.500000000 -10.000000000 NAPH 1 cp C -0.128 8 | C3 8.288980000 -8.262840000 -10.000000000 NAPH 1 cp C -0.127 9 | C4 9.661860000 -8.228710000 -10.001500000 NAPH 1 cp C -0.117 10 | C5 10.406020000 -9.440000000 -10.006040000 NAPH 1 cp C -0.037 11 | C6 9.719960000 -10.680950000 -10.004000000 NAPH 1 cp C -0.036 12 | C7 8.297670000 -10.682850000 -10.001160000 NAPH 1 cp C -0.117 13 | H8 7.705780000 -7.329930000 -9.996380000 NAPH 1 h H 0.131 14 | H9 10.206130000 -7.272850000 -10.002830000 NAPH 1 h H 0.133 15 | H10 7.770540000 -11.648530000 -10.000400000 NAPH 1 h H 0.132 16 | C11 11.828680000 -9.441740000 -10.010130000 NAPH 1 cp C -0.119 17 | C12 12.527620000 -10.622850000 -10.015250000 NAPH 1 cp C -0.127 18 | C13 11.844840000 -11.863540000 -10.015940000 NAPH 1 cp C -0.127 19 | C14 10.470950000 -11.888220000 -10.009030000 NAPH 1 cp C -0.118 20 | H15 12.355170000 -8.475370000 -10.009670000 NAPH 1 h H 0.132 21 | H16 13.627550000 -10.611020000 -10.018380000 NAPH 1 h H 0.131 22 | H17 12.414260000 -12.804680000 -10.020060000 NAPH 1 h H 0.133 23 | H18 9.938140000 -12.850570000 -10.009550000 NAPH 1 h H 0.131 24 | end 25 | end 26 | -------------------------------------------------------------------------------- /msi2lmp/test/naphthalene-class2b.mdf: -------------------------------------------------------------------------------- 1 | !BIOSYM molecular_data 4 2 | 3 | !Date: Tue Jul 02 12:43:30 2013 Materials Studio Generated MDF file 4 | 5 | #topology 6 | 7 | @column 1 element 8 | @column 2 atom_type 9 | @column 3 charge_group 10 | @column 4 isotope 11 | @column 5 formal_charge 12 | @column 6 charge 13 | @column 7 switching_atom 14 | @column 8 oop_flag 15 | @column 9 chirality_flag 16 | @column 10 occupancy 17 | @column 11 xray_temp_factor 18 | @column 12 connections 19 | 20 | @molecule naphthalene 21 | 22 | NAPH_1:H1 H h 1 0 0 0.1320 0 0 8 1.0000 0.0000 C2 23 | NAPH_1:C2 C cp 1 0 0 -0.1280 0 0 8 1.0000 0.0000 H1 C3/1.5 C7/1.5 24 | NAPH_1:C3 C cp 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C2/1.5 C4/1.5 H8 25 | NAPH_1:C4 C cp 1 0 0 -0.1170 0 0 8 1.0000 0.0000 C3/1.5 C5/1.5 H9 26 | NAPH_1:C5 C cp 1 0 0 -0.0370 0 0 8 1.0000 0.0000 C4/1.5 C6/1.5 C11/1.5 27 | NAPH_1:C6 C cp 1 0 0 -0.0360 0 0 8 1.0000 0.0000 C5/1.5 C7/1.5 C14/1.5 28 | NAPH_1:C7 C cp 1 0 0 -0.1170 0 0 8 1.0000 0.0000 C2/1.5 C6/1.5 H10 29 | NAPH_1:H8 H h 1 0 0 0.1310 0 0 8 1.0000 0.0000 C3 30 | NAPH_1:H9 H h 1 0 0 0.1330 0 0 8 1.0000 0.0000 C4 31 | NAPH_1:H10 H h 1 0 0 0.1320 0 0 8 1.0000 0.0000 C7 32 | NAPH_1:C11 C cp 1 0 0 -0.1190 0 0 8 1.0000 0.0000 C5/1.5 C12/1.5 H15 33 | NAPH_1:C12 C cp 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C11/1.5 C13/1.5 H16 34 | NAPH_1:C13 C cp 1 0 0 -0.1270 0 0 8 1.0000 0.0000 C12/1.5 C14/1.5 H17 35 | NAPH_1:C14 C cp 1 0 0 -0.1180 0 0 8 1.0000 0.0000 C6/1.5 C13/1.5 H18 36 | NAPH_1:H15 H h 1 0 0 0.1320 0 0 8 1.0000 0.0000 C11 37 | NAPH_1:H16 H h 1 0 0 0.1310 0 0 8 1.0000 0.0000 C12 38 | NAPH_1:H17 H h 1 0 0 0.1330 0 0 8 1.0000 0.0000 C13 39 | NAPH_1:H18 H h 1 0 0 0.1310 0 0 8 1.0000 0.0000 C14 40 | 41 | ! 42 | #symmetry 43 | @periodicity 3 xyz 44 | @group (P1) 45 | 46 | #end 47 | -------------------------------------------------------------------------------- /msi2lmp/test/phen3_cff97-class1.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=OFF 3 | input file for discover 4 | !DATE Tue Jul 15 15:14:54 1997 5 | N 0.109592088 -0.199880913 0.000000478 PHEN 1 n+ N -0.0450 6 | HN1 -0.124733858 -1.202872038 -0.000001981 PHEN 1 h+ H 0.2800 7 | HN2 -0.285811990 0.244572327 0.840843439 PHEN 1 h+ H 0.2800 8 | HN3 -0.285812497 0.244576558 -0.840839982 PHEN 1 h+ H 0.2800 9 | CA 1.560634732 -0.038402185 0.000000465 PHEN 1 c C -0.0780 10 | HA 1.972637177 -0.500293911 0.916701555 PHEN 1 h H 0.0530 11 | C 1.942531705 1.422506809 0.000000450 PHEN 1 c- C 0.2974 12 | OXT 3.187694550 1.672445178 0.000000438 PHEN 1 o- O -0.5337 13 | O 1.070737839 2.346019268 0.000000449 PHEN 1 o- O -0.5337 14 | CB 2.174581766 -0.718786478 -1.261021852 PHEN 1 c C -0.1060 15 | HB1 1.839982390 -0.182426706 -2.172762394 PHEN 1 h H 0.0530 16 | HB2 3.272250891 -0.569177628 -1.261509657 PHEN 1 h H 0.0530 17 | CG 1.889680982 -2.218492746 -1.435816169 PHEN 1 cp C 0.0000 18 | CD1 0.737977445 -2.629161119 -2.116767168 PHEN 1 cp C -0.1305 19 | HD1 0.061427273 -1.894254208 -2.533302307 PHEN 1 h H 0.1305 20 | CE1 0.424228579 -3.980331659 -2.214080095 PHEN 1 cp C -0.1305 21 | HE1 -0.483345032 -4.285143852 -2.715474367 PHEN 1 h H 0.1305 22 | CZ 1.268485427 -4.931880474 -1.646431088 PHEN 1 cp C -0.1305 23 | HZ 1.020345688 -5.980008125 -1.718327641 PHEN 1 h H 0.1305 24 | CE2 2.423752546 -4.531005859 -0.977356374 PHEN 1 cp C -0.1305 25 | HE2 3.074717045 -5.268786907 -0.531340718 PHEN 1 h H 0.1305 26 | CD2 2.733307123 -3.177516222 -0.869901538 PHEN 1 cp C -0.1305 27 | HD2 3.619415522 -2.873045444 -0.331384182 PHEN 1 h H 0.1305 28 | end 29 | end 30 | -------------------------------------------------------------------------------- /msi2lmp/test/phen3_cff97-class1.mdf: -------------------------------------------------------------------------------- 1 | !BIOSYM molecular_data 4 2 | 3 | !DATE: Tue Jul 15 15:14:54 1997 INSIGHT generated molecular data file 4 | 5 | #topology 6 | 7 | @column 1 element 8 | @column 2 atom_type cvff 9 | @column 3 charge_group cvff 10 | @column 4 isotope 11 | @column 5 formal_charge 12 | @column 6 charge cvff 13 | @column 7 switching_atom cvff 14 | @column 8 oop_flag cvff 15 | @column 9 chirality_flag 16 | @column 10 occupancy 17 | @column 11 xray_temp_factor 18 | @column 12 connections 19 | 20 | @molecule PHE_CVFF 21 | 22 | PHEN_1:N N n+ pepN 0 0 -0.04500 1 0 8 1.0000 0.0000 CA HN1 HN2 HN3 23 | PHEN_1:HN1 H h+ pepN 0 0 0.28000 0 0 8 1.0000 0.0000 N 24 | PHEN_1:HN2 H h+ pepN 0 0 0.28000 0 0 8 1.0000 0.0000 N 25 | PHEN_1:HN3 H h+ pepN 0 0 0.28000 0 0 8 1.0000 0.0000 N 26 | PHEN_1:CA C c pepN 0 0 -0.07800 0 0 8 1.0000 0.0000 N HA C CB 27 | PHEN_1:HA H h pepN 0 0 0.05300 0 0 8 1.0000 0.0000 CA 28 | PHEN_1:C C c- pepC 0 0 0.29740 1 1 8 1.0000 0.0000 CA O/1.5 OXT/1.5 29 | PHEN_1:OXT O o- pepC 0 0 -0.53370 0 0 8 1.0000 0.0000 C/1.5 30 | PHEN_1:O O o- pepC 0 0 -0.53370 0 0 8 1.0000 0.0000 C/1.5 31 | PHEN_1:CB C c meB 0 0 -0.10600 1 0 8 1.0000 0.0000 CA HB1 HB2 CG 32 | PHEN_1:HB1 H h meB 0 0 0.05300 0 0 8 1.0000 0.0000 CB 33 | PHEN_1:HB2 H h meB 0 0 0.05300 0 0 8 1.0000 0.0000 CB 34 | PHEN_1:CG C cp arG 0 0 0.00000 1 1 8 1.0000 0.0000 CB CD1/1.5 CD2/1.5 35 | PHEN_1:CD1 C cp arD1 0 0 -0.13053 1 1 8 1.0000 0.0000 CG/1.5 HD1 CE1/1.5 36 | PHEN_1:HD1 H h arD1 0 0 0.13053 0 0 8 1.0000 0.0000 CD1 37 | PHEN_1:CE1 C cp arE1 0 0 -0.13053 1 1 8 1.0000 0.0000 CD1/1.5 HE1 CZ/1.5 38 | PHEN_1:HE1 H h arE1 0 0 0.13053 0 0 8 1.0000 0.0000 CE1 39 | PHEN_1:CZ C cp arZ 0 0 -0.13053 1 1 8 1.0000 0.0000 CE1/1.5 HZ CE2/1.5 40 | PHEN_1:HZ H h arZ 0 0 0.13053 0 0 8 1.0000 0.0000 CZ 41 | PHEN_1:CE2 C cp arE2 0 0 -0.13053 1 1 8 1.0000 0.0000 CZ/1.5 HE2 CD2/1.5 42 | PHEN_1:HE2 H h arE2 0 0 0.13053 0 0 8 1.0000 0.0000 CE2 43 | PHEN_1:CD2 C cp arD2 0 0 -0.13053 1 1 8 1.0000 0.0000 CE2/1.5 HD2 CG/1.5 44 | PHEN_1:HD2 H h arD2 0 0 0.13053 0 0 8 1.0000 0.0000 CD2 45 | 46 | 47 | #atomset 48 | 49 | 50 | @quartet torsion *:PHEN_1:chi1 51 | N CA CB CG 52 | 53 | @quartet torsion *:PHEN_1:chi2 54 | CA CB CG CD1 55 | 56 | #end 57 | 58 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/benzene-class1.data: -------------------------------------------------------------------------------- 1 | LAMMPS data file. msi2lmp v3.9.7 / 24 Oct 2015 / CGCMM for benzene-class1 2 | 3 | 12 atoms 4 | 12 bonds 5 | 18 angles 6 | 24 dihedrals 7 | 6 impropers 8 | 9 | 2 atom types 10 | 2 bond types 11 | 2 angle types 12 | 3 dihedral types 13 | 1 improper types 14 | 15 | -0.014180000 9.985820000 xlo xhi 16 | -0.000000000 10.000000000 ylo yhi 17 | -10.000000000 0.000000000 zlo zhi 18 | 19 | Masses 20 | 21 | 1 1.007970 # h 22 | 2 12.011150 # cp 23 | 24 | Pair Coeffs # lj/cut/coul/long 25 | 26 | 1 0.0380000011 2.4499714540 # h 27 | 2 0.1479999981 3.6170487995 # cp 28 | 29 | Bond Coeffs # harmonic 30 | 31 | 1 363.4164 1.0800 # h-cp 32 | 2 480.0000 1.3400 # cp-cp 33 | 34 | Angle Coeffs # harmonic 35 | 36 | 1 37.0000 120.0000 # h-cp-cp 37 | 2 90.0000 120.0000 # cp-cp-cp 38 | 39 | Dihedral Coeffs # harmonic 40 | 41 | 1 3.0000 -1 2 # h-cp-cp-cp 42 | 2 3.0000 -1 2 # h-cp-cp-h 43 | 3 3.0000 -1 2 # cp-cp-cp-cp 44 | 45 | Improper Coeffs # cvff 46 | 47 | 1 0.3700 -1 2 # h-cp-cp-cp 48 | 49 | Atoms # full 50 | 51 | 1 1 1 0.102000 2.500000000 5.000000000 -5.000000000 0 0 0 # h 52 | 2 1 2 -0.102000 3.594720000 5.000000000 -5.000000000 0 0 0 # cp 53 | 3 1 2 -0.102000 4.290270000 6.204730000 -5.000000000 0 0 0 # cp 54 | 4 1 2 -0.102000 5.681370000 6.204730000 -5.000000000 0 0 0 # cp 55 | 5 1 2 -0.102000 6.376920000 5.000000000 -5.000000000 0 0 0 # cp 56 | 6 1 2 -0.102000 5.681370000 3.795270000 -5.000000000 0 0 0 # cp 57 | 7 1 2 -0.102000 4.290270000 3.795270000 -5.000000000 0 0 0 # cp 58 | 8 1 1 0.102000 7.471640000 5.000000000 -5.000000000 0 0 0 # h 59 | 9 1 1 0.102000 3.742910000 7.152785000 -5.000000000 0 0 0 # h 60 | 10 1 1 0.102000 6.228730000 7.152785000 -5.000000000 0 0 0 # h 61 | 11 1 1 0.102000 6.228730000 2.847215000 -5.000000000 0 0 0 # h 62 | 12 1 1 0.102000 3.742910000 2.847215000 -5.000000000 0 0 0 # h 63 | 64 | Bonds 65 | 66 | 1 1 1 2 67 | 2 2 2 3 68 | 3 2 2 7 69 | 4 2 3 4 70 | 5 1 9 3 71 | 6 2 4 5 72 | 7 1 10 4 73 | 8 1 8 5 74 | 9 2 5 6 75 | 10 2 6 7 76 | 11 1 11 6 77 | 12 1 12 7 78 | 79 | Angles 80 | 81 | 1 1 1 2 3 82 | 2 1 1 2 7 83 | 3 2 3 2 7 84 | 4 2 2 3 4 85 | 5 1 9 3 2 86 | 6 1 9 3 4 87 | 7 2 3 4 5 88 | 8 1 10 4 3 89 | 9 1 10 4 5 90 | 10 1 8 5 4 91 | 11 2 4 5 6 92 | 12 1 8 5 6 93 | 13 2 5 6 7 94 | 14 1 11 6 5 95 | 15 1 11 6 7 96 | 16 2 2 7 6 97 | 17 1 12 7 2 98 | 18 1 12 7 6 99 | 100 | Dihedrals 101 | 102 | 1 1 1 2 3 4 103 | 2 2 1 2 3 9 104 | 3 3 7 2 3 4 105 | 4 1 9 3 2 7 106 | 5 1 1 2 7 6 107 | 6 2 1 2 7 12 108 | 7 3 3 2 7 6 109 | 8 1 12 7 2 3 110 | 9 3 2 3 4 5 111 | 10 1 10 4 3 2 112 | 11 1 9 3 4 5 113 | 12 2 9 3 4 10 114 | 13 1 8 5 4 3 115 | 14 3 3 4 5 6 116 | 15 2 10 4 5 8 117 | 16 1 10 4 5 6 118 | 17 3 4 5 6 7 119 | 18 1 11 6 5 4 120 | 19 1 8 5 6 7 121 | 20 2 8 5 6 11 122 | 21 3 5 6 7 2 123 | 22 1 12 7 6 5 124 | 23 1 11 6 7 2 125 | 24 2 11 6 7 12 126 | 127 | Impropers 128 | 129 | 1 1 1 2 3 7 130 | 2 1 9 3 4 2 131 | 3 1 10 4 5 3 132 | 4 1 8 5 4 6 133 | 5 1 11 6 7 5 134 | 6 1 12 7 6 2 135 | 136 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/benzene-class1.data2: -------------------------------------------------------------------------------- 1 | LAMMPS data file via write_data, version 24 Oct 2015-ICMS, timestep = 100 2 | 3 | 12 atoms 4 | 2 atom types 5 | 12 bonds 6 | 2 bond types 7 | 18 angles 8 | 2 angle types 9 | 24 dihedrals 10 | 3 dihedral types 11 | 6 impropers 12 | 1 improper types 13 | 14 | -1.4180000000000000e-02 9.9858200000000004e+00 xlo xhi 15 | -0.0000000000000000e+00 1.0000000000000000e+01 ylo yhi 16 | -1.0000000000000000e+01 0.0000000000000000e+00 zlo zhi 17 | 18 | Masses 19 | 20 | 1 1.00797 21 | 2 12.0112 22 | 23 | Pair Coeffs # lj/cut/coul/cut 24 | 25 | 1 0.038 2.44997 26 | 2 0.148 3.61705 27 | 28 | Bond Coeffs # harmonic 29 | 30 | 1 363.416 1.08 31 | 2 480 1.34 32 | 33 | Angle Coeffs # harmonic 34 | 35 | 1 37 120 36 | 2 90 120 37 | 38 | Dihedral Coeffs # harmonic 39 | 40 | 1 3 -1 2 41 | 2 3 -1 2 42 | 3 3 -1 2 43 | 44 | Improper Coeffs # cvff 45 | 46 | 1 0.37 -1 2 47 | 48 | Atoms # full 49 | 50 | 1 1 1 1.0199999999999999e-01 2.5658050685389746e+00 5.0000000000000000e+00 -5.0000000000000000e+00 0 0 0 51 | 2 1 2 -1.0199999999999999e-01 3.6459860339265049e+00 5.0000000000000000e+00 -5.0000000000000000e+00 0 0 0 52 | 3 1 2 -1.0199999999999999e-01 4.3158891913221265e+00 6.1603977365242004e+00 -5.0000000000000000e+00 0 0 0 53 | 4 1 2 -1.0199999999999999e-01 5.6557508086778734e+00 6.1603977365242013e+00 -5.0000000000000000e+00 0 0 0 54 | 5 1 2 -1.0199999999999999e-01 6.3256539660734958e+00 5.0000000000000000e+00 -5.0000000000000000e+00 0 0 0 55 | 6 1 2 -1.0199999999999999e-01 5.6557508086778734e+00 3.8396022634757996e+00 -5.0000000000000000e+00 0 0 0 56 | 7 1 2 -1.0199999999999999e-01 4.3158891913221265e+00 3.8396022634757991e+00 -5.0000000000000000e+00 0 0 0 57 | 8 1 1 1.0199999999999999e-01 7.4058349314610261e+00 5.0000000000000000e+00 -5.0000000000000000e+00 0 0 0 58 | 9 1 1 1.0199999999999999e-01 3.7757549564922894e+00 7.0959459039705521e+00 -5.0000000000000000e+00 0 0 0 59 | 10 1 1 1.0199999999999999e-01 6.1958850435077109e+00 7.0959459039705530e+00 -5.0000000000000000e+00 0 0 0 60 | 11 1 1 1.0199999999999999e-01 6.1958850435077109e+00 2.9040540960294479e+00 -5.0000000000000000e+00 0 0 0 61 | 12 1 1 1.0199999999999999e-01 3.7757549564922899e+00 2.9040540960294474e+00 -5.0000000000000000e+00 0 0 0 62 | 63 | Velocities 64 | 65 | 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 66 | 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 67 | 3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 68 | 4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 69 | 5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 70 | 6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 71 | 7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 72 | 8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 73 | 9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 74 | 10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 75 | 11 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 76 | 12 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 77 | 78 | Bonds 79 | 80 | 1 1 1 2 81 | 2 2 2 3 82 | 3 2 2 7 83 | 4 2 3 4 84 | 5 2 4 5 85 | 6 2 5 6 86 | 7 2 6 7 87 | 8 1 8 5 88 | 9 1 9 3 89 | 10 1 10 4 90 | 11 1 11 6 91 | 12 1 12 7 92 | 93 | Angles 94 | 95 | 1 1 1 2 3 96 | 2 1 1 2 7 97 | 3 2 3 2 7 98 | 4 2 2 3 4 99 | 5 1 9 3 2 100 | 6 1 9 3 4 101 | 7 2 3 4 5 102 | 8 1 10 4 3 103 | 9 1 10 4 5 104 | 10 1 8 5 4 105 | 11 2 4 5 6 106 | 12 1 8 5 6 107 | 13 2 5 6 7 108 | 14 1 11 6 5 109 | 15 1 11 6 7 110 | 16 2 2 7 6 111 | 17 1 12 7 2 112 | 18 1 12 7 6 113 | 114 | Dihedrals 115 | 116 | 1 1 1 2 3 4 117 | 2 2 1 2 3 9 118 | 3 3 7 2 3 4 119 | 4 1 1 2 7 6 120 | 5 2 1 2 7 12 121 | 6 3 3 2 7 6 122 | 7 1 9 3 2 7 123 | 8 3 2 3 4 5 124 | 9 1 9 3 4 5 125 | 10 2 9 3 4 10 126 | 11 1 10 4 3 2 127 | 12 3 3 4 5 6 128 | 13 2 10 4 5 8 129 | 14 1 10 4 5 6 130 | 15 1 8 5 4 3 131 | 16 3 4 5 6 7 132 | 17 1 8 5 6 7 133 | 18 2 8 5 6 11 134 | 19 1 11 6 5 4 135 | 20 3 5 6 7 2 136 | 21 1 11 6 7 2 137 | 22 2 11 6 7 12 138 | 23 1 12 7 2 3 139 | 24 1 12 7 6 5 140 | 141 | Impropers 142 | 143 | 1 1 1 2 3 7 144 | 2 1 9 3 4 2 145 | 3 1 10 4 5 3 146 | 4 1 8 5 4 6 147 | 5 1 11 6 7 5 148 | 6 1 12 7 6 2 149 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/benzene-class1.data3: -------------------------------------------------------------------------------- 1 | LAMMPS data file from msi2lmp v3.8 for benzene-class1 2 | 3 | 12 atoms 4 | 12 bonds 5 | 18 angles 6 | 24 dihedrals 7 | 6 impropers 8 | 9 | 2 atom types 10 | 2 bond types 11 | 2 angle types 12 | 3 dihedral types 13 | 1 improper types 14 | 15 | -0.014180000 9.985820000 xlo xhi 16 | -0.000000000 10.000000000 ylo yhi 17 | -10.000000000 0.000000000 zlo zhi 18 | 19 | Masses 20 | 21 | 1 1.007970 22 | 2 12.011150 23 | 24 | Pair Coeffs 25 | 26 | 1 0.0380000011 2.4499714540 27 | 2 0.1479999981 3.6170487995 28 | 29 | Bond Coeffs 30 | 31 | 1 363.4164 1.0800 32 | 2 480.0000 1.3400 33 | 34 | Angle Coeffs 35 | 36 | 1 37.0000 120.0000 37 | 2 90.0000 120.0000 38 | 39 | Dihedral Coeffs 40 | 41 | 1 3.0000 -1 2 42 | 2 3.0000 -1 2 43 | 3 3.0000 -1 2 44 | 45 | Improper Coeffs 46 | 47 | 1 0.3700 -1 2 48 | 49 | Atoms 50 | 51 | 1 1 1 0.102000 2.500000000 5.000000000 -5.000000000 52 | 2 1 2 -0.102000 3.594720000 5.000000000 -5.000000000 53 | 3 1 2 -0.102000 4.290270000 6.204730000 -5.000000000 54 | 4 1 2 -0.102000 5.681370000 6.204730000 -5.000000000 55 | 5 1 2 -0.102000 6.376920000 5.000000000 -5.000000000 56 | 6 1 2 -0.102000 5.681370000 3.795270000 -5.000000000 57 | 7 1 2 -0.102000 4.290270000 3.795270000 -5.000000000 58 | 8 1 1 0.102000 7.471640000 5.000000000 -5.000000000 59 | 9 1 1 0.102000 3.742910000 7.152785000 -5.000000000 60 | 10 1 1 0.102000 6.228730000 7.152785000 -5.000000000 61 | 11 1 1 0.102000 6.228730000 2.847215000 -5.000000000 62 | 12 1 1 0.102000 3.742910000 2.847215000 -5.000000000 63 | 64 | Bonds 65 | 66 | 1 1 1 2 67 | 2 2 2 3 68 | 3 2 2 7 69 | 4 2 3 4 70 | 5 1 9 3 71 | 6 2 4 5 72 | 7 1 10 4 73 | 8 1 8 5 74 | 9 2 5 6 75 | 10 2 6 7 76 | 11 1 11 6 77 | 12 1 12 7 78 | 79 | Angles 80 | 81 | 1 1 1 2 3 82 | 2 1 1 2 7 83 | 3 2 3 2 7 84 | 4 2 2 3 4 85 | 5 1 9 3 2 86 | 6 1 9 3 4 87 | 7 2 3 4 5 88 | 8 1 10 4 3 89 | 9 1 10 4 5 90 | 10 1 8 5 4 91 | 11 2 4 5 6 92 | 12 1 8 5 6 93 | 13 2 5 6 7 94 | 14 1 11 6 5 95 | 15 1 11 6 7 96 | 16 2 2 7 6 97 | 17 1 12 7 2 98 | 18 1 12 7 6 99 | 100 | Dihedrals 101 | 102 | 1 1 1 2 3 4 103 | 2 2 1 2 3 9 104 | 3 3 7 2 3 4 105 | 4 1 9 3 2 7 106 | 5 1 1 2 7 6 107 | 6 2 1 2 7 12 108 | 7 3 3 2 7 6 109 | 8 1 12 7 2 3 110 | 9 3 2 3 4 5 111 | 10 1 10 4 3 2 112 | 11 1 9 3 4 5 113 | 12 2 9 3 4 10 114 | 13 1 8 5 4 3 115 | 14 3 3 4 5 6 116 | 15 2 10 4 5 8 117 | 16 1 10 4 5 6 118 | 17 3 4 5 6 7 119 | 18 1 11 6 5 4 120 | 19 1 8 5 6 7 121 | 20 2 8 5 6 11 122 | 21 3 5 6 7 2 123 | 22 1 12 7 6 5 124 | 23 1 11 6 7 2 125 | 24 2 11 6 7 12 126 | 127 | Impropers 128 | 129 | 1 1 1 2 3 7 130 | 2 1 9 3 4 2 131 | 3 1 10 4 5 3 132 | 4 1 8 5 4 6 133 | 5 1 11 6 7 5 134 | 6 1 12 7 6 2 135 | 136 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/benzene-class2a.data: -------------------------------------------------------------------------------- 1 | LAMMPS data file from msi2lmp v3.8 for benzene-class2 2 | 3 | 12 atoms 4 | 12 bonds 5 | 18 angles 6 | 24 dihedrals 7 | 6 impropers 8 | 9 | 2 atom types 10 | 2 bond types 11 | 2 angle types 12 | 3 dihedral types 13 | 1 improper types 14 | 15 | -0.014180000 9.985820000 xlo xhi 16 | -0.000000000 10.000000000 ylo yhi 17 | -10.000000000 0.000000000 zlo zhi 18 | 19 | Masses 20 | 21 | 1 1.007970 22 | 2 12.011150 23 | 24 | Pair Coeffs 25 | 26 | 1 0.0230000000 2.8780000000 27 | 2 0.0680000000 3.9150000000 28 | 29 | Bond Coeffs 30 | 31 | 1 1.0982 372.8251 -803.4526 894.3173 32 | 2 1.4170 470.8361 -627.6179 1327.6345 33 | 34 | Angle Coeffs 35 | 36 | 1 117.9400 35.1558 -12.4682 0.0000 37 | 2 118.9000 61.0226 -34.9931 0.0000 38 | 39 | Dihedral Coeffs 40 | 41 | 1 0.0000 0.0000 3.9661 0.0000 0.0000 0.0000 42 | 2 0.0000 0.0000 2.3500 0.0000 0.0000 0.0000 43 | 3 8.3667 0.0000 1.2000 0.0000 0.0000 0.0000 44 | 45 | Improper Coeffs 46 | 47 | 1 4.8912 0.0000 48 | 49 | BondBond Coeffs 50 | 51 | 1 1.0795 1.0982 1.4170 52 | 2 68.2856 1.4170 1.4170 53 | 54 | BondAngle Coeffs 55 | 56 | 1 24.2183 20.0033 1.0982 1.4170 57 | 2 28.8708 28.8708 1.4170 1.4170 58 | 59 | AngleAngle Coeffs 60 | 61 | 1 0.0000 0.0000 0.0000 117.9400 118.9000 117.9400 62 | 63 | AngleAngleTorsion Coeffs 64 | 65 | 1 -4.8141 117.9400 118.9000 66 | 2 0.3598 117.9400 117.9400 67 | 3 0.0000 118.9000 118.9000 68 | 69 | EndBondTorsion Coeffs 70 | 71 | 1 0.0000 -0.4669 0.0000 0.0000 -6.8958 0.0000 1.0982 1.4170 72 | 2 0.0000 -0.6890 0.0000 0.0000 -0.6890 0.0000 1.0982 1.0982 73 | 3 -0.1185 6.3204 0.0000 -0.1185 6.3204 0.0000 1.4170 1.4170 74 | 75 | MiddleBondTorsion Coeffs 76 | 77 | 1 0.0000 -1.1521 0.0000 1.4170 78 | 2 0.0000 4.8228 0.0000 1.4170 79 | 3 27.5989 -2.3120 0.0000 1.4170 80 | 81 | BondBond13 Coeffs 82 | 83 | 1 0.0000 1.0982 1.4170 84 | 2 0.0000 1.0982 1.0982 85 | 3 0.0000 1.4170 1.4170 86 | 87 | AngleTorsion Coeffs 88 | 89 | 1 0.0000 2.7147 0.0000 0.0000 2.5014 0.0000 117.9400 118.9000 90 | 2 0.0000 2.4501 0.0000 0.0000 2.4501 0.0000 117.9400 117.9400 91 | 3 1.9767 1.0239 0.0000 1.9767 1.0239 0.0000 118.9000 118.9000 92 | 93 | Atoms 94 | 95 | 1 1 1 0.102000 2.500000000 5.000000000 -5.000000000 96 | 2 1 2 -0.102000 3.594720000 5.000000000 -5.000000000 97 | 3 1 2 -0.102000 4.290270000 6.204730000 -5.000000000 98 | 4 1 2 -0.102000 5.681370000 6.204730000 -5.000000000 99 | 5 1 2 -0.102000 6.376920000 5.000000000 -5.000000000 100 | 6 1 2 -0.102000 5.681370000 3.795270000 -5.000000000 101 | 7 1 2 -0.102000 4.290270000 3.795270000 -5.000000000 102 | 8 1 1 0.102000 7.471640000 5.000000000 -5.000000000 103 | 9 1 1 0.102000 3.742910000 7.152785000 -5.000000000 104 | 10 1 1 0.102000 6.228730000 7.152785000 -5.000000000 105 | 11 1 1 0.102000 6.228730000 2.847215000 -5.000000000 106 | 12 1 1 0.102000 3.742910000 2.847215000 -5.000000000 107 | 108 | Bonds 109 | 110 | 1 1 1 2 111 | 2 2 2 3 112 | 3 2 2 7 113 | 4 2 3 4 114 | 5 1 9 3 115 | 6 2 4 5 116 | 7 1 10 4 117 | 8 1 8 5 118 | 9 2 5 6 119 | 10 2 6 7 120 | 11 1 11 6 121 | 12 1 12 7 122 | 123 | Angles 124 | 125 | 1 1 1 2 3 126 | 2 1 1 2 7 127 | 3 2 3 2 7 128 | 4 2 2 3 4 129 | 5 1 9 3 2 130 | 6 1 9 3 4 131 | 7 2 3 4 5 132 | 8 1 10 4 3 133 | 9 1 10 4 5 134 | 10 1 8 5 4 135 | 11 2 4 5 6 136 | 12 1 8 5 6 137 | 13 2 5 6 7 138 | 14 1 11 6 5 139 | 15 1 11 6 7 140 | 16 2 2 7 6 141 | 17 1 12 7 2 142 | 18 1 12 7 6 143 | 144 | Dihedrals 145 | 146 | 1 1 1 2 3 4 147 | 2 2 1 2 3 9 148 | 3 3 7 2 3 4 149 | 4 1 9 3 2 7 150 | 5 1 1 2 7 6 151 | 6 2 1 2 7 12 152 | 7 3 3 2 7 6 153 | 8 1 12 7 2 3 154 | 9 3 2 3 4 5 155 | 10 1 10 4 3 2 156 | 11 1 9 3 4 5 157 | 12 2 9 3 4 10 158 | 13 1 8 5 4 3 159 | 14 3 3 4 5 6 160 | 15 2 10 4 5 8 161 | 16 1 10 4 5 6 162 | 17 3 4 5 6 7 163 | 18 1 11 6 5 4 164 | 19 1 8 5 6 7 165 | 20 2 8 5 6 11 166 | 21 3 5 6 7 2 167 | 22 1 12 7 6 5 168 | 23 1 11 6 7 2 169 | 24 2 11 6 7 12 170 | 171 | Impropers 172 | 173 | 1 1 1 2 3 7 174 | 2 1 9 3 4 2 175 | 3 1 10 4 5 3 176 | 4 1 8 5 4 6 177 | 5 1 11 6 7 5 178 | 6 1 12 7 6 2 179 | 180 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/benzene-class2a.data2: -------------------------------------------------------------------------------- 1 | LAMMPS data file via write_data, version 8 Jul 2013-ICMS, timestep = 11 2 | 3 | 12 atoms 4 | 2 atom types 5 | 12 bonds 6 | 2 bond types 7 | 18 angles 8 | 2 angle types 9 | 24 dihedrals 10 | 3 dihedral types 11 | 6 impropers 12 | 1 improper types 13 | 14 | -1.4180000000000000e-02 9.9858200000000004e+00 xlo xhi 15 | -0.0000000000000000e+00 1.0000000000000000e+01 ylo yhi 16 | -1.0000000000000000e+01 0.0000000000000000e+00 zlo zhi 17 | 18 | Masses 19 | 20 | 1 1.00797 21 | 2 12.0112 22 | 23 | Pair Coeffs 24 | 25 | 1 0.023 2.878 26 | 2 0.068 3.915 27 | 28 | Bond Coeffs 29 | 30 | 1 1.0982 372.825 -803.453 894.317 31 | 2 1.417 470.836 -627.618 1327.63 32 | 33 | Angle Coeffs 34 | 35 | 1 117.94 35.1558 -12.4682 0 36 | 2 118.9 61.0226 -34.9931 0 37 | 38 | BondBond Coeffs 39 | 40 | 1 1.0795 1.0982 1.417 41 | 2 68.2856 1.417 1.417 42 | 43 | BondAngle Coeffs 44 | 45 | 1 24.2183 20.0033 1.0982 1.417 46 | 2 28.8708 28.8708 1.417 1.417 47 | 48 | Dihedral Coeffs 49 | 50 | 1 0 0 3.9661 0 0 0 51 | 2 0 0 2.35 0 0 0 52 | 3 8.3667 0 1.2 0 0 0 53 | 54 | AngleAngleTorsion Coeffs 55 | 56 | 1 -4.8141 117.94 118.9 57 | 2 0.3598 117.94 117.94 58 | 3 0 118.9 118.9 59 | 60 | EndBondTorsion Coeffs 61 | 62 | 1 0 -0.4669 0 0 -6.8958 0 1.0982 1.417 63 | 2 0 -0.689 0 0 -0.689 0 1.0982 1.0982 64 | 3 -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417 65 | 66 | MiddleBondTorsion Coeffs 67 | 68 | 1 0 -1.1521 0 1.417 69 | 2 0 4.8228 0 1.417 70 | 3 27.5989 -2.312 0 1.417 71 | 72 | BondBond13 Coeffs 73 | 74 | 1 0 1.0982 1.417 75 | 2 0 1.0982 1.0982 76 | 3 0 1.417 1.417 77 | 78 | AngleTorsion Coeffs 79 | 80 | 1 0 2.7147 0 0 2.5014 0 117.94 118.9 81 | 2 0 2.4501 0 0 2.4501 0 117.94 117.94 82 | 3 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9 83 | 84 | Improper Coeffs 85 | 86 | 1 4.8912 0 87 | 88 | AngleAngle Coeffs 89 | 90 | 1 0 0 0 117.94 118.9 117.94 91 | 92 | Atoms 93 | 94 | 1 1 1 1.0199999999999999e-01 2.4952054314002501e+00 5.0000000000000000e+00 -5.0000000000000000e+00 0 0 0 95 | 2 1 2 -1.0199999999999999e-01 3.5945091269535197e+00 5.0000000000000009e+00 -5.0000000000000000e+00 0 0 0 96 | 3 1 2 -1.0199999999999999e-01 4.2901451050500334e+00 6.2049812477418866e+00 -5.0000000000000000e+00 0 0 0 97 | 4 1 2 -1.0199999999999999e-01 5.6814948949499664e+00 6.2049812477418858e+00 -5.0000000000000000e+00 0 0 0 98 | 5 1 2 -1.0199999999999999e-01 6.3771308730464789e+00 5.0000000000000018e+00 -5.0000000000000000e+00 0 0 0 99 | 6 1 2 -1.0199999999999999e-01 5.6814948949499628e+00 3.7950187522581120e+00 -5.0000000000000000e+00 0 0 0 100 | 7 1 2 -1.0199999999999999e-01 4.2901451050500370e+00 3.7950187522581116e+00 -5.0000000000000000e+00 0 0 0 101 | 8 1 1 1.0199999999999999e-01 7.4764345685997498e+00 5.0000000000000000e+00 -5.0000000000000000e+00 0 0 0 102 | 9 1 1 1.0199999999999999e-01 3.7404633343978420e+00 7.1570474148571899e+00 -5.0000000000000000e+00 0 0 0 103 | 10 1 1 1.0199999999999999e-01 6.2311766656021588e+00 7.1570474148571908e+00 -5.0000000000000000e+00 0 0 0 104 | 11 1 1 1.0199999999999999e-01 6.2311766656021579e+00 2.8429525851428088e+00 -5.0000000000000000e+00 0 0 0 105 | 12 1 1 1.0199999999999999e-01 3.7404633343978411e+00 2.8429525851428092e+00 -5.0000000000000000e+00 0 0 0 106 | 107 | Velocities 108 | 109 | 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 110 | 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 111 | 3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 112 | 4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 113 | 5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 114 | 6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 115 | 7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 116 | 8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 117 | 9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 118 | 10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 119 | 11 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 120 | 12 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 121 | 122 | Bonds 123 | 124 | 1 1 1 2 125 | 2 2 2 3 126 | 3 2 2 7 127 | 4 2 3 4 128 | 5 2 4 5 129 | 6 2 5 6 130 | 7 2 6 7 131 | 8 1 8 5 132 | 9 1 9 3 133 | 10 1 10 4 134 | 11 1 11 6 135 | 12 1 12 7 136 | 137 | Angles 138 | 139 | 1 1 1 2 3 140 | 2 1 1 2 7 141 | 3 2 3 2 7 142 | 4 2 2 3 4 143 | 5 1 9 3 2 144 | 6 1 9 3 4 145 | 7 2 3 4 5 146 | 8 1 10 4 3 147 | 9 1 10 4 5 148 | 10 1 8 5 4 149 | 11 2 4 5 6 150 | 12 1 8 5 6 151 | 13 2 5 6 7 152 | 14 1 11 6 5 153 | 15 1 11 6 7 154 | 16 2 2 7 6 155 | 17 1 12 7 2 156 | 18 1 12 7 6 157 | 158 | Dihedrals 159 | 160 | 1 1 1 2 3 4 161 | 2 2 1 2 3 9 162 | 3 3 7 2 3 4 163 | 4 1 1 2 7 6 164 | 5 2 1 2 7 12 165 | 6 3 3 2 7 6 166 | 7 1 9 3 2 7 167 | 8 3 2 3 4 5 168 | 9 1 9 3 4 5 169 | 10 2 9 3 4 10 170 | 11 1 10 4 3 2 171 | 12 3 3 4 5 6 172 | 13 2 10 4 5 8 173 | 14 1 10 4 5 6 174 | 15 1 8 5 4 3 175 | 16 3 4 5 6 7 176 | 17 1 8 5 6 7 177 | 18 2 8 5 6 11 178 | 19 1 11 6 5 4 179 | 20 3 5 6 7 2 180 | 21 1 11 6 7 2 181 | 22 2 11 6 7 12 182 | 23 1 12 7 2 3 183 | 24 1 12 7 6 5 184 | 185 | Impropers 186 | 187 | 1 1 1 2 3 7 188 | 2 1 9 3 4 2 189 | 3 1 10 4 5 3 190 | 4 1 8 5 4 6 191 | 5 1 11 6 7 5 192 | 6 1 12 7 6 2 193 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/benzene-class2b.data: -------------------------------------------------------------------------------- 1 | LAMMPS data file from msi2lmp v3.8 for benzene-class2b 2 | 3 | 12 atoms 4 | 12 bonds 5 | 18 angles 6 | 24 dihedrals 7 | 6 impropers 8 | 9 | 2 atom types 10 | 2 bond types 11 | 2 angle types 12 | 3 dihedral types 13 | 1 improper types 14 | 15 | -0.014180000 9.985820000 xlo xhi 16 | -0.000000000 10.000000000 ylo yhi 17 | -10.000000000 0.000000000 zlo zhi 18 | 19 | Masses 20 | 21 | 1 1.007970 22 | 2 12.011150 23 | 24 | Pair Coeffs 25 | 26 | 1 0.0200000000 2.9950000000 27 | 2 0.0640000000 4.0100000000 28 | 29 | Bond Coeffs 30 | 31 | 1 1.0982 372.8251 -803.4526 894.3173 32 | 2 1.4170 470.8361 -627.6179 1327.6345 33 | 34 | Angle Coeffs 35 | 36 | 1 117.9400 35.1558 -12.4682 0.0000 37 | 2 118.9000 61.0226 -34.9931 0.0000 38 | 39 | Dihedral Coeffs 40 | 41 | 1 0.0000 0.0000 3.9661 0.0000 0.0000 0.0000 42 | 2 0.0000 0.0000 1.8769 0.0000 0.0000 0.0000 43 | 3 8.3667 0.0000 1.1932 0.0000 0.0000 0.0000 44 | 45 | Improper Coeffs 46 | 47 | 1 4.8912 0.0000 48 | 49 | BondBond Coeffs 50 | 51 | 1 1.0795 1.0982 1.4170 52 | 2 68.2856 1.4170 1.4170 53 | 54 | BondAngle Coeffs 55 | 56 | 1 24.2183 20.0033 1.0982 1.4170 57 | 2 28.8708 28.8708 1.4170 1.4170 58 | 59 | AngleAngle Coeffs 60 | 61 | 1 0.0000 0.0000 0.0000 117.9400 118.9000 117.9400 62 | 63 | AngleAngleTorsion Coeffs 64 | 65 | 1 -4.8141 117.9400 118.9000 66 | 2 0.3598 117.9400 117.9400 67 | 3 0.0000 118.9000 118.9000 68 | 69 | EndBondTorsion Coeffs 70 | 71 | 1 0.0000 -0.4669 0.0000 0.0000 -6.8958 0.0000 1.0982 1.4170 72 | 2 0.0000 -0.6890 0.0000 0.0000 -0.6890 0.0000 1.0982 1.0982 73 | 3 -0.1185 6.3204 0.0000 -0.1185 6.3204 0.0000 1.4170 1.4170 74 | 75 | MiddleBondTorsion Coeffs 76 | 77 | 1 0.0000 -1.1521 0.0000 1.4170 78 | 2 0.0000 4.8228 0.0000 1.4170 79 | 3 27.5989 -2.3120 0.0000 1.4170 80 | 81 | BondBond13 Coeffs 82 | 83 | 1 -6.2741 1.0982 1.4170 84 | 2 -1.7077 1.0982 1.0982 85 | 3 53.0000 1.4170 1.4170 86 | 87 | AngleTorsion Coeffs 88 | 89 | 1 0.0000 2.7147 0.0000 0.0000 2.5014 0.0000 117.9400 118.9000 90 | 2 0.0000 2.4501 0.0000 0.0000 2.4501 0.0000 117.9400 117.9400 91 | 3 1.9767 1.0239 0.0000 1.9767 1.0239 0.0000 118.9000 118.9000 92 | 93 | Atoms 94 | 95 | 1 1 1 0.102000 2.500000000 5.000000000 -5.000000000 96 | 2 1 2 -0.102000 3.594720000 5.000000000 -5.000000000 97 | 3 1 2 -0.102000 4.290270000 6.204730000 -5.000000000 98 | 4 1 2 -0.102000 5.681370000 6.204730000 -5.000000000 99 | 5 1 2 -0.102000 6.376920000 5.000000000 -5.000000000 100 | 6 1 2 -0.102000 5.681370000 3.795270000 -5.000000000 101 | 7 1 2 -0.102000 4.290270000 3.795270000 -5.000000000 102 | 8 1 1 0.102000 7.471640000 5.000000000 -5.000000000 103 | 9 1 1 0.102000 3.742910000 7.152785000 -5.000000000 104 | 10 1 1 0.102000 6.228730000 7.152785000 -5.000000000 105 | 11 1 1 0.102000 6.228730000 2.847215000 -5.000000000 106 | 12 1 1 0.102000 3.742910000 2.847215000 -5.000000000 107 | 108 | Bonds 109 | 110 | 1 1 1 2 111 | 2 2 2 3 112 | 3 2 2 7 113 | 4 2 3 4 114 | 5 1 9 3 115 | 6 2 4 5 116 | 7 1 10 4 117 | 8 1 8 5 118 | 9 2 5 6 119 | 10 2 6 7 120 | 11 1 11 6 121 | 12 1 12 7 122 | 123 | Angles 124 | 125 | 1 1 1 2 3 126 | 2 1 1 2 7 127 | 3 2 3 2 7 128 | 4 2 2 3 4 129 | 5 1 9 3 2 130 | 6 1 9 3 4 131 | 7 2 3 4 5 132 | 8 1 10 4 3 133 | 9 1 10 4 5 134 | 10 1 8 5 4 135 | 11 2 4 5 6 136 | 12 1 8 5 6 137 | 13 2 5 6 7 138 | 14 1 11 6 5 139 | 15 1 11 6 7 140 | 16 2 2 7 6 141 | 17 1 12 7 2 142 | 18 1 12 7 6 143 | 144 | Dihedrals 145 | 146 | 1 1 1 2 3 4 147 | 2 2 1 2 3 9 148 | 3 3 7 2 3 4 149 | 4 1 9 3 2 7 150 | 5 1 1 2 7 6 151 | 6 2 1 2 7 12 152 | 7 3 3 2 7 6 153 | 8 1 12 7 2 3 154 | 9 3 2 3 4 5 155 | 10 1 10 4 3 2 156 | 11 1 9 3 4 5 157 | 12 2 9 3 4 10 158 | 13 1 8 5 4 3 159 | 14 3 3 4 5 6 160 | 15 2 10 4 5 8 161 | 16 1 10 4 5 6 162 | 17 3 4 5 6 7 163 | 18 1 11 6 5 4 164 | 19 1 8 5 6 7 165 | 20 2 8 5 6 11 166 | 21 3 5 6 7 2 167 | 22 1 12 7 6 5 168 | 23 1 11 6 7 2 169 | 24 2 11 6 7 12 170 | 171 | Impropers 172 | 173 | 1 1 1 2 3 7 174 | 2 1 9 3 4 2 175 | 3 1 10 4 5 3 176 | 4 1 8 5 4 6 177 | 5 1 11 6 7 5 178 | 6 1 12 7 6 2 179 | 180 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/benzene-class2b.data2: -------------------------------------------------------------------------------- 1 | LAMMPS data file via write_data, version 8 Jul 2013-ICMS, timestep = 13 2 | 3 | 12 atoms 4 | 2 atom types 5 | 12 bonds 6 | 2 bond types 7 | 18 angles 8 | 2 angle types 9 | 24 dihedrals 10 | 3 dihedral types 11 | 6 impropers 12 | 1 improper types 13 | 14 | -1.4180000000000000e-02 9.9858200000000004e+00 xlo xhi 15 | -0.0000000000000000e+00 1.0000000000000000e+01 ylo yhi 16 | -1.0000000000000000e+01 0.0000000000000000e+00 zlo zhi 17 | 18 | Masses 19 | 20 | 1 1.00797 21 | 2 12.0112 22 | 23 | Pair Coeffs 24 | 25 | 1 0.02 2.995 26 | 2 0.064 4.01 27 | 28 | Bond Coeffs 29 | 30 | 1 1.0982 372.825 -803.453 894.317 31 | 2 1.417 470.836 -627.618 1327.63 32 | 33 | Angle Coeffs 34 | 35 | 1 117.94 35.1558 -12.4682 0 36 | 2 118.9 61.0226 -34.9931 0 37 | 38 | BondBond Coeffs 39 | 40 | 1 1.0795 1.0982 1.417 41 | 2 68.2856 1.417 1.417 42 | 43 | BondAngle Coeffs 44 | 45 | 1 24.2183 20.0033 1.0982 1.417 46 | 2 28.8708 28.8708 1.417 1.417 47 | 48 | Dihedral Coeffs 49 | 50 | 1 0 0 3.9661 0 0 0 51 | 2 0 0 1.8769 0 0 0 52 | 3 8.3667 0 1.1932 0 0 0 53 | 54 | AngleAngleTorsion Coeffs 55 | 56 | 1 -4.8141 117.94 118.9 57 | 2 0.3598 117.94 117.94 58 | 3 0 118.9 118.9 59 | 60 | EndBondTorsion Coeffs 61 | 62 | 1 0 -0.4669 0 0 -6.8958 0 1.0982 1.417 63 | 2 0 -0.689 0 0 -0.689 0 1.0982 1.0982 64 | 3 -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417 65 | 66 | MiddleBondTorsion Coeffs 67 | 68 | 1 0 -1.1521 0 1.417 69 | 2 0 4.8228 0 1.417 70 | 3 27.5989 -2.312 0 1.417 71 | 72 | BondBond13 Coeffs 73 | 74 | 1 -6.2741 1.0982 1.417 75 | 2 -1.7077 1.0982 1.0982 76 | 3 53 1.417 1.417 77 | 78 | AngleTorsion Coeffs 79 | 80 | 1 0 2.7147 0 0 2.5014 0 117.94 118.9 81 | 2 0 2.4501 0 0 2.4501 0 117.94 117.94 82 | 3 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9 83 | 84 | Improper Coeffs 85 | 86 | 1 4.8912 0 87 | 88 | AngleAngle Coeffs 89 | 90 | 1 0 0 0 117.94 118.9 117.94 91 | 92 | Atoms 93 | 94 | 1 1 1 1.0199999999999999e-01 2.4934740594722666e+00 5.0000000000000000e+00 -5.0000000000000000e+00 0 0 0 95 | 2 1 2 -1.0199999999999999e-01 3.5923803339560756e+00 4.9999999999999982e+00 -5.0000000000000000e+00 0 0 0 96 | 3 1 2 -1.0199999999999999e-01 4.2890818316483230e+00 6.2068241003441083e+00 -5.0000000000000000e+00 0 0 0 97 | 4 1 2 -1.0199999999999999e-01 5.6825581683516759e+00 6.2068241003441074e+00 -5.0000000000000000e+00 0 0 0 98 | 5 1 2 -1.0199999999999999e-01 6.3792596660439251e+00 4.9999999999999982e+00 -5.0000000000000000e+00 0 0 0 99 | 6 1 2 -1.0199999999999999e-01 5.6825581683516804e+00 3.7931758996558931e+00 -5.0000000000000000e+00 0 0 0 100 | 7 1 2 -1.0199999999999999e-01 4.2890818316483195e+00 3.7931758996558931e+00 -5.0000000000000000e+00 0 0 0 101 | 8 1 1 1.0199999999999999e-01 7.4781659405277336e+00 5.0000000000000000e+00 -5.0000000000000000e+00 0 0 0 102 | 9 1 1 1.0199999999999999e-01 3.7395991894266301e+00 7.1585464568095123e+00 -5.0000000000000000e+00 0 0 0 103 | 10 1 1 1.0199999999999999e-01 6.2320408105733698e+00 7.1585464568095132e+00 -5.0000000000000000e+00 0 0 0 104 | 11 1 1 1.0199999999999999e-01 6.2320408105733698e+00 2.8414535431904864e+00 -5.0000000000000000e+00 0 0 0 105 | 12 1 1 1.0199999999999999e-01 3.7395991894266305e+00 2.8414535431904868e+00 -5.0000000000000000e+00 0 0 0 106 | 107 | Velocities 108 | 109 | 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 110 | 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 111 | 3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 112 | 4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 113 | 5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 114 | 6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 115 | 7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 116 | 8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 117 | 9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 118 | 10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 119 | 11 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 120 | 12 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 121 | 122 | Bonds 123 | 124 | 1 1 1 2 125 | 2 2 2 3 126 | 3 2 2 7 127 | 4 2 3 4 128 | 5 2 4 5 129 | 6 2 5 6 130 | 7 2 6 7 131 | 8 1 8 5 132 | 9 1 9 3 133 | 10 1 10 4 134 | 11 1 11 6 135 | 12 1 12 7 136 | 137 | Angles 138 | 139 | 1 1 1 2 3 140 | 2 1 1 2 7 141 | 3 2 3 2 7 142 | 4 2 2 3 4 143 | 5 1 9 3 2 144 | 6 1 9 3 4 145 | 7 2 3 4 5 146 | 8 1 10 4 3 147 | 9 1 10 4 5 148 | 10 1 8 5 4 149 | 11 2 4 5 6 150 | 12 1 8 5 6 151 | 13 2 5 6 7 152 | 14 1 11 6 5 153 | 15 1 11 6 7 154 | 16 2 2 7 6 155 | 17 1 12 7 2 156 | 18 1 12 7 6 157 | 158 | Dihedrals 159 | 160 | 1 1 1 2 3 4 161 | 2 2 1 2 3 9 162 | 3 3 7 2 3 4 163 | 4 1 1 2 7 6 164 | 5 2 1 2 7 12 165 | 6 3 3 2 7 6 166 | 7 1 9 3 2 7 167 | 8 3 2 3 4 5 168 | 9 1 9 3 4 5 169 | 10 2 9 3 4 10 170 | 11 1 10 4 3 2 171 | 12 3 3 4 5 6 172 | 13 2 10 4 5 8 173 | 14 1 10 4 5 6 174 | 15 1 8 5 4 3 175 | 16 3 4 5 6 7 176 | 17 1 8 5 6 7 177 | 18 2 8 5 6 11 178 | 19 1 11 6 5 4 179 | 20 3 5 6 7 2 180 | 21 1 11 6 7 2 181 | 22 2 11 6 7 12 182 | 23 1 12 7 2 3 183 | 24 1 12 7 6 5 184 | 185 | Impropers 186 | 187 | 1 1 1 2 3 7 188 | 2 1 9 3 4 2 189 | 3 1 10 4 5 3 190 | 4 1 8 5 4 6 191 | 5 1 11 6 7 5 192 | 6 1 12 7 6 2 193 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/ethane-class1.data: -------------------------------------------------------------------------------- 1 | LAMMPS data file. msi2lmp v3.9.7 / 24 Oct 2015 / CGCMM for ethane-class1 2 | 3 | 8 atoms 4 | 7 bonds 5 | 12 angles 6 | 9 dihedrals 7 | 0 impropers 8 | 9 | 2 atom types 10 | 2 bond types 11 | 2 angle types 12 | 1 dihedral types 13 | 14 | 0.214545000 10.214545000 xlo xhi 15 | 0.114180000 10.114180000 ylo yhi 16 | -10.000145000 -0.000145000 zlo zhi 17 | 18 | Masses 19 | 20 | 1 12.011150 # c 21 | 2 1.007970 # h 22 | 23 | Pair Coeffs # lj/cut/coul/long 24 | 25 | 1 0.1599999990 3.4745050026 # c 26 | 2 0.0380000011 2.4499714540 # h 27 | 28 | Bond Coeffs # harmonic 29 | 30 | 1 322.7158 1.5260 # c-c 31 | 2 340.6175 1.1050 # c-h 32 | 33 | Angle Coeffs # harmonic 34 | 35 | 1 44.4000 110.0000 # c-c-h 36 | 2 39.5000 106.4000 # h-c-h 37 | 38 | Dihedral Coeffs # harmonic 39 | 40 | 1 0.1581 1 3 # h-c-c-h 41 | 42 | Atoms # full 43 | 44 | 1 1 1 -0.080000 4.462910000 5.148330000 -5.000410000 0 0 0 # c 45 | 2 1 1 -0.080000 5.965490000 5.079930000 -4.999750000 0 0 0 # c 46 | 3 1 2 0.027000 4.099550000 6.054480000 -5.502500000 0 0 0 # h 47 | 4 1 2 0.027000 4.020330000 4.288350000 -5.519840000 0 0 0 # h 48 | 5 1 2 0.027000 4.057610000 5.156680000 -3.980190000 0 0 0 # h 49 | 6 1 2 0.027000 6.409980000 5.944880000 -4.490510000 0 0 0 # h 50 | 7 1 2 0.027000 6.329880000 4.179410000 -4.488110000 0 0 0 # h 51 | 8 1 2 0.027000 6.370610000 5.061380000 -6.019850000 0 0 0 # h 52 | 53 | Bonds 54 | 55 | 1 1 1 2 56 | 2 2 1 3 57 | 3 2 1 4 58 | 4 2 1 5 59 | 5 2 2 6 60 | 6 2 2 7 61 | 7 2 2 8 62 | 63 | Angles 64 | 65 | 1 1 2 1 3 66 | 2 1 2 1 4 67 | 3 1 2 1 5 68 | 4 2 3 1 4 69 | 5 2 3 1 5 70 | 6 2 4 1 5 71 | 7 1 1 2 6 72 | 8 1 1 2 7 73 | 9 1 1 2 8 74 | 10 2 6 2 7 75 | 11 2 6 2 8 76 | 12 2 7 2 8 77 | 78 | Dihedrals 79 | 80 | 1 1 3 1 2 6 81 | 2 1 3 1 2 7 82 | 3 1 3 1 2 8 83 | 4 1 4 1 2 6 84 | 5 1 4 1 2 7 85 | 6 1 4 1 2 8 86 | 7 1 5 1 2 6 87 | 8 1 5 1 2 7 88 | 9 1 5 1 2 8 89 | 90 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/ethane-class1.data2: -------------------------------------------------------------------------------- 1 | LAMMPS data file via write_data, version 24 Oct 2015-ICMS, timestep = 16 2 | 3 | 8 atoms 4 | 2 atom types 5 | 7 bonds 6 | 2 bond types 7 | 12 angles 8 | 2 angle types 9 | 9 dihedrals 10 | 1 dihedral types 11 | 12 | 2.1454500000000001e-01 1.0214544999999999e+01 xlo xhi 13 | 1.1418000000000000e-01 1.0114179999999999e+01 ylo yhi 14 | -1.0000145000000000e+01 -1.4500000000000000e-04 zlo zhi 15 | 16 | Masses 17 | 18 | 1 12.0112 19 | 2 1.00797 20 | 21 | Pair Coeffs # lj/cut/coul/cut 22 | 23 | 1 0.16 3.47451 24 | 2 0.038 2.44997 25 | 26 | Bond Coeffs # harmonic 27 | 28 | 1 322.716 1.526 29 | 2 340.618 1.105 30 | 31 | Angle Coeffs # harmonic 32 | 33 | 1 44.4 110 34 | 2 39.5 106.4 35 | 36 | Dihedral Coeffs # harmonic 37 | 38 | 1 0.1581 1 3 39 | 40 | Atoms # full 41 | 42 | 1 1 1 -8.0000000000000002e-02 4.4524466695000546e+00 5.1487002164026885e+00 -5.0006302347485345e+00 0 0 0 43 | 2 1 1 -8.0000000000000002e-02 5.9766896892153030e+00 5.0796889426210985e+00 -4.9996544827175731e+00 0 0 0 44 | 3 1 2 2.7000000000000000e-02 4.0938947910110901e+00 6.0620658648029728e+00 -5.5084975543469561e+00 0 0 0 45 | 4 1 2 2.7000000000000000e-02 4.0131227861508476e+00 4.2799775608175219e+00 -5.5231947126945471e+00 0 0 0 46 | 5 1 2 2.7000000000000000e-02 4.0519859498275457e+00 5.1583490086462893e+00 -3.9709421079082223e+00 0 0 0 47 | 6 1 2 2.7000000000000000e-02 6.4161294697399160e+00 5.9524744856787599e+00 -4.4838711524807371e+00 0 0 0 48 | 7 1 2 2.7000000000000000e-02 6.3353624851758052e+00 4.1701774309268549e+00 -4.4849204427200817e+00 0 0 0 49 | 8 1 2 2.7000000000000000e-02 6.3767281593794412e+00 5.0620064901038129e+00 -6.0294493123833437e+00 0 0 0 50 | 51 | Velocities 52 | 53 | 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 54 | 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 55 | 3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 56 | 4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 57 | 5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 58 | 6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 59 | 7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 60 | 8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 61 | 62 | Bonds 63 | 64 | 1 1 1 2 65 | 2 2 1 3 66 | 3 2 1 4 67 | 4 2 1 5 68 | 5 2 2 6 69 | 6 2 2 7 70 | 7 2 2 8 71 | 72 | Angles 73 | 74 | 1 1 2 1 3 75 | 2 1 2 1 4 76 | 3 1 2 1 5 77 | 4 2 3 1 4 78 | 5 2 3 1 5 79 | 6 2 4 1 5 80 | 7 1 1 2 6 81 | 8 1 1 2 7 82 | 9 1 1 2 8 83 | 10 2 6 2 7 84 | 11 2 6 2 8 85 | 12 2 7 2 8 86 | 87 | Dihedrals 88 | 89 | 1 1 3 1 2 6 90 | 2 1 3 1 2 7 91 | 3 1 3 1 2 8 92 | 4 1 4 1 2 6 93 | 5 1 4 1 2 7 94 | 6 1 4 1 2 8 95 | 7 1 5 1 2 6 96 | 8 1 5 1 2 7 97 | 9 1 5 1 2 8 98 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/ethane-class2a.data: -------------------------------------------------------------------------------- 1 | LAMMPS data file. msi2lmp v3.9.7 / 24 Oct 2015 / CGCMM for ethane-class2a 2 | 3 | 8 atoms 4 | 7 bonds 5 | 12 angles 6 | 9 dihedrals 7 | 8 impropers 8 | 9 | 2 atom types 10 | 2 bond types 11 | 2 angle types 12 | 1 dihedral types 13 | 2 improper types 14 | 15 | 0.214545000 10.214545000 xlo xhi 16 | 0.114180000 10.114180000 ylo yhi 17 | -10.000145000 -0.000145000 zlo zhi 18 | 19 | Masses 20 | 21 | 1 12.011150 # c4 22 | 2 1.007970 # h1 23 | 24 | Pair Coeffs # lj/class2/coul/long 25 | 26 | 1 0.0620000000 3.8540000000 # c4 27 | 2 0.0230000000 2.8780000000 # h1 28 | 29 | Bond Coeffs # class2 30 | 31 | 1 1.5300 299.6700 -501.7700 679.8100 # c4-c4 32 | 2 1.1010 345.0000 -691.8900 844.6000 # c4-h1 33 | 34 | Angle Coeffs # class2 35 | 36 | 1 110.7700 41.4530 -10.6040 5.1290 # c4-c4-h1 37 | 2 107.6600 39.6410 -12.9210 -2.4318 # h1-c4-h1 38 | 39 | Dihedral Coeffs # class2 40 | 41 | 1 -0.1432 0.0000 0.0617 0.0000 -0.1530 0.0000# h1-c4-c4-h1 42 | 43 | Improper Coeffs # class2 44 | 45 | 1 0.0000 0.0000 46 | 2 0.0000 0.0000 47 | 48 | BondBond Coeffs 49 | 50 | 1 3.3872 1.5300 1.1010 51 | 2 5.3316 1.1010 1.1010 52 | 53 | BondAngle Coeffs 54 | 55 | 1 20.7540 11.4210 1.5300 1.1010 56 | 2 18.1030 18.1030 1.1010 1.1010 57 | 58 | AngleAngle Coeffs 59 | 60 | 1 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700 61 | 2 -0.3157 -0.3157 -0.3157 107.6600 107.6600 107.6600 62 | 63 | AngleAngleTorsion Coeffs 64 | 65 | 1 -12.5640 110.7700 110.7700 66 | 67 | EndBondTorsion Coeffs 68 | 69 | 1 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010 70 | 71 | MiddleBondTorsion Coeffs 72 | 73 | 1 -14.2610 -0.5322 -0.4864 1.5300 74 | 75 | BondBond13 Coeffs 76 | 77 | 1 0.0000 1.1010 1.1010 78 | 79 | AngleTorsion Coeffs 80 | 81 | 1 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700 82 | 83 | Atoms # full 84 | 85 | 1 1 1 -0.080000 4.462910000 5.148330000 -5.000410000 0 0 0 # c4 86 | 2 1 1 -0.080000 5.965490000 5.079930000 -4.999750000 0 0 0 # c4 87 | 3 1 2 0.027000 4.099550000 6.054480000 -5.502500000 0 0 0 # h1 88 | 4 1 2 0.027000 4.020330000 4.288350000 -5.519840000 0 0 0 # h1 89 | 5 1 2 0.027000 4.057610000 5.156680000 -3.980190000 0 0 0 # h1 90 | 6 1 2 0.027000 6.409980000 5.944880000 -4.490510000 0 0 0 # h1 91 | 7 1 2 0.027000 6.329880000 4.179410000 -4.488110000 0 0 0 # h1 92 | 8 1 2 0.027000 6.370610000 5.061380000 -6.019850000 0 0 0 # h1 93 | 94 | Bonds 95 | 96 | 1 1 1 2 97 | 2 2 1 3 98 | 3 2 1 4 99 | 4 2 1 5 100 | 5 2 2 6 101 | 6 2 2 7 102 | 7 2 2 8 103 | 104 | Angles 105 | 106 | 1 1 2 1 3 107 | 2 1 2 1 4 108 | 3 1 2 1 5 109 | 4 2 3 1 4 110 | 5 2 3 1 5 111 | 6 2 4 1 5 112 | 7 1 1 2 6 113 | 8 1 1 2 7 114 | 9 1 1 2 8 115 | 10 2 6 2 7 116 | 11 2 6 2 8 117 | 12 2 7 2 8 118 | 119 | Dihedrals 120 | 121 | 1 1 3 1 2 6 122 | 2 1 3 1 2 7 123 | 3 1 3 1 2 8 124 | 4 1 4 1 2 6 125 | 5 1 4 1 2 7 126 | 6 1 4 1 2 8 127 | 7 1 5 1 2 6 128 | 8 1 5 1 2 7 129 | 9 1 5 1 2 8 130 | 131 | Impropers 132 | 133 | 1 1 2 1 3 4 134 | 2 1 2 1 3 5 135 | 3 1 2 1 4 5 136 | 4 2 3 1 4 5 137 | 5 1 1 2 6 7 138 | 6 1 1 2 6 8 139 | 7 1 1 2 7 8 140 | 8 2 6 2 7 8 141 | 142 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/ethane-class2a.data2: -------------------------------------------------------------------------------- 1 | LAMMPS data file via write_data, version 24 Oct 2015-ICMS, timestep = 100 2 | 3 | 8 atoms 4 | 2 atom types 5 | 7 bonds 6 | 2 bond types 7 | 12 angles 8 | 2 angle types 9 | 9 dihedrals 10 | 1 dihedral types 11 | 8 impropers 12 | 2 improper types 13 | 14 | 2.1454500000000001e-01 1.0214544999999999e+01 xlo xhi 15 | 1.1418000000000000e-01 1.0114179999999999e+01 ylo yhi 16 | -1.0000145000000000e+01 -1.4500000000000000e-04 zlo zhi 17 | 18 | Masses 19 | 20 | 1 12.0112 21 | 2 1.00797 22 | 23 | Pair Coeffs # lj/class2/coul/cut 24 | 25 | 1 0.062 3.854 26 | 2 0.023 2.878 27 | 28 | Bond Coeffs # class2 29 | 30 | 1 1.53 299.67 -501.77 679.81 31 | 2 1.101 345 -691.89 844.6 32 | 33 | Angle Coeffs # class2 34 | 35 | 1 110.77 41.453 -10.604 5.129 36 | 2 107.66 39.641 -12.921 -2.4318 37 | 38 | BondBond Coeffs 39 | 40 | 1 3.3872 1.53 1.101 41 | 2 5.3316 1.101 1.101 42 | 43 | BondAngle Coeffs 44 | 45 | 1 20.754 11.421 1.53 1.101 46 | 2 18.103 18.103 1.101 1.101 47 | 48 | Dihedral Coeffs # class2 49 | 50 | 1 -0.1432 0 0.0617 0 -0.153 0 51 | 52 | AngleAngleTorsion Coeffs 53 | 54 | 1 -12.564 110.77 110.77 55 | 56 | EndBondTorsion Coeffs 57 | 58 | 1 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101 59 | 60 | MiddleBondTorsion Coeffs 61 | 62 | 1 -14.261 -0.5322 -0.4864 1.53 63 | 64 | BondBond13 Coeffs 65 | 66 | 1 0 1.101 1.101 67 | 68 | AngleTorsion Coeffs 69 | 70 | 1 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77 71 | 72 | Improper Coeffs # class2 73 | 74 | 1 0 0 75 | 2 0 0 76 | 77 | AngleAngle Coeffs 78 | 79 | 1 0.2738 -0.4825 0.2738 110.77 107.66 110.77 80 | 2 -0.3157 -0.3157 -0.3157 107.66 107.66 107.66 81 | 82 | Atoms # full 83 | 84 | 1 1 1 -8.0000000000000002e-02 4.4544123665337896e+00 5.1486516372092170e+00 -5.0006962362392784e+00 0 0 0 85 | 2 1 1 -8.0000000000000002e-02 5.9747371453052525e+00 5.0799344018788561e+00 -4.9995040022823884e+00 0 0 0 86 | 3 1 2 2.7000000000000000e-02 4.1025609324394567e+00 6.0613274359488347e+00 -5.5070580540513703e+00 0 0 0 87 | 4 1 2 2.7000000000000000e-02 4.0222670265180884e+00 4.2808733867818995e+00 -5.5237599275364175e+00 0 0 0 88 | 5 1 2 2.7000000000000000e-02 4.0608188439305533e+00 5.1567248480305103e+00 -3.9719768549622634e+00 0 0 0 89 | 6 1 2 2.7000000000000000e-02 6.4075897652590026e+00 5.9527908182889586e+00 -4.4851804392097590e+00 0 0 0 90 | 7 1 2 2.7000000000000000e-02 6.3265284020976820e+00 4.1718477784918555e+00 -4.4843929146465413e+00 0 0 0 91 | 8 1 2 2.7000000000000000e-02 6.3674455179161704e+00 5.0612896933698677e+00 -6.0285915710719840e+00 0 0 0 92 | 93 | Velocities 94 | 95 | 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 96 | 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 97 | 3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 98 | 4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 99 | 5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 100 | 6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 101 | 7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 102 | 8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 103 | 104 | Bonds 105 | 106 | 1 1 1 2 107 | 2 2 1 3 108 | 3 2 1 4 109 | 4 2 1 5 110 | 5 2 2 6 111 | 6 2 2 7 112 | 7 2 2 8 113 | 114 | Angles 115 | 116 | 1 1 2 1 3 117 | 2 1 2 1 4 118 | 3 1 2 1 5 119 | 4 2 3 1 4 120 | 5 2 3 1 5 121 | 6 2 4 1 5 122 | 7 1 1 2 6 123 | 8 1 1 2 7 124 | 9 1 1 2 8 125 | 10 2 6 2 7 126 | 11 2 6 2 8 127 | 12 2 7 2 8 128 | 129 | Dihedrals 130 | 131 | 1 1 3 1 2 6 132 | 2 1 3 1 2 7 133 | 3 1 3 1 2 8 134 | 4 1 4 1 2 6 135 | 5 1 4 1 2 7 136 | 6 1 4 1 2 8 137 | 7 1 5 1 2 6 138 | 8 1 5 1 2 7 139 | 9 1 5 1 2 8 140 | 141 | Impropers 142 | 143 | 1 1 2 1 3 4 144 | 2 1 2 1 3 5 145 | 3 1 2 1 4 5 146 | 4 2 3 1 4 5 147 | 5 1 1 2 6 7 148 | 6 1 1 2 6 8 149 | 7 1 1 2 7 8 150 | 8 2 6 2 7 8 151 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/ethane-class2b.data: -------------------------------------------------------------------------------- 1 | LAMMPS data file. msi2lmp v3.9.7 / 24 Oct 2015 / CGCMM for ethane-class2b 2 | 3 | 8 atoms 4 | 7 bonds 5 | 12 angles 6 | 9 dihedrals 7 | 8 impropers 8 | 9 | 2 atom types 10 | 2 bond types 11 | 2 angle types 12 | 1 dihedral types 13 | 2 improper types 14 | 15 | 0.214545000 10.214545000 xlo xhi 16 | 0.114180000 10.114180000 ylo yhi 17 | -10.000145000 -0.000145000 zlo zhi 18 | 19 | Masses 20 | 21 | 1 12.011150 # c 22 | 2 1.007970 # h 23 | 24 | Pair Coeffs # lj/class2/coul/long 25 | 26 | 1 0.0540000000 4.0100000000 # c 27 | 2 0.0200000000 2.9950000000 # h 28 | 29 | Bond Coeffs # class2 30 | 31 | 1 1.5300 299.6700 -501.7700 679.8100 # c-c 32 | 2 1.1010 345.0000 -691.8900 844.6000 # c-h 33 | 34 | Angle Coeffs # class2 35 | 36 | 1 110.7700 41.4530 -10.6040 5.1290 # c-c-h 37 | 2 107.6600 39.6410 -12.9210 -2.4318 # h-c-h 38 | 39 | Dihedral Coeffs # class2 40 | 41 | 1 -0.1432 0.0000 0.0617 0.0000 -0.1083 0.0000# h-c-c-h 42 | 43 | Improper Coeffs # class2 44 | 45 | 1 0.0000 0.0000 46 | 2 0.0000 0.0000 47 | 48 | BondBond Coeffs 49 | 50 | 1 3.3872 1.5300 1.1010 51 | 2 5.3316 1.1010 1.1010 52 | 53 | BondAngle Coeffs 54 | 55 | 1 20.7540 11.4210 1.5300 1.1010 56 | 2 18.1030 18.1030 1.1010 1.1010 57 | 58 | AngleAngle Coeffs 59 | 60 | 1 0.2738 -0.4825 0.2738 110.7700 107.6600 110.7700 61 | 2 -0.3157 -0.3157 -0.3157 107.6600 107.6600 107.6600 62 | 63 | AngleAngleTorsion Coeffs 64 | 65 | 1 -12.5640 110.7700 110.7700 66 | 67 | EndBondTorsion Coeffs 68 | 69 | 1 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010 70 | 71 | MiddleBondTorsion Coeffs 72 | 73 | 1 -14.2610 -0.5322 -0.4864 1.5300 74 | 75 | BondBond13 Coeffs 76 | 77 | 1 0.0000 1.1010 1.1010 78 | 79 | AngleTorsion Coeffs 80 | 81 | 1 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700 82 | 83 | Atoms # full 84 | 85 | 1 1 1 -0.080000 4.462910000 5.148330000 -5.000410000 0 0 0 # c 86 | 2 1 1 -0.080000 5.965490000 5.079930000 -4.999750000 0 0 0 # c 87 | 3 1 2 0.027000 4.099550000 6.054480000 -5.502500000 0 0 0 # h 88 | 4 1 2 0.027000 4.020330000 4.288350000 -5.519840000 0 0 0 # h 89 | 5 1 2 0.027000 4.057610000 5.156680000 -3.980190000 0 0 0 # h 90 | 6 1 2 0.027000 6.409980000 5.944880000 -4.490510000 0 0 0 # h 91 | 7 1 2 0.027000 6.329880000 4.179410000 -4.488110000 0 0 0 # h 92 | 8 1 2 0.027000 6.370610000 5.061380000 -6.019850000 0 0 0 # h 93 | 94 | Bonds 95 | 96 | 1 1 1 2 97 | 2 2 1 3 98 | 3 2 1 4 99 | 4 2 1 5 100 | 5 2 2 6 101 | 6 2 2 7 102 | 7 2 2 8 103 | 104 | Angles 105 | 106 | 1 1 2 1 3 107 | 2 1 2 1 4 108 | 3 1 2 1 5 109 | 4 2 3 1 4 110 | 5 2 3 1 5 111 | 6 2 4 1 5 112 | 7 1 1 2 6 113 | 8 1 1 2 7 114 | 9 1 1 2 8 115 | 10 2 6 2 7 116 | 11 2 6 2 8 117 | 12 2 7 2 8 118 | 119 | Dihedrals 120 | 121 | 1 1 3 1 2 6 122 | 2 1 3 1 2 7 123 | 3 1 3 1 2 8 124 | 4 1 4 1 2 6 125 | 5 1 4 1 2 7 126 | 6 1 4 1 2 8 127 | 7 1 5 1 2 6 128 | 8 1 5 1 2 7 129 | 9 1 5 1 2 8 130 | 131 | Impropers 132 | 133 | 1 1 2 1 3 4 134 | 2 1 2 1 3 5 135 | 3 1 2 1 4 5 136 | 4 2 3 1 4 5 137 | 5 1 1 2 6 7 138 | 6 1 1 2 6 8 139 | 7 1 1 2 7 8 140 | 8 2 6 2 7 8 141 | 142 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/ethane-class2b.data2: -------------------------------------------------------------------------------- 1 | LAMMPS data file via write_data, version 24 Oct 2015-ICMS, timestep = 11 2 | 3 | 8 atoms 4 | 2 atom types 5 | 7 bonds 6 | 2 bond types 7 | 12 angles 8 | 2 angle types 9 | 9 dihedrals 10 | 1 dihedral types 11 | 8 impropers 12 | 2 improper types 13 | 14 | 2.1454500000000001e-01 1.0214544999999999e+01 xlo xhi 15 | 1.1418000000000000e-01 1.0114179999999999e+01 ylo yhi 16 | -1.0000145000000000e+01 -1.4500000000000000e-04 zlo zhi 17 | 18 | Masses 19 | 20 | 1 12.0112 21 | 2 1.00797 22 | 23 | Pair Coeffs # lj/class2/coul/cut 24 | 25 | 1 0.054 4.01 26 | 2 0.02 2.995 27 | 28 | Bond Coeffs # class2 29 | 30 | 1 1.53 299.67 -501.77 679.81 31 | 2 1.101 345 -691.89 844.6 32 | 33 | Angle Coeffs # class2 34 | 35 | 1 110.77 41.453 -10.604 5.129 36 | 2 107.66 39.641 -12.921 -2.4318 37 | 38 | BondBond Coeffs 39 | 40 | 1 3.3872 1.53 1.101 41 | 2 5.3316 1.101 1.101 42 | 43 | BondAngle Coeffs 44 | 45 | 1 20.754 11.421 1.53 1.101 46 | 2 18.103 18.103 1.101 1.101 47 | 48 | Dihedral Coeffs # class2 49 | 50 | 1 -0.1432 0 0.0617 0 -0.1083 0 51 | 52 | AngleAngleTorsion Coeffs 53 | 54 | 1 -12.564 110.77 110.77 55 | 56 | EndBondTorsion Coeffs 57 | 58 | 1 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101 59 | 60 | MiddleBondTorsion Coeffs 61 | 62 | 1 -14.261 -0.5322 -0.4864 1.53 63 | 64 | BondBond13 Coeffs 65 | 66 | 1 0 1.101 1.101 67 | 68 | AngleTorsion Coeffs 69 | 70 | 1 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77 71 | 72 | Improper Coeffs # class2 73 | 74 | 1 0 0 75 | 2 0 0 76 | 77 | AngleAngle Coeffs 78 | 79 | 1 0.2738 -0.4825 0.2738 110.77 107.66 110.77 80 | 2 -0.3157 -0.3157 -0.3157 107.66 107.66 107.66 81 | 82 | Atoms # full 83 | 84 | 1 1 1 -8.0000000000000002e-02 4.4541504448288123e+00 5.1486715981549755e+00 -5.0007109878435214e+00 0 0 0 85 | 2 1 1 -8.0000000000000002e-02 5.9750405660608887e+00 5.0798943241546031e+00 -4.9995076367000628e+00 0 0 0 86 | 3 1 2 2.7000000000000000e-02 4.1036706029623886e+00 6.0613108544497596e+00 -5.5071821074104745e+00 0 0 0 87 | 4 1 2 2.7000000000000000e-02 4.0233947566823307e+00 4.2807839467327344e+00 -5.5237351329632576e+00 0 0 0 88 | 5 1 2 2.7000000000000000e-02 4.0620677456311283e+00 5.1567196976631307e+00 -3.9718963609010816e+00 0 0 0 89 | 6 1 2 2.7000000000000000e-02 6.4063899019512558e+00 5.9527037106765199e+00 -4.4851566090466166e+00 0 0 0 90 | 7 1 2 2.7000000000000000e-02 6.3253329542276440e+00 4.1719698649751500e+00 -4.4844570638742756e+00 0 0 0 91 | 8 1 2 2.7000000000000000e-02 6.3663130276555524e+00 5.0613860031931273e+00 -6.0285141012607104e+00 0 0 0 92 | 93 | Velocities 94 | 95 | 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 96 | 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 97 | 3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 98 | 4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 99 | 5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 100 | 6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 101 | 7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 102 | 8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 103 | 104 | Bonds 105 | 106 | 1 1 1 2 107 | 2 2 1 3 108 | 3 2 1 4 109 | 4 2 1 5 110 | 5 2 2 6 111 | 6 2 2 7 112 | 7 2 2 8 113 | 114 | Angles 115 | 116 | 1 1 2 1 3 117 | 2 1 2 1 4 118 | 3 1 2 1 5 119 | 4 2 3 1 4 120 | 5 2 3 1 5 121 | 6 2 4 1 5 122 | 7 1 1 2 6 123 | 8 1 1 2 7 124 | 9 1 1 2 8 125 | 10 2 6 2 7 126 | 11 2 6 2 8 127 | 12 2 7 2 8 128 | 129 | Dihedrals 130 | 131 | 1 1 3 1 2 6 132 | 2 1 3 1 2 7 133 | 3 1 3 1 2 8 134 | 4 1 4 1 2 6 135 | 5 1 4 1 2 7 136 | 6 1 4 1 2 8 137 | 7 1 5 1 2 6 138 | 8 1 5 1 2 7 139 | 9 1 5 1 2 8 140 | 141 | Impropers 142 | 143 | 1 1 2 1 3 4 144 | 2 1 2 1 3 5 145 | 3 1 2 1 4 5 146 | 4 2 3 1 4 5 147 | 5 1 1 2 6 7 148 | 6 1 1 2 6 8 149 | 7 1 1 2 7 8 150 | 8 2 6 2 7 8 151 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/ethane-oplsaa.data: -------------------------------------------------------------------------------- 1 | LAMMPS data file. msi2lmp v3.9.7 / 24 Oct 2015 / CGCMM for ethane-oplsaa 2 | 3 | 8 atoms 4 | 7 bonds 5 | 12 angles 6 | 9 dihedrals 7 | 0 impropers 8 | 9 | 2 atom types 10 | 2 bond types 11 | 2 angle types 12 | 1 dihedral types 13 | 14 | -5.000000000 5.000000000 xlo xhi 15 | -5.000000000 5.000000000 ylo yhi 16 | -5.000000000 5.000000000 zlo zhi 17 | 18 | Masses 19 | 20 | 1 12.011150 # CT 21 | 2 1.007970 # HC 22 | 23 | Pair Coeffs # lj/cut/coul/long 24 | 25 | 1 0.0659999660 3.5000001502 # CT 26 | 2 0.0300002576 2.4999982005 # HC 27 | 28 | Bond Coeffs # harmonic 29 | 30 | 1 268.0000 1.5290 # CT-CT 31 | 2 340.0000 1.0900 # CT-HC 32 | 33 | Angle Coeffs # harmonic 34 | 35 | 1 37.5000 110.7000 # CT-CT-HC 36 | 2 33.0000 107.8000 # HC-CT-HC 37 | 38 | Dihedral Coeffs # opls 39 | 40 | 1 0.0000 0.0000 0.3180 0.0000 # HC-CT-CT-HC 41 | 42 | Atoms # full 43 | 44 | 1 1 1 -0.180000 4.462910000 -4.851670000 4.999590000 0 1 -1 # CT 45 | 2 1 1 -0.180000 -4.034510000 -4.920070000 -4.999750000 1 1 0 # CT 46 | 3 1 2 0.060000 4.099550000 -3.945520000 4.497500000 0 1 -1 # HC 47 | 4 1 2 0.060000 4.020330000 4.288350000 4.480160000 0 0 -1 # HC 48 | 5 1 2 0.060000 4.057610000 -4.843320000 -3.980190000 0 1 0 # HC 49 | 6 1 2 0.060000 -3.590020000 -4.055120000 -4.490510000 1 1 0 # HC 50 | 7 1 2 0.060000 -3.670120000 4.179410000 -4.488110000 1 0 0 # HC 51 | 8 1 2 0.060000 -3.629390000 -4.938620000 3.980150000 1 1 -1 # HC 52 | 53 | Bonds 54 | 55 | 1 1 1 2 56 | 2 2 1 3 57 | 3 2 1 4 58 | 4 2 1 5 59 | 5 2 2 6 60 | 6 2 2 7 61 | 7 2 2 8 62 | 63 | Angles 64 | 65 | 1 1 2 1 3 66 | 2 1 2 1 4 67 | 3 1 2 1 5 68 | 4 2 3 1 4 69 | 5 2 3 1 5 70 | 6 2 4 1 5 71 | 7 1 1 2 6 72 | 8 1 1 2 7 73 | 9 1 1 2 8 74 | 10 2 6 2 7 75 | 11 2 6 2 8 76 | 12 2 7 2 8 77 | 78 | Dihedrals 79 | 80 | 1 1 3 1 2 6 81 | 2 1 3 1 2 7 82 | 3 1 3 1 2 8 83 | 4 1 4 1 2 6 84 | 5 1 4 1 2 7 85 | 6 1 4 1 2 8 86 | 7 1 5 1 2 6 87 | 8 1 5 1 2 7 88 | 9 1 5 1 2 8 89 | 90 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/ethane-oplsaa.data2: -------------------------------------------------------------------------------- 1 | LAMMPS data file via write_data, version 24 Oct 2015-ICMS, timestep = 60 2 | 3 | 8 atoms 4 | 2 atom types 5 | 7 bonds 6 | 2 bond types 7 | 12 angles 8 | 2 angle types 9 | 9 dihedrals 10 | 1 dihedral types 11 | 12 | -5.0000000000000000e+00 5.0000000000000000e+00 xlo xhi 13 | -5.0000000000000000e+00 5.0000000000000000e+00 ylo yhi 14 | -5.0000000000000000e+00 5.0000000000000000e+00 zlo zhi 15 | 16 | Masses 17 | 18 | 1 12.0112 19 | 2 1.00797 20 | 21 | Pair Coeffs # lj/cut/coul/cut 22 | 23 | 1 0.066 3.5 24 | 2 0.0300003 2.5 25 | 26 | Bond Coeffs # harmonic 27 | 28 | 1 268 1.529 29 | 2 340 1.09 30 | 31 | Angle Coeffs # harmonic 32 | 33 | 1 37.5 110.7 34 | 2 33 107.8 35 | 36 | Dihedral Coeffs # opls 37 | 38 | 1 0 0 0.318 0 39 | 40 | Atoms # full 41 | 42 | 1 1 1 -1.7999999999999999e-01 4.4520961794662339e+00 -4.8331316055118139e+00 4.9921953697666774e+00 0 1 -1 43 | 2 1 1 -1.7999999999999999e-01 -4.0208267456132498e+00 -4.9408970766661060e+00 -4.9962668603193716e+00 1 1 0 44 | 3 1 2 5.9999999999999998e-02 4.1241637410618237e+00 -3.9187715229527775e+00 4.4953501727331462e+00 0 1 -1 45 | 4 1 2 5.9999999999999998e-02 3.9927847754165149e+00 4.3246628372301563e+00 4.4708516600772406e+00 0 0 -1 46 | 5 1 2 5.9999999999999998e-02 4.0591846610420355e+00 -4.8176278098672096e+00 -3.9904372631272924e+00 0 1 0 47 | 6 1 2 5.9999999999999998e-02 -3.5762405194770461e+00 -4.0716394256255244e+00 -4.5137080084717223e+00 1 1 0 48 | 7 1 2 5.9999999999999998e-02 -3.6936651570105905e+00 4.1740778258698201e+00 -4.4511582014826949e+00 1 0 0 49 | 8 1 2 5.9999999999999998e-02 -3.6211369348857190e+00 4.9967667775234554e+00 3.9920131308240276e+00 1 0 -1 50 | 51 | Velocities 52 | 53 | 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 54 | 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 55 | 3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 56 | 4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 57 | 5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 58 | 6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 59 | 7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 60 | 8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 61 | 62 | Bonds 63 | 64 | 1 1 1 2 65 | 2 2 1 3 66 | 3 2 1 4 67 | 4 2 1 5 68 | 5 2 2 6 69 | 6 2 2 7 70 | 7 2 2 8 71 | 72 | Angles 73 | 74 | 1 1 2 1 3 75 | 2 1 2 1 4 76 | 3 1 2 1 5 77 | 4 2 3 1 4 78 | 5 2 3 1 5 79 | 6 2 4 1 5 80 | 7 1 1 2 6 81 | 8 1 1 2 7 82 | 9 1 1 2 8 83 | 10 2 6 2 7 84 | 11 2 6 2 8 85 | 12 2 7 2 8 86 | 87 | Dihedrals 88 | 89 | 1 1 3 1 2 6 90 | 2 1 3 1 2 7 91 | 3 1 3 1 2 8 92 | 4 1 4 1 2 6 93 | 5 1 4 1 2 7 94 | 6 1 4 1 2 8 95 | 7 1 5 1 2 6 96 | 8 1 5 1 2 7 97 | 9 1 5 1 2 8 98 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/h2-h2o-class1.data: -------------------------------------------------------------------------------- 1 | LAMMPS data file. msi2lmp v3.9.7 / 24 Oct 2015 / CGCMM for h2-h2o-class1 2 | 3 | 5 atoms 4 | 3 bonds 5 | 1 angles 6 | 0 dihedrals 7 | 0 impropers 8 | 9 | 3 atom types 10 | 2 bond types 11 | 1 angle types 12 | 13 | -0.200000000 9.800000000 xlo xhi 14 | -0.200000000 9.800000000 ylo yhi 15 | 0.500000000 10.500000000 zlo zhi 16 | 17 | Masses 18 | 19 | 1 1.007970 # h 20 | 2 15.999400 # otip 21 | 3 1.007970 # htip 22 | 23 | Pair Coeffs # lj/cut/coul/long 24 | 25 | 1 0.0380000011 2.4499714540 # h 26 | 2 0.1520725945 3.1506561105 # otip 27 | 3 0.0000000000 0.0000000000 # htip 28 | 29 | Bond Coeffs # harmonic 30 | 31 | 1 398.7500 0.7461 # h-h 32 | 2 540.6336 0.9570 # otip-htip 33 | 34 | Angle Coeffs # harmonic 35 | 36 | 1 50.0000 104.5200 # htip-otip-htip 37 | 38 | Atoms # full 39 | 40 | 1 1 1 0.000000 4.600000000 5.000000000 2.500000000 0 0 0 # h 41 | 2 1 1 0.000000 5.400000000 5.000000000 2.500000000 0 0 0 # h 42 | 3 2 2 -0.834000 5.000000000 5.000000000 7.500000000 0 0 0 # otip 43 | 4 2 3 0.417000 4.000000000 5.000000000 7.500000000 0 0 0 # htip 44 | 5 2 3 0.417000 5.000000000 4.000000000 7.500000000 0 0 0 # htip 45 | 46 | Bonds 47 | 48 | 1 1 1 2 49 | 2 2 3 4 50 | 3 2 3 5 51 | 52 | Angles 53 | 54 | 1 1 4 3 5 55 | 56 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/h2-h2o-class1.data2: -------------------------------------------------------------------------------- 1 | LAMMPS data file via write_data, version 24 Oct 2015-ICMS, timestep = 16 2 | 3 | 5 atoms 4 | 3 atom types 5 | 3 bonds 6 | 2 bond types 7 | 1 angles 8 | 1 angle types 9 | 10 | -2.0000000000000001e-01 9.8000000000000007e+00 xlo xhi 11 | -2.0000000000000001e-01 9.8000000000000007e+00 ylo yhi 12 | 5.0000000000000000e-01 1.0500000000000000e+01 zlo zhi 13 | 14 | Masses 15 | 16 | 1 1.00797 17 | 2 15.9994 18 | 3 1.00797 19 | 20 | Pair Coeffs # lj/cut/coul/cut 21 | 22 | 1 0.038 2.44997 23 | 2 0.152073 3.15066 24 | 3 0 0 25 | 26 | Bond Coeffs # harmonic 27 | 28 | 1 398.75 0.7461 29 | 2 540.634 0.957 30 | 31 | Angle Coeffs # harmonic 32 | 33 | 1 50 104.52 34 | 35 | Atoms # full 36 | 37 | 1 1 1 0.0000000000000000e+00 4.6360793448580777e+00 4.9999989751288503e+00 2.5000000000000000e+00 0 0 0 38 | 2 1 1 0.0000000000000000e+00 5.3639187040369425e+00 4.9999989859260383e+00 2.5000000000000000e+00 0 0 0 39 | 3 2 2 -8.3399999999999996e-01 4.9272370060124890e+00 4.9272370489778368e+00 7.5000000000000000e+00 0 0 0 40 | 4 2 3 4.1699999999999998e-01 3.9745202805917161e+00 5.0982446721165102e+00 7.5000000000000000e+00 0 0 0 41 | 5 2 3 4.1699999999999998e-01 5.0982446645007720e+00 3.9745203178507658e+00 7.5000000000000000e+00 0 0 0 42 | 43 | Velocities 44 | 45 | 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 46 | 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 47 | 3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 48 | 4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 49 | 5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 50 | 51 | Bonds 52 | 53 | 1 1 1 2 54 | 2 2 3 4 55 | 3 2 3 5 56 | 57 | Angles 58 | 59 | 1 1 4 3 5 60 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/h2-h2o-class2b.data: -------------------------------------------------------------------------------- 1 | LAMMPS data file. msi2lmp v3.9.7 / 24 Oct 2015 / CGCMM for h2-h2o-class2b 2 | 3 | 5 atoms 4 | 3 bonds 5 | 1 angles 6 | 0 dihedrals 7 | 0 impropers 8 | 9 | 3 atom types 10 | 2 bond types 11 | 1 angle types 12 | 13 | -0.200000000 9.800000000 xlo xhi 14 | -0.200000000 9.800000000 ylo yhi 15 | -0.500000000 9.500000000 zlo zhi 16 | 17 | Masses 18 | 19 | 1 15.999400 # o* 20 | 2 1.007970 # h* 21 | 3 1.007970 # h 22 | 23 | Pair Coeffs # lj/class2/coul/long 24 | 25 | 1 0.2740000000 3.6080000000 # o* 26 | 2 0.0130000000 1.0980000000 # h* 27 | 3 0.0200000000 2.9950000000 # h 28 | 29 | Bond Coeffs # class2 30 | 31 | 1 0.9700 563.2800 -1428.2200 1902.1200 # o*-h* 32 | 2 0.7414 414.0000 0.0000 0.0000 # h-h 33 | 34 | Angle Coeffs # class2 35 | 36 | 1 103.7000 49.8400 -11.6000 -8.0000 # h*-o*-h* 37 | 38 | BondBond Coeffs 39 | 40 | 1 -9.5000 0.9700 0.9700 41 | 42 | BondAngle Coeffs 43 | 44 | 1 22.3500 22.3500 0.9700 0.9700 45 | 46 | Atoms # full 47 | 48 | 1 2 1 -0.834000 5.000000000 5.000000000 2.500000000 0 0 0 # o* 49 | 2 2 2 0.417000 4.000000000 5.000000000 2.500000000 0 0 0 # h* 50 | 3 2 2 0.417000 5.000000000 4.000000000 2.500000000 0 0 0 # h* 51 | 4 1 3 0.000000 4.600000000 5.000000000 7.500000000 0 0 0 # h 52 | 5 1 3 0.000000 5.400000000 5.000000000 7.500000000 0 0 0 # h 53 | 54 | Bonds 55 | 56 | 1 1 1 2 57 | 2 1 1 3 58 | 3 2 4 5 59 | 60 | Angles 61 | 62 | 1 1 2 1 3 63 | 64 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/h2-h2o-class2b.data2: -------------------------------------------------------------------------------- 1 | LAMMPS data file via write_data, version 24 Oct 2015-ICMS, timestep = 16 2 | 3 | 5 atoms 4 | 3 atom types 5 | 3 bonds 6 | 2 bond types 7 | 1 angles 8 | 1 angle types 9 | 10 | -2.0000000000000001e-01 9.8000000000000007e+00 xlo xhi 11 | -2.0000000000000001e-01 9.8000000000000007e+00 ylo yhi 12 | -5.0000000000000000e-01 9.5000000000000000e+00 zlo zhi 13 | 14 | Masses 15 | 16 | 1 15.9994 17 | 2 1.00797 18 | 3 1.00797 19 | 20 | Pair Coeffs # lj/class2/coul/cut 21 | 22 | 1 0.274 3.608 23 | 2 0.013 1.098 24 | 3 0.02 2.995 25 | 26 | Bond Coeffs # class2 27 | 28 | 1 0.97 563.28 -1428.22 1902.12 29 | 2 0.7414 414 0 0 30 | 31 | Angle Coeffs # class2 32 | 33 | 1 103.7 49.84 -11.6 -8 34 | 35 | BondBond Coeffs 36 | 37 | 1 -9.5 0.97 0.97 38 | 39 | BondAngle Coeffs 40 | 41 | 1 22.35 22.35 0.97 0.97 42 | 43 | Atoms # full 44 | 45 | 1 2 1 -8.3399999999999996e-01 4.9290882176945097e+00 4.9290882639548759e+00 2.5000000000000000e+00 0 0 0 46 | 2 2 2 4.1699999999999998e-01 3.9735950727002165e+00 5.0973194765083036e+00 2.5000000000000000e+00 0 0 0 47 | 3 2 2 4.1699999999999998e-01 5.0973194689799799e+00 3.9735951232668252e+00 2.5000000000000000e+00 0 0 0 48 | 4 1 3 0.0000000000000000e+00 4.6251317425574490e+00 4.9999985647449563e+00 7.5000000000000000e+00 0 0 0 49 | 5 1 3 0.0000000000000000e+00 5.3748654980678428e+00 4.9999985715250368e+00 7.5000000000000000e+00 0 0 0 50 | 51 | Velocities 52 | 53 | 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 54 | 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 55 | 3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 56 | 4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 57 | 5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 58 | 59 | Bonds 60 | 61 | 1 1 1 2 62 | 2 1 1 3 63 | 3 2 4 5 64 | 65 | Angles 66 | 67 | 1 1 2 1 3 68 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/hydrogen-class1.data: -------------------------------------------------------------------------------- 1 | LAMMPS data file from msi2lmp v3.8 for hydrogen-class1 2 | 3 | 2 atoms 4 | 1 bonds 5 | 0 angles 6 | 0 dihedrals 7 | 0 impropers 8 | 9 | 1 atom types 10 | 1 bond types 11 | 12 | 0.000000000 10.000000000 xlo xhi 13 | 0.000000000 10.000000000 ylo yhi 14 | 0.000000000 10.000000000 zlo zhi 15 | 16 | Masses 17 | 18 | 1 1.007970 19 | 20 | Pair Coeffs 21 | 22 | 1 0.0380000011 2.4499714540 23 | 24 | Bond Coeffs 25 | 26 | 1 398.7500 0.7461 27 | 28 | Atoms 29 | 30 | 1 1 1 0.000000 4.600000000 5.000000000 5.000000000 31 | 2 1 1 0.000000 5.400000000 5.000000000 5.000000000 32 | 33 | Bonds 34 | 35 | 1 1 1 2 36 | 37 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/hydrogen-class1.data2: -------------------------------------------------------------------------------- 1 | LAMMPS data file via write_data, version 8 Jul 2013-ICMS, timestep = 5 2 | 3 | 2 atoms 4 | 1 atom types 5 | 1 bonds 6 | 1 bond types 7 | 8 | 0.0000000000000000e+00 1.0000000000000000e+01 xlo xhi 9 | 0.0000000000000000e+00 1.0000000000000000e+01 ylo yhi 10 | 0.0000000000000000e+00 1.0000000000000000e+01 zlo zhi 11 | 12 | Masses 13 | 14 | 1 1.00797 15 | 16 | Pair Coeffs 17 | 18 | 1 0.038 2.44997 19 | 20 | Bond Coeffs 21 | 22 | 1 398.75 0.7461 23 | 24 | Atoms 25 | 26 | 1 1 1 0.0000000000000000e+00 4.6269506823868030e+00 5.0000000000000000e+00 5.0000000000000000e+00 0 0 0 27 | 2 1 1 0.0000000000000000e+00 5.3730493176131970e+00 5.0000000000000000e+00 5.0000000000000000e+00 0 0 0 28 | 29 | Velocities 30 | 31 | 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 32 | 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 33 | 34 | Bonds 35 | 36 | 1 1 1 2 37 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/hydrogen-class2a.data: -------------------------------------------------------------------------------- 1 | LAMMPS data file from msi2lmp v3.8 for hydrogen-class2a 2 | 3 | 2 atoms 4 | 1 bonds 5 | 0 angles 6 | 0 dihedrals 7 | 0 impropers 8 | 9 | 1 atom types 10 | 1 bond types 11 | 12 | 0.000000000 10.000000000 xlo xhi 13 | 0.000000000 10.000000000 ylo yhi 14 | 0.000000000 10.000000000 zlo zhi 15 | 16 | Masses 17 | 18 | 1 1.007970 19 | 20 | Pair Coeffs 21 | 22 | 1 0.0216000000 1.4210000000 23 | 24 | Bond Coeffs 25 | 26 | 1 0.7412 414.2185 -805.6549 914.1296 27 | 28 | Atoms 29 | 30 | 1 1 1 0.000000 4.600000000 5.000000000 5.000000000 31 | 2 1 1 0.000000 5.400000000 5.000000000 5.000000000 32 | 33 | Bonds 34 | 35 | 1 1 1 2 36 | 37 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/hydrogen-class2a.data2: -------------------------------------------------------------------------------- 1 | LAMMPS data file via write_data, version 8 Jul 2013-ICMS, timestep = 7 2 | 3 | 2 atoms 4 | 1 atom types 5 | 1 bonds 6 | 1 bond types 7 | 8 | 0.0000000000000000e+00 1.0000000000000000e+01 xlo xhi 9 | 0.0000000000000000e+00 1.0000000000000000e+01 ylo yhi 10 | 0.0000000000000000e+00 1.0000000000000000e+01 zlo zhi 11 | 12 | Masses 13 | 14 | 1 1.00797 15 | 16 | Pair Coeffs 17 | 18 | 1 0.0216 1.421 19 | 20 | Bond Coeffs 21 | 22 | 1 0.7412 414.219 -805.655 914.13 23 | 24 | Atoms 25 | 26 | 1 1 1 0.0000000000000000e+00 4.6293989552979129e+00 5.0000000000000000e+00 5.0000000000000000e+00 0 0 0 27 | 2 1 1 0.0000000000000000e+00 5.3706010447020871e+00 5.0000000000000000e+00 5.0000000000000000e+00 0 0 0 28 | 29 | Velocities 30 | 31 | 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 32 | 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 33 | 34 | Bonds 35 | 36 | 1 1 1 2 37 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/naphthalene-class1.data: -------------------------------------------------------------------------------- 1 | LAMMPS data file. msi2lmp v3.9.7 / 24 Oct 2015 / CGCMM for naphthalene-class1 2 | 3 | 18 atoms 4 | 19 bonds 5 | 30 angles 6 | 44 dihedrals 7 | 10 impropers 8 | 9 | 2 atom types 10 | 2 bond types 11 | 2 angle types 12 | 3 dihedral types 13 | 2 improper types 14 | 15 | 0.064669444 20.064669444 xlo xhi 16 | -20.061369444 -0.061369444 ylo yhi 17 | -20.006684444 -0.006684444 zlo zhi 18 | 19 | Masses 20 | 21 | 1 1.007970 # h 22 | 2 12.011150 # cp 23 | 24 | Pair Coeffs # lj/cut/coul/long 25 | 26 | 1 0.0380000011 2.4499714540 # h 27 | 2 0.1479999981 3.6170487995 # cp 28 | 29 | Bond Coeffs # harmonic 30 | 31 | 1 363.4164 1.0800 # h-cp 32 | 2 480.0000 1.3400 # cp-cp 33 | 34 | Angle Coeffs # harmonic 35 | 36 | 1 37.0000 120.0000 # h-cp-cp 37 | 2 90.0000 120.0000 # cp-cp-cp 38 | 39 | Dihedral Coeffs # harmonic 40 | 41 | 1 3.0000 -1 2 # h-cp-cp-cp 42 | 2 3.0000 -1 2 # h-cp-cp-h 43 | 3 3.0000 -1 2 # cp-cp-cp-cp 44 | 45 | Improper Coeffs # cvff 46 | 47 | 1 0.3700 -1 2 # h-cp-cp-cp 48 | 2 0.3700 -1 2 # cp-cp-cp-cp 49 | 50 | Atoms # full 51 | 52 | 1 1 1 0.132000 6.500000000 -9.500000000 -10.000000000 0 0 0 # h 53 | 2 1 2 -0.128000 7.599900000 -9.500000000 -10.000000000 0 0 0 # cp 54 | 3 1 2 -0.127000 8.288980000 -8.262840000 -10.000000000 0 0 0 # cp 55 | 4 1 2 -0.117000 9.661860000 -8.228710000 -10.001500000 0 0 0 # cp 56 | 5 1 2 -0.037000 10.406020000 -9.440000000 -10.006040000 0 0 0 # cp 57 | 6 1 2 -0.036000 9.719960000 -10.680950000 -10.004000000 0 0 0 # cp 58 | 7 1 2 -0.117000 8.297670000 -10.682850000 -10.001160000 0 0 0 # cp 59 | 8 1 1 0.131000 7.705780000 -7.329930000 -9.996380000 0 0 0 # h 60 | 9 1 1 0.133000 10.206130000 -7.272850000 -10.002830000 0 0 0 # h 61 | 10 1 1 0.132000 7.770540000 -11.648530000 -10.000400000 0 0 0 # h 62 | 11 1 2 -0.119000 11.828680000 -9.441740000 -10.010130000 0 0 0 # cp 63 | 12 1 2 -0.127000 12.527620000 -10.622850000 -10.015250000 0 0 0 # cp 64 | 13 1 2 -0.127000 11.844840000 -11.863540000 -10.015940000 0 0 0 # cp 65 | 14 1 2 -0.118000 10.470950000 -11.888220000 -10.009030000 0 0 0 # cp 66 | 15 1 1 0.132000 12.355170000 -8.475370000 -10.009670000 0 0 0 # h 67 | 16 1 1 0.131000 13.627550000 -10.611020000 -10.018380000 0 0 0 # h 68 | 17 1 1 0.133000 12.414260000 -12.804680000 -10.020060000 0 0 0 # h 69 | 18 1 1 0.131000 9.938140000 -12.850570000 -10.009550000 0 0 0 # h 70 | 71 | Bonds 72 | 73 | 1 1 1 2 74 | 2 2 2 3 75 | 3 2 2 7 76 | 4 2 3 4 77 | 5 1 8 3 78 | 6 2 4 5 79 | 7 1 9 4 80 | 8 2 5 6 81 | 9 2 5 11 82 | 10 2 6 7 83 | 11 2 6 14 84 | 12 1 10 7 85 | 13 2 11 12 86 | 14 1 15 11 87 | 15 2 12 13 88 | 16 1 16 12 89 | 17 2 13 14 90 | 18 1 17 13 91 | 19 1 18 14 92 | 93 | Angles 94 | 95 | 1 1 1 2 3 96 | 2 1 1 2 7 97 | 3 2 3 2 7 98 | 4 2 2 3 4 99 | 5 1 8 3 2 100 | 6 1 8 3 4 101 | 7 2 3 4 5 102 | 8 1 9 4 3 103 | 9 1 9 4 5 104 | 10 2 4 5 6 105 | 11 2 4 5 11 106 | 12 2 6 5 11 107 | 13 2 5 6 7 108 | 14 2 5 6 14 109 | 15 2 7 6 14 110 | 16 2 2 7 6 111 | 17 1 10 7 2 112 | 18 1 10 7 6 113 | 19 2 5 11 12 114 | 20 1 15 11 5 115 | 21 1 15 11 12 116 | 22 2 11 12 13 117 | 23 1 16 12 11 118 | 24 1 16 12 13 119 | 25 2 12 13 14 120 | 26 1 17 13 12 121 | 27 1 17 13 14 122 | 28 2 6 14 13 123 | 29 1 18 14 6 124 | 30 1 18 14 13 125 | 126 | Dihedrals 127 | 128 | 1 1 1 2 3 4 129 | 2 2 1 2 3 8 130 | 3 3 7 2 3 4 131 | 4 1 8 3 2 7 132 | 5 1 1 2 7 6 133 | 6 2 1 2 7 10 134 | 7 3 3 2 7 6 135 | 8 1 10 7 2 3 136 | 9 3 2 3 4 5 137 | 10 1 9 4 3 2 138 | 11 1 8 3 4 5 139 | 12 2 8 3 4 9 140 | 13 3 3 4 5 6 141 | 14 3 3 4 5 11 142 | 15 1 9 4 5 6 143 | 16 1 9 4 5 11 144 | 17 3 4 5 6 7 145 | 18 3 4 5 6 14 146 | 19 3 11 5 6 7 147 | 20 3 11 5 6 14 148 | 21 3 4 5 11 12 149 | 22 1 15 11 5 4 150 | 23 3 6 5 11 12 151 | 24 1 15 11 5 6 152 | 25 3 5 6 7 2 153 | 26 1 10 7 6 5 154 | 27 3 14 6 7 2 155 | 28 1 10 7 6 14 156 | 29 3 5 6 14 13 157 | 30 1 18 14 6 5 158 | 31 3 7 6 14 13 159 | 32 1 18 14 6 7 160 | 33 3 5 11 12 13 161 | 34 1 16 12 11 5 162 | 35 1 15 11 12 13 163 | 36 2 15 11 12 16 164 | 37 3 11 12 13 14 165 | 38 1 17 13 12 11 166 | 39 1 16 12 13 14 167 | 40 2 16 12 13 17 168 | 41 3 12 13 14 6 169 | 42 1 18 14 13 12 170 | 43 1 17 13 14 6 171 | 44 2 17 13 14 18 172 | 173 | Impropers 174 | 175 | 1 1 1 2 3 7 176 | 2 1 8 3 4 2 177 | 3 1 9 4 5 3 178 | 4 2 4 5 6 11 179 | 5 2 5 6 7 14 180 | 6 1 10 7 6 2 181 | 7 1 15 11 12 5 182 | 8 1 16 12 13 11 183 | 9 1 17 13 14 12 184 | 10 1 18 14 13 6 185 | 186 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/naphthalene-class1.data2: -------------------------------------------------------------------------------- 1 | LAMMPS data file via write_data, version 24 Oct 2015-ICMS, timestep = 15 2 | 3 | 18 atoms 4 | 2 atom types 5 | 19 bonds 6 | 2 bond types 7 | 30 angles 8 | 2 angle types 9 | 44 dihedrals 10 | 3 dihedral types 11 | 10 impropers 12 | 2 improper types 13 | 14 | 6.4669444000000006e-02 2.0064669444000000e+01 xlo xhi 15 | -2.0061369444000000e+01 -6.1369444000000002e-02 ylo yhi 16 | -2.0006684444000001e+01 -6.6844440000000003e-03 zlo zhi 17 | 18 | Masses 19 | 20 | 1 1.00797 21 | 2 12.0112 22 | 23 | Pair Coeffs # lj/cut/coul/cut 24 | 25 | 1 0.038 2.44997 26 | 2 0.148 3.61705 27 | 28 | Bond Coeffs # harmonic 29 | 30 | 1 363.416 1.08 31 | 2 480 1.34 32 | 33 | Angle Coeffs # harmonic 34 | 35 | 1 37 120 36 | 2 90 120 37 | 38 | Dihedral Coeffs # harmonic 39 | 40 | 1 3 -1 2 41 | 2 3 -1 2 42 | 3 3 -1 2 43 | 44 | Improper Coeffs # cvff 45 | 46 | 1 0.37 -1 2 47 | 2 0.37 -1 2 48 | 49 | Atoms # full 50 | 51 | 18 1 1 1.3100000000000001e-01 9.9618951061052083e+00 -1.2757510840317650e+01 -1.0009363546664854e+01 0 0 0 52 | 12 1 2 -1.2700000000000000e-01 1.2434163464289064e+01 -1.0619224947056749e+01 -1.0014620094082913e+01 0 0 0 53 | 13 1 2 -1.2700000000000000e-01 1.1789493602619283e+01 -1.1779792146565503e+01 -1.0014756756801232e+01 0 0 0 54 | 14 1 2 -1.1799999999999999e-01 1.0451783491408802e+01 -1.1796832592410674e+01 -1.0009565445392903e+01 0 0 0 55 | 16 1 1 1.3100000000000001e-01 1.3512822757503637e+01 -1.0607414781638862e+01 -1.0018330619949849e+01 0 0 0 56 | 17 1 1 1.3300000000000001e-01 1.2348302035167473e+01 -1.2701932016500484e+01 -1.0019374868605887e+01 0 0 0 57 | 11 1 2 -1.1899999999999999e-01 1.1741641676022077e+01 -9.4744686477619471e+00 -1.0009738880381777e+01 0 0 0 58 | 15 1 1 1.3200000000000001e-01 1.2295771349754121e+01 -8.5493716043086465e+00 -1.0009853503656768e+01 0 0 0 59 | 6 1 2 -3.5999999999999997e-02 9.7391193737490021e+00 -1.0646115965439973e+01 -1.0005189216959286e+01 0 0 0 60 | 7 1 2 -1.1700000000000001e-01 8.3872861032350201e+00 -1.0648980116387495e+01 -1.0001815657561217e+01 0 0 0 61 | 10 1 1 1.3200000000000001e-01 7.8324302037216587e+00 -1.1572465202265569e+01 -1.0000854039340906e+01 0 0 0 62 | 1 1 1 1.3200000000000001e-01 6.6169196593512458e+00 -9.5110484958740145e+00 -9.9993042850123004e+00 0 0 0 63 | 2 1 2 -1.2800000000000000e-01 7.6956989806808282e+00 -9.5024478453623402e+00 -9.9999857993938690e+00 0 0 0 64 | 3 1 2 -1.2700000000000000e-01 8.3407748181977635e+00 -8.3429947691588691e+00 -9.9996277206777506e+00 0 0 0 65 | 4 1 2 -1.1700000000000001e-01 9.6776654343172712e+00 -8.3267399222715675e+00 -1.0002266165754046e+01 0 0 0 66 | 8 1 1 1.3100000000000001e-01 7.7778648310552443e+00 -7.4220431795187904e+00 -9.9972704073578349e+00 0 0 0 67 | 5 1 2 -3.6999999999999998e-02 1.0389324985930516e+01 -9.4771642328275494e+00 -1.0005827497015289e+01 0 0 0 68 | 9 1 1 1.3300000000000001e-01 1.0171092126891777e+01 -7.3681026943333148e+00 -1.0002575495391330e+01 0 0 0 69 | 70 | Velocities 71 | 72 | 18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 73 | 12 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 74 | 13 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 75 | 14 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 76 | 16 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 77 | 17 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 78 | 11 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 79 | 15 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 80 | 6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 81 | 7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 82 | 10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 83 | 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 84 | 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 85 | 3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 86 | 4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 87 | 8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 88 | 5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 89 | 9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 90 | 91 | Bonds 92 | 93 | 1 1 18 14 94 | 2 2 12 13 95 | 3 2 13 14 96 | 4 1 16 12 97 | 5 1 17 13 98 | 6 2 11 12 99 | 7 1 15 11 100 | 8 2 6 7 101 | 9 2 6 14 102 | 10 1 10 7 103 | 11 1 1 2 104 | 12 2 2 3 105 | 13 2 2 7 106 | 14 2 3 4 107 | 15 2 4 5 108 | 16 1 8 3 109 | 17 2 5 6 110 | 18 2 5 11 111 | 19 1 9 4 112 | 113 | Angles 114 | 115 | 1 2 11 12 13 116 | 2 1 16 12 11 117 | 3 1 16 12 13 118 | 4 2 12 13 14 119 | 5 1 17 13 12 120 | 6 1 17 13 14 121 | 7 2 6 14 13 122 | 8 1 18 14 6 123 | 9 1 18 14 13 124 | 10 2 5 11 12 125 | 11 1 15 11 5 126 | 12 1 15 11 12 127 | 13 2 5 6 7 128 | 14 2 5 6 14 129 | 15 2 7 6 14 130 | 16 2 2 7 6 131 | 17 1 10 7 2 132 | 18 1 10 7 6 133 | 19 1 1 2 3 134 | 20 1 1 2 7 135 | 21 2 3 2 7 136 | 22 2 2 3 4 137 | 23 1 8 3 2 138 | 24 1 8 3 4 139 | 25 2 3 4 5 140 | 26 1 9 4 3 141 | 27 1 9 4 5 142 | 28 2 4 5 6 143 | 29 2 4 5 11 144 | 30 2 6 5 11 145 | 146 | Dihedrals 147 | 148 | 1 1 16 12 11 5 149 | 2 3 11 12 13 14 150 | 3 1 16 12 13 14 151 | 4 2 16 12 13 17 152 | 5 1 17 13 12 11 153 | 6 3 12 13 14 6 154 | 7 1 17 13 14 6 155 | 8 2 17 13 14 18 156 | 9 1 18 14 6 5 157 | 10 1 18 14 6 7 158 | 11 1 18 14 13 12 159 | 12 1 15 11 5 4 160 | 13 1 15 11 5 6 161 | 14 3 5 11 12 13 162 | 15 1 15 11 12 13 163 | 16 2 15 11 12 16 164 | 17 3 5 6 7 2 165 | 18 3 14 6 7 2 166 | 19 3 5 6 14 13 167 | 20 3 7 6 14 13 168 | 21 1 10 7 2 3 169 | 22 1 10 7 6 5 170 | 23 1 10 7 6 14 171 | 24 1 1 2 3 4 172 | 25 2 1 2 3 8 173 | 26 3 7 2 3 4 174 | 27 1 1 2 7 6 175 | 28 2 1 2 7 10 176 | 29 3 3 2 7 6 177 | 30 1 8 3 2 7 178 | 31 3 2 3 4 5 179 | 32 1 8 3 4 5 180 | 33 2 8 3 4 9 181 | 34 1 9 4 3 2 182 | 35 3 3 4 5 6 183 | 36 3 3 4 5 11 184 | 37 1 9 4 5 6 185 | 38 1 9 4 5 11 186 | 39 3 4 5 6 7 187 | 40 3 4 5 6 14 188 | 41 3 11 5 6 7 189 | 42 3 11 5 6 14 190 | 43 3 4 5 11 12 191 | 44 3 6 5 11 12 192 | 193 | Impropers 194 | 195 | 1 1 16 12 13 11 196 | 2 1 17 13 14 12 197 | 3 1 18 14 13 6 198 | 4 1 15 11 12 5 199 | 5 2 5 6 7 14 200 | 6 1 10 7 6 2 201 | 7 1 1 2 3 7 202 | 8 1 8 3 4 2 203 | 9 1 9 4 5 3 204 | 10 2 4 5 6 11 205 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/naphthalene-class2a.data2: -------------------------------------------------------------------------------- 1 | LAMMPS data file via write_data, version 24 Oct 2015-ICMS, timestep = 100 2 | 3 | 18 atoms 4 | 2 atom types 5 | 19 bonds 6 | 2 bond types 7 | 30 angles 8 | 2 angle types 9 | 44 dihedrals 10 | 3 dihedral types 11 | 10 impropers 12 | 2 improper types 13 | 14 | 6.4669444000000006e-02 2.0064669444000000e+01 xlo xhi 15 | -2.0061369444000000e+01 -6.1369444000000002e-02 ylo yhi 16 | -2.0006684444000001e+01 -6.6844440000000003e-03 zlo zhi 17 | 18 | Masses 19 | 20 | 1 1.00797 21 | 2 12.0112 22 | 23 | Pair Coeffs # lj/class2/coul/cut 24 | 25 | 1 0.023 2.878 26 | 2 0.068 3.915 27 | 28 | Bond Coeffs # class2 29 | 30 | 1 1.0982 372.825 -803.453 894.317 31 | 2 1.417 470.836 -627.618 1327.63 32 | 33 | Angle Coeffs # class2 34 | 35 | 1 117.94 35.1558 -12.4682 0 36 | 2 118.9 61.0226 -34.9931 0 37 | 38 | BondBond Coeffs 39 | 40 | 1 1.0795 1.0982 1.417 41 | 2 68.2856 1.417 1.417 42 | 43 | BondAngle Coeffs 44 | 45 | 1 24.2183 20.0033 1.0982 1.417 46 | 2 28.8708 28.8708 1.417 1.417 47 | 48 | Dihedral Coeffs # class2 49 | 50 | 1 0 0 3.9661 0 0 0 51 | 2 0 0 2.35 0 0 0 52 | 3 8.3667 0 1.2 0 0 0 53 | 54 | AngleAngleTorsion Coeffs 55 | 56 | 1 -4.8141 117.94 118.9 57 | 2 0.3598 117.94 117.94 58 | 3 0 118.9 118.9 59 | 60 | EndBondTorsion Coeffs 61 | 62 | 1 0 -0.4669 0 0 -6.8958 0 1.0982 1.417 63 | 2 0 -0.689 0 0 -0.689 0 1.0982 1.0982 64 | 3 -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417 65 | 66 | MiddleBondTorsion Coeffs 67 | 68 | 1 0 -1.1521 0 1.417 69 | 2 0 4.8228 0 1.417 70 | 3 27.5989 -2.312 0 1.417 71 | 72 | BondBond13 Coeffs 73 | 74 | 1 0 1.0982 1.417 75 | 2 0 1.0982 1.0982 76 | 3 0 1.417 1.417 77 | 78 | AngleTorsion Coeffs 79 | 80 | 1 0 2.7147 0 0 2.5014 0 117.94 118.9 81 | 2 0 2.4501 0 0 2.4501 0 117.94 117.94 82 | 3 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9 83 | 84 | Improper Coeffs # class2 85 | 86 | 1 4.8912 0 87 | 2 7.1794 0 88 | 89 | AngleAngle Coeffs 90 | 91 | 1 0 0 0 117.94 118.9 117.94 92 | 2 0 0 0 118.9 118.9 118.9 93 | 94 | Atoms # full 95 | 96 | 18 1 1 1.3100000000000001e-01 1.0032362752100944e+01 -1.2850872457944025e+01 -1.0014072691976034e+01 0 0 0 97 | 12 1 2 -1.2700000000000000e-01 1.2537032816978714e+01 -1.0551070704115340e+01 -1.0013222696752699e+01 0 0 0 98 | 13 1 2 -1.2700000000000000e-01 1.1897661261740154e+01 -1.1790868716774206e+01 -1.0011666036389959e+01 0 0 0 99 | 14 1 2 -1.1799999999999999e-01 1.0521733489465674e+01 -1.1866957953113106e+01 -1.0014645375595610e+01 0 0 0 100 | 16 1 1 1.3100000000000001e-01 1.3635211503951460e+01 -1.0504644137864680e+01 -1.0012607443532412e+01 0 0 0 101 | 17 1 1 1.3300000000000001e-01 1.2496246242651550e+01 -1.2712938767230884e+01 -1.0008017486622476e+01 0 0 0 102 | 11 1 2 -1.1899999999999999e-01 1.1801344930238916e+01 -9.3856119751428917e+00 -1.0015402694750533e+01 0 0 0 103 | 15 1 1 1.3200000000000001e-01 1.2320246478960698e+01 -8.4165672485623446e+00 -1.0015522359025409e+01 0 0 0 104 | 6 1 2 -3.5999999999999997e-02 9.7384404501559292e+00 -1.0694334361385316e+01 -1.0014577811303761e+01 0 0 0 105 | 7 1 2 -1.1700000000000001e-01 8.3289051008280008e+00 -1.0736828465297775e+01 -1.0007099895934864e+01 0 0 0 106 | 10 1 1 1.3200000000000001e-01 7.8115345677910000e+00 -1.1706626818692703e+01 -1.0007194315863302e+01 0 0 0 107 | 1 1 1 1.3200000000000001e-01 6.4941686848437516e+00 -9.6201232611557437e+00 -9.9883895846937563e+00 0 0 0 108 | 2 1 2 -1.2800000000000000e-01 7.5923273335064989e+00 -9.5723085661895944e+00 -9.9968287768198927e+00 0 0 0 109 | 3 1 2 -1.2700000000000000e-01 8.2312889333738042e+00 -8.3322087518588788e+00 -9.9956627056362581e+00 0 0 0 110 | 4 1 2 -1.1700000000000001e-01 9.6072935742507113e+00 -8.2548632320642561e+00 -1.0003654663559724e+01 0 0 0 111 | 8 1 1 1.3100000000000001e-01 7.6317658715267713e+00 -7.4105826788806439e+00 -9.9885680376332981e+00 0 0 0 112 | 5 1 2 -3.6999999999999998e-02 1.0391489516609976e+01 -9.4270307576481098e+00 -1.0012988749237229e+01 0 0 0 113 | 9 1 1 1.3300000000000001e-01 1.0094996491025443e+01 -7.2702111460794043e+00 -1.0000198674672777e+01 0 0 0 114 | 115 | Velocities 116 | 117 | 18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 118 | 12 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 119 | 13 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 120 | 14 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 121 | 16 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 122 | 17 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 123 | 11 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 124 | 15 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 125 | 6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 126 | 7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 127 | 10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 128 | 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 129 | 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 130 | 3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 131 | 4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 132 | 8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 133 | 5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 134 | 9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 135 | 136 | Bonds 137 | 138 | 1 1 18 14 139 | 2 2 12 13 140 | 3 2 13 14 141 | 4 1 16 12 142 | 5 1 17 13 143 | 6 2 11 12 144 | 7 1 15 11 145 | 8 2 6 7 146 | 9 2 6 14 147 | 10 1 10 7 148 | 11 1 1 2 149 | 12 2 2 3 150 | 13 2 2 7 151 | 14 2 3 4 152 | 15 2 4 5 153 | 16 1 8 3 154 | 17 2 5 6 155 | 18 2 5 11 156 | 19 1 9 4 157 | 158 | Angles 159 | 160 | 1 2 11 12 13 161 | 2 1 16 12 11 162 | 3 1 16 12 13 163 | 4 2 12 13 14 164 | 5 1 17 13 12 165 | 6 1 17 13 14 166 | 7 2 6 14 13 167 | 8 1 18 14 6 168 | 9 1 18 14 13 169 | 10 2 5 11 12 170 | 11 1 15 11 5 171 | 12 1 15 11 12 172 | 13 2 5 6 7 173 | 14 2 5 6 14 174 | 15 2 7 6 14 175 | 16 2 2 7 6 176 | 17 1 10 7 2 177 | 18 1 10 7 6 178 | 19 1 1 2 3 179 | 20 1 1 2 7 180 | 21 2 3 2 7 181 | 22 2 2 3 4 182 | 23 1 8 3 2 183 | 24 1 8 3 4 184 | 25 2 3 4 5 185 | 26 1 9 4 3 186 | 27 1 9 4 5 187 | 28 2 4 5 6 188 | 29 2 4 5 11 189 | 30 2 6 5 11 190 | 191 | Dihedrals 192 | 193 | 1 1 16 12 11 5 194 | 2 3 11 12 13 14 195 | 3 1 16 12 13 14 196 | 4 2 16 12 13 17 197 | 5 1 17 13 12 11 198 | 6 3 12 13 14 6 199 | 7 1 17 13 14 6 200 | 8 2 17 13 14 18 201 | 9 1 18 14 6 5 202 | 10 1 18 14 6 7 203 | 11 1 18 14 13 12 204 | 12 1 15 11 5 4 205 | 13 1 15 11 5 6 206 | 14 3 5 11 12 13 207 | 15 1 15 11 12 13 208 | 16 2 15 11 12 16 209 | 17 3 5 6 7 2 210 | 18 3 14 6 7 2 211 | 19 3 5 6 14 13 212 | 20 3 7 6 14 13 213 | 21 1 10 7 2 3 214 | 22 1 10 7 6 5 215 | 23 1 10 7 6 14 216 | 24 1 1 2 3 4 217 | 25 2 1 2 3 8 218 | 26 3 7 2 3 4 219 | 27 1 1 2 7 6 220 | 28 2 1 2 7 10 221 | 29 3 3 2 7 6 222 | 30 1 8 3 2 7 223 | 31 3 2 3 4 5 224 | 32 1 8 3 4 5 225 | 33 2 8 3 4 9 226 | 34 1 9 4 3 2 227 | 35 3 3 4 5 6 228 | 36 3 3 4 5 11 229 | 37 1 9 4 5 6 230 | 38 1 9 4 5 11 231 | 39 3 4 5 6 7 232 | 40 3 4 5 6 14 233 | 41 3 11 5 6 7 234 | 42 3 11 5 6 14 235 | 43 3 4 5 11 12 236 | 44 3 6 5 11 12 237 | 238 | Impropers 239 | 240 | 1 1 16 12 13 11 241 | 2 1 17 13 14 12 242 | 3 1 18 14 13 6 243 | 4 1 15 11 12 5 244 | 5 2 5 6 7 14 245 | 6 1 10 7 6 2 246 | 7 1 1 2 3 7 247 | 8 1 8 3 4 2 248 | 9 1 9 4 5 3 249 | 10 2 4 5 6 11 250 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/naphthalene-class2b.data2: -------------------------------------------------------------------------------- 1 | LAMMPS data file via write_data, version 24 Oct 2015-ICMS, timestep = 100 2 | 3 | 18 atoms 4 | 2 atom types 5 | 19 bonds 6 | 2 bond types 7 | 30 angles 8 | 2 angle types 9 | 44 dihedrals 10 | 3 dihedral types 11 | 10 impropers 12 | 2 improper types 13 | 14 | 6.4669444000000006e-02 2.0064669444000000e+01 xlo xhi 15 | -2.0061369444000000e+01 -6.1369444000000002e-02 ylo yhi 16 | -2.0006684444000001e+01 -6.6844440000000003e-03 zlo zhi 17 | 18 | Masses 19 | 20 | 1 1.00797 21 | 2 12.0112 22 | 23 | Pair Coeffs # lj/class2/coul/cut 24 | 25 | 1 0.02 2.995 26 | 2 0.064 4.01 27 | 28 | Bond Coeffs # class2 29 | 30 | 1 1.0982 372.825 -803.453 894.317 31 | 2 1.417 470.836 -627.618 1327.63 32 | 33 | Angle Coeffs # class2 34 | 35 | 1 117.94 35.1558 -12.4682 0 36 | 2 118.9 61.0226 -34.9931 0 37 | 38 | BondBond Coeffs 39 | 40 | 1 1.0795 1.0982 1.417 41 | 2 68.2856 1.417 1.417 42 | 43 | BondAngle Coeffs 44 | 45 | 1 24.2183 20.0033 1.0982 1.417 46 | 2 28.8708 28.8708 1.417 1.417 47 | 48 | Dihedral Coeffs # class2 49 | 50 | 1 0 0 3.9661 0 0 0 51 | 2 0 0 1.8769 0 0 0 52 | 3 8.3667 0 1.1932 0 0 0 53 | 54 | AngleAngleTorsion Coeffs 55 | 56 | 1 -4.8141 117.94 118.9 57 | 2 0.3598 117.94 117.94 58 | 3 0 118.9 118.9 59 | 60 | EndBondTorsion Coeffs 61 | 62 | 1 0 -0.4669 0 0 -6.8958 0 1.0982 1.417 63 | 2 0 -0.689 0 0 -0.689 0 1.0982 1.0982 64 | 3 -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417 65 | 66 | MiddleBondTorsion Coeffs 67 | 68 | 1 0 -1.1521 0 1.417 69 | 2 0 4.8228 0 1.417 70 | 3 27.5989 -2.312 0 1.417 71 | 72 | BondBond13 Coeffs 73 | 74 | 1 -6.2741 1.0982 1.417 75 | 2 -1.7077 1.0982 1.0982 76 | 3 53 1.417 1.417 77 | 78 | AngleTorsion Coeffs 79 | 80 | 1 0 2.7147 0 0 2.5014 0 117.94 118.9 81 | 2 0 2.4501 0 0 2.4501 0 117.94 117.94 82 | 3 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9 83 | 84 | Improper Coeffs # class2 85 | 86 | 1 4.8912 0 87 | 2 7.1794 0 88 | 89 | AngleAngle Coeffs 90 | 91 | 1 0 0 0 117.94 118.9 117.94 92 | 2 0 0 0 118.9 118.9 118.9 93 | 94 | Atoms # full 95 | 96 | 18 1 1 1.3100000000000001e-01 9.9818272866175075e+00 -1.2855663774939638e+01 -1.0009450787367086e+01 0 0 0 97 | 12 1 2 -1.2700000000000000e-01 1.2529554285474092e+01 -1.0600284104727114e+01 -1.0015641735668074e+01 0 0 0 98 | 13 1 2 -1.2700000000000000e-01 1.1865863545075193e+01 -1.1827817347686510e+01 -1.0016143204504594e+01 0 0 0 99 | 14 1 2 -1.1799999999999999e-01 1.0487865315056842e+01 -1.1880432841090798e+01 -1.0009012204129904e+01 0 0 0 100 | 16 1 1 1.3100000000000001e-01 1.3628255119027907e+01 -1.0576671759443403e+01 -1.0021108442715054e+01 0 0 0 101 | 17 1 1 1.3300000000000001e-01 1.2447159073366381e+01 -1.2760449226419150e+01 -1.0022295739921258e+01 0 0 0 102 | 11 1 2 -1.1899999999999999e-01 1.1818885067538572e+01 -9.4183522267797972e+00 -1.0008343871912928e+01 0 0 0 103 | 15 1 1 1.3200000000000001e-01 1.2358875775045824e+01 -8.4612075353333474e+00 -1.0009150930845982e+01 0 0 0 104 | 6 1 2 -3.5999999999999997e-02 9.7240210515250567e+00 -1.0691686309928613e+01 -1.0003158357277508e+01 0 0 0 105 | 7 1 2 -1.1700000000000001e-01 8.3110279035699222e+00 -1.0704259833711575e+01 -1.0000636527566915e+01 0 0 0 106 | 10 1 1 1.3200000000000001e-01 7.7723715155681719e+00 -1.1662033535268330e+01 -1.0001512310543106e+01 0 0 0 107 | 1 1 1 1.3200000000000001e-01 6.5011854619891860e+00 -9.5478500109020548e+00 -9.9989203564295472e+00 0 0 0 108 | 2 1 2 -1.2800000000000000e-01 7.5998512893161774e+00 -9.5228176924598156e+00 -1.0000021098941344e+01 0 0 0 109 | 3 1 2 -1.2700000000000000e-01 8.2631706048357252e+00 -8.2949498179280834e+00 -1.0000156396747084e+01 0 0 0 110 | 4 1 2 -1.1700000000000001e-01 9.6412569424707293e+00 -8.2416500367266643e+00 -1.0000802350457274e+01 0 0 0 111 | 8 1 1 1.3100000000000001e-01 7.6811503230314129e+00 -7.3627183952227666e+00 -1.0000267698314738e+01 0 0 0 112 | 5 1 2 -3.6999999999999998e-02 1.0405736096337888e+01 -9.4303209683888376e+00 -1.0002576434550440e+01 0 0 0 113 | 9 1 1 1.3300000000000001e-01 1.0145993344153458e+01 -7.2654845830434924e+00 -1.0001121552107151e+01 0 0 0 114 | 115 | Velocities 116 | 117 | 18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 118 | 12 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 119 | 13 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 120 | 14 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 121 | 16 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 122 | 17 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 123 | 11 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 124 | 15 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 125 | 6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 126 | 7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 127 | 10 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 128 | 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 129 | 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 130 | 3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 131 | 4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 132 | 8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 133 | 5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 134 | 9 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 135 | 136 | Bonds 137 | 138 | 1 1 18 14 139 | 2 2 12 13 140 | 3 2 13 14 141 | 4 1 16 12 142 | 5 1 17 13 143 | 6 2 11 12 144 | 7 1 15 11 145 | 8 2 6 7 146 | 9 2 6 14 147 | 10 1 10 7 148 | 11 1 1 2 149 | 12 2 2 3 150 | 13 2 2 7 151 | 14 2 3 4 152 | 15 2 4 5 153 | 16 1 8 3 154 | 17 2 5 6 155 | 18 2 5 11 156 | 19 1 9 4 157 | 158 | Angles 159 | 160 | 1 2 11 12 13 161 | 2 1 16 12 11 162 | 3 1 16 12 13 163 | 4 2 12 13 14 164 | 5 1 17 13 12 165 | 6 1 17 13 14 166 | 7 2 6 14 13 167 | 8 1 18 14 6 168 | 9 1 18 14 13 169 | 10 2 5 11 12 170 | 11 1 15 11 5 171 | 12 1 15 11 12 172 | 13 2 5 6 7 173 | 14 2 5 6 14 174 | 15 2 7 6 14 175 | 16 2 2 7 6 176 | 17 1 10 7 2 177 | 18 1 10 7 6 178 | 19 1 1 2 3 179 | 20 1 1 2 7 180 | 21 2 3 2 7 181 | 22 2 2 3 4 182 | 23 1 8 3 2 183 | 24 1 8 3 4 184 | 25 2 3 4 5 185 | 26 1 9 4 3 186 | 27 1 9 4 5 187 | 28 2 4 5 6 188 | 29 2 4 5 11 189 | 30 2 6 5 11 190 | 191 | Dihedrals 192 | 193 | 1 1 16 12 11 5 194 | 2 3 11 12 13 14 195 | 3 1 16 12 13 14 196 | 4 2 16 12 13 17 197 | 5 1 17 13 12 11 198 | 6 3 12 13 14 6 199 | 7 1 17 13 14 6 200 | 8 2 17 13 14 18 201 | 9 1 18 14 6 5 202 | 10 1 18 14 6 7 203 | 11 1 18 14 13 12 204 | 12 1 15 11 5 4 205 | 13 1 15 11 5 6 206 | 14 3 5 11 12 13 207 | 15 1 15 11 12 13 208 | 16 2 15 11 12 16 209 | 17 3 5 6 7 2 210 | 18 3 14 6 7 2 211 | 19 3 5 6 14 13 212 | 20 3 7 6 14 13 213 | 21 1 10 7 2 3 214 | 22 1 10 7 6 5 215 | 23 1 10 7 6 14 216 | 24 1 1 2 3 4 217 | 25 2 1 2 3 8 218 | 26 3 7 2 3 4 219 | 27 1 1 2 7 6 220 | 28 2 1 2 7 10 221 | 29 3 3 2 7 6 222 | 30 1 8 3 2 7 223 | 31 3 2 3 4 5 224 | 32 1 8 3 4 5 225 | 33 2 8 3 4 9 226 | 34 1 9 4 3 2 227 | 35 3 3 4 5 6 228 | 36 3 3 4 5 11 229 | 37 1 9 4 5 6 230 | 38 1 9 4 5 11 231 | 39 3 4 5 6 7 232 | 40 3 4 5 6 14 233 | 41 3 11 5 6 7 234 | 42 3 11 5 6 14 235 | 43 3 4 5 11 12 236 | 44 3 6 5 11 12 237 | 238 | Impropers 239 | 240 | 1 1 16 12 13 11 241 | 2 1 17 13 14 12 242 | 3 1 18 14 13 6 243 | 4 1 15 11 12 5 244 | 5 2 5 6 7 14 245 | 6 1 10 7 6 2 246 | 7 1 1 2 3 7 247 | 8 1 8 3 4 2 248 | 9 1 9 4 5 3 249 | 10 2 4 5 6 11 250 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/water-class1.data: -------------------------------------------------------------------------------- 1 | LAMMPS data file. msi2lmp v3.9.7 / 24 Oct 2015 / CGCMM for water-class1 2 | 3 | 3 atoms 4 | 2 bonds 5 | 1 angles 6 | 0 dihedrals 7 | 0 impropers 8 | 9 | 2 atom types 10 | 1 bond types 11 | 1 angle types 12 | 13 | -0.333333333 9.666666667 xlo xhi 14 | -0.333333333 9.666666667 ylo yhi 15 | 0.000000000 10.000000000 zlo zhi 16 | 17 | Masses 18 | 19 | 1 15.999400 # otip 20 | 2 1.007970 # htip 21 | 22 | Pair Coeffs # lj/cut/coul/long 23 | 24 | 1 0.1520725945 3.1506561105 # otip 25 | 2 0.0000000000 0.0000000000 # htip 26 | 27 | Bond Coeffs # harmonic 28 | 29 | 1 540.6336 0.9570 # otip-htip 30 | 31 | Angle Coeffs # harmonic 32 | 33 | 1 50.0000 104.5200 # htip-otip-htip 34 | 35 | Atoms # full 36 | 37 | 1 1 1 -0.834000 5.000000000 5.000000000 5.000000000 0 0 0 # otip 38 | 2 1 2 0.417000 4.000000000 5.000000000 5.000000000 0 0 0 # htip 39 | 3 1 2 0.417000 5.000000000 4.000000000 5.000000000 0 0 0 # htip 40 | 41 | Bonds 42 | 43 | 1 1 1 2 44 | 2 1 1 3 45 | 46 | Angles 47 | 48 | 1 1 2 1 3 49 | 50 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/water-class1.data2: -------------------------------------------------------------------------------- 1 | LAMMPS data file via write_data, version 24 Oct 2015-ICMS, timestep = 16 2 | 3 | 3 atoms 4 | 2 atom types 5 | 2 bonds 6 | 1 bond types 7 | 1 angles 8 | 1 angle types 9 | 10 | -3.3333333300000001e-01 9.6666666669999994e+00 xlo xhi 11 | -3.3333333300000001e-01 9.6666666669999994e+00 ylo yhi 12 | 0.0000000000000000e+00 1.0000000000000000e+01 zlo zhi 13 | 14 | Masses 15 | 16 | 1 15.9994 17 | 2 1.00797 18 | 19 | Pair Coeffs # lj/cut/coul/cut 20 | 21 | 1 0.152073 3.15066 22 | 2 0 0 23 | 24 | Bond Coeffs # harmonic 25 | 26 | 1 540.634 0.957 27 | 28 | Angle Coeffs # harmonic 29 | 30 | 1 50 104.52 31 | 32 | Atoms # full 33 | 34 | 1 1 1 -8.3399999999999996e-01 4.9246007359428710e+00 4.9246007359428710e+00 5.0000000000000000e+00 0 0 0 35 | 2 1 2 4.1699999999999998e-01 3.9758374534980736e+00 5.0995618105590559e+00 5.0000000000000000e+00 0 0 0 36 | 3 1 2 4.1699999999999998e-01 5.0995618105590559e+00 3.9758374534980736e+00 5.0000000000000000e+00 0 0 0 37 | 38 | Velocities 39 | 40 | 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 41 | 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 42 | 3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 43 | 44 | Bonds 45 | 46 | 1 1 1 2 47 | 2 1 1 3 48 | 49 | Angles 50 | 51 | 1 1 2 1 3 52 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/water-class2b.data: -------------------------------------------------------------------------------- 1 | LAMMPS data file. msi2lmp v3.9.7 / 24 Oct 2015 / CGCMM for water-class2b 2 | 3 | 3 atoms 4 | 2 bonds 5 | 1 angles 6 | 0 dihedrals 7 | 0 impropers 8 | 9 | 2 atom types 10 | 1 bond types 11 | 1 angle types 12 | 13 | -0.333333333 9.666666667 xlo xhi 14 | -0.333333333 9.666666667 ylo yhi 15 | 0.000000000 10.000000000 zlo zhi 16 | 17 | Masses 18 | 19 | 1 15.999400 # o* 20 | 2 1.007970 # h* 21 | 22 | Pair Coeffs # lj/class2/coul/long 23 | 24 | 1 0.2740000000 3.6080000000 # o* 25 | 2 0.0130000000 1.0980000000 # h* 26 | 27 | Bond Coeffs # class2 28 | 29 | 1 0.9700 563.2800 -1428.2200 1902.1200 # o*-h* 30 | 31 | Angle Coeffs # class2 32 | 33 | 1 103.7000 49.8400 -11.6000 -8.0000 # h*-o*-h* 34 | 35 | BondBond Coeffs 36 | 37 | 1 -9.5000 0.9700 0.9700 38 | 39 | BondAngle Coeffs 40 | 41 | 1 22.3500 22.3500 0.9700 0.9700 42 | 43 | Atoms # full 44 | 45 | 1 1 1 -0.834000 5.000000000 5.000000000 5.000000000 0 0 0 # o* 46 | 2 1 2 0.417000 4.000000000 5.000000000 5.000000000 0 0 0 # h* 47 | 3 1 2 0.417000 5.000000000 4.000000000 5.000000000 0 0 0 # h* 48 | 49 | Bonds 50 | 51 | 1 1 1 2 52 | 2 1 1 3 53 | 54 | Angles 55 | 56 | 1 1 2 1 3 57 | 58 | -------------------------------------------------------------------------------- /msi2lmp/test/reference/water-class2b.data2: -------------------------------------------------------------------------------- 1 | LAMMPS data file via write_data, version 24 Oct 2015-ICMS, timestep = 15 2 | 3 | 3 atoms 4 | 2 atom types 5 | 2 bonds 6 | 1 bond types 7 | 1 angles 8 | 1 angle types 9 | 10 | -3.3333333300000001e-01 9.6666666669999994e+00 xlo xhi 11 | -3.3333333300000001e-01 9.6666666669999994e+00 ylo yhi 12 | 0.0000000000000000e+00 1.0000000000000000e+01 zlo zhi 13 | 14 | Masses 15 | 16 | 1 15.9994 17 | 2 1.00797 18 | 19 | Pair Coeffs # lj/class2/coul/cut 20 | 21 | 1 0.274 3.608 22 | 2 0.013 1.098 23 | 24 | Bond Coeffs # class2 25 | 26 | 1 0.97 563.28 -1428.22 1902.12 27 | 28 | Angle Coeffs # class2 29 | 30 | 1 103.7 49.84 -11.6 -8 31 | 32 | BondBond Coeffs 33 | 34 | 1 -9.5 0.97 0.97 35 | 36 | BondAngle Coeffs 37 | 38 | 1 22.35 22.35 0.97 0.97 39 | 40 | Atoms # full 41 | 42 | 1 1 1 -8.3399999999999996e-01 4.9317110579061119e+00 4.9317110579061119e+00 5.0000000000000000e+00 0 0 0 43 | 2 1 2 4.1699999999999998e-01 3.9722822924820522e+00 5.0960066496118355e+00 5.0000000000000000e+00 0 0 0 44 | 3 1 2 4.1699999999999998e-01 5.0960066496118355e+00 3.9722822924820522e+00 5.0000000000000000e+00 0 0 0 45 | 46 | Velocities 47 | 48 | 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 49 | 2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 50 | 3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 51 | 52 | Bonds 53 | 54 | 1 1 1 2 55 | 2 1 1 3 56 | 57 | Angles 58 | 59 | 1 1 2 1 3 60 | -------------------------------------------------------------------------------- /msi2lmp/test/runtests.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | MSI2LMP_LIBRARY=../frc_files 4 | VALGRIND='valgrind -v --track-origins=yes --show-reachable=yes --leak-check=full' 5 | MSI2LMP=../src/msi2lmp.exe 6 | LAMMPS=../../../src/lmp_serial 7 | CHECKDATA=./data-compare.pl 8 | 9 | if [ ! -x $MSI2LMP ] 10 | then 11 | echo "No executable $MSI2LMP" 12 | exit 1 13 | fi 14 | 15 | if [ ! -d $MSI2LMP_LIBRARY ] 16 | then 17 | echo "No directory $MSI2LMP_LIBRARY" 18 | exit 1 19 | fi 20 | 21 | if [ ! -x $LAMMPS ] 22 | then 23 | echo "No executable $LAMMPS" 24 | exit 1 25 | fi 26 | 27 | verbose=1 28 | counter=0 29 | errors=0 30 | 31 | # Class1 tests with cvff 32 | for m in hydrogen water h2-h2o ethane benzene naphthalene cnt-hexagonal crambin nylon phen3_cff97 hap_crystal 33 | do \ 34 | before=$errors 35 | vglog=${m}-class1.chk 36 | ${VALGRIND} --log-file=${vglog} \ 37 | ${MSI2LMP} ${m}-class1 -c 1 -p ${verbose} \ 38 | || errors=$(expr $errors + 1) 39 | ${LAMMPS} -log none -screen none -in in.${m}-class1 \ 40 | || errors=$(expr $errors + 1) 41 | ${CHECKDATA} ${m}-class1.data reference/${m}-class1.data \ 42 | || errors=$(expr $errors + 1) 43 | ${CHECKDATA} ${m}-class1.data2 reference/${m}-class1.data2 \ 44 | || errors=$(expr $errors + 1) 45 | [ $before -eq $errors ] && rm ${m}-class1.data ${m}-class1.data2 log.${m}-class1 46 | leak=$(awk '/in use at exit:/ {num=$6;} END {print num;}' $vglog) 47 | [ $leak != 0 ] && echo "Memory still used: $leak" \ 48 | && errors=$(expr $errors + 1) 49 | viol=$(awk '/ERROR SUMMARY/ {num=$4;} END {print num;}' $vglog) 50 | [ $viol != 0 ] && echo "Valgrind errors: $viol" \ 51 | && errors=$(expr $errors + 1) 52 | [ $leak = 0 ] && [ $viol = 0 ] && rm ${vglog} 53 | counter=$(expr $counter + 6) 54 | done 55 | 56 | # Class1 tests with clayff 57 | for m in PyAC_bulk 58 | do \ 59 | before=$errors 60 | vglog=${m}-clayff.chk 61 | ${VALGRIND} --log-file=${vglog} \ 62 | ${MSI2LMP} ${m}-clayff -c 1 -p ${verbose} -f clayff -n \ 63 | || errors=$(expr $errors + 1) 64 | ${LAMMPS} -log none -screen none -in in.${m}-clayff \ 65 | || errors=$(expr $errors + 1) 66 | ${CHECKDATA} ${m}-clayff.data reference/${m}-clayff.data \ 67 | || errors=$(expr $errors + 1) 68 | ${CHECKDATA} ${m}-clayff.data2 reference/${m}-clayff.data2 \ 69 | || errors=$(expr $errors + 1) 70 | [ $before -eq $errors ] && rm ${m}-clayff.data ${m}-clayff.data2 log.${m}-clayff 71 | leak=$(awk '/in use at exit:/ {num=$6;} END {print num;}' $vglog) 72 | [ $leak != 0 ] && echo "Memory still used: $leak" \ 73 | && errors=$(expr $errors + 1) 74 | viol=$(awk '/ERROR SUMMARY/ {num=$4;} END {print num;}' $vglog) 75 | [ $viol != 0 ] && echo "Valgrind errors: $viol" \ 76 | && errors=$(expr $errors + 1) 77 | [ $leak = 0 ] && [ $viol = 0 ] && rm ${vglog} 78 | counter=$(expr $counter + 6) 79 | done 80 | 81 | # OPLS-AA tests 82 | for m in ethane decane 83 | do \ 84 | before=$errors 85 | vglog=${m}-oplsaa.chk 86 | ${VALGRIND} --log-file=${vglog} \ 87 | ${MSI2LMP} ${m}-oplsaa -c 0 -p ${verbose} -f oplsaa -n \ 88 | || errors=$(expr $errors + 1) 89 | ${LAMMPS} -log none -screen none -in in.${m}-oplsaa \ 90 | || errors=$(expr $errors + 1) 91 | ${CHECKDATA} ${m}-oplsaa.data reference/${m}-oplsaa.data \ 92 | || errors=$(expr $errors + 1) 93 | ${CHECKDATA} ${m}-oplsaa.data2 reference/${m}-oplsaa.data2 \ 94 | || errors=$(expr $errors + 1) 95 | [ $before -eq $errors ] && rm ${m}-oplsaa.data ${m}-oplsaa.data2 log.${m}-oplsaa 96 | leak=$(awk '/in use at exit:/ {num=$6;} END {print num;}' $vglog) 97 | [ $leak != 0 ] && echo "Memory still used: $leak" \ 98 | && errors=$(expr $errors + 1) 99 | viol=$(awk '/ERROR SUMMARY/ {num=$4;} END {print num;}' $vglog) 100 | [ $viol != 0 ] && echo "Valgrind errors: $viol" \ 101 | && errors=$(expr $errors + 1) 102 | [ $leak = 0 ] && [ $viol = 0 ] && rm ${vglog} 103 | counter=$(expr $counter + 6) 104 | done 105 | 106 | # Class2 tests with compass 107 | for m in hydrogen ethane benzene naphthalene cnt-hexagonal 108 | do \ 109 | before=$errors 110 | vglog=${m}-class2a.chk 111 | ${VALGRIND} --log-file=${vglog} \ 112 | ${MSI2LMP} ${m}-class2a -c 2 -p ${verbose} -f compass_published \ 113 | || errors=$(expr $errors + 1) 114 | ${LAMMPS} -log none -screen none -in in.${m}-class2a \ 115 | || errors=$(expr $errors + 1) 116 | ${CHECKDATA} ${m}-class2a.data reference/${m}-class2a.data \ 117 | || errors=$(expr $errors + 1) 118 | ${CHECKDATA} ${m}-class2a.data2 reference/${m}-class2a.data2 \ 119 | || errors=$(expr $errors + 1) 120 | [ $before -eq $errors ] && rm ${m}-class2a.data ${m}-class2a.data2 log.${m}-class2a 121 | leak=$(awk '/in use at exit:/ {num=$6;} END {print num;}' $vglog) 122 | [ $leak != 0 ] && echo "Memory still used: $leak" \ 123 | && errors=$(expr $errors + 1) 124 | viol=$(awk '/ERROR SUMMARY/ {num=$4;} END {print num;}' $vglog) 125 | [ $viol != 0 ] && echo "Valgrind errors: $viol" \ 126 | && errors=$(expr $errors + 1) 127 | [ $leak = 0 ] && [ $viol = 0 ] && rm ${vglog} 128 | counter=$(expr $counter + 6) 129 | done 130 | 131 | # Class2 tests with pcff 132 | for m in water h2-h2o ethane benzene naphthalene cnt-hexagonal hap_crystal 133 | do \ 134 | before=$errors 135 | vglog=${m}-class2b.chk 136 | ${VALGRIND} --log-file=${vglog} \ 137 | ${MSI2LMP} ${m}-class2b -c 2 -p ${verbose} -f pcff \ 138 | || errors=$(expr $errors + 1) 139 | ${LAMMPS} -log none -screen none -in in.${m}-class2b \ 140 | || errors=$(expr $errors + 1) 141 | ${CHECKDATA} ${m}-class2b.data reference/${m}-class2b.data \ 142 | || errors=$(expr $errors + 1) 143 | ${CHECKDATA} ${m}-class2b.data2 reference/${m}-class2b.data2 \ 144 | || errors=$(expr $errors + 1) 145 | [ $before -eq $errors ] && rm ${m}-class2b.data ${m}-class2b.data2 log.${m}-class2b 146 | leak=$(awk '/in use at exit:/ {num=$6;} END {print num;}' $vglog) 147 | [ $leak != 0 ] && echo "Memory still used: $leak" \ 148 | && errors=$(expr $errors + 1) 149 | viol=$(awk '/ERROR SUMMARY/ {num=$4;} END {print num;}' $vglog) 150 | [ $viol != 0 ] && echo "Valgrind errors: $viol" \ 151 | && errors=$(expr $errors + 1) 152 | [ $leak = 0 ] && [ $viol = 0 ] && rm ${vglog} 153 | counter=$(expr $counter + 6) 154 | done 155 | 156 | echo "Total error count: $errors / $counter" 157 | echo 158 | 159 | echo "Total error count: $errors / $counter" 160 | echo 161 | 162 | -------------------------------------------------------------------------------- /msi2lmp/test/water-class1.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Tue Jul 02 12:42:22 2013 5 | PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1) 6 | O1 5.000000000 5.000000000 5.000000000 TIP3 1 otip O -0.834 7 | H2 4.000000000 5.000000000 5.000000000 TIP3 1 htip H 0.417 8 | H3 5.000000000 4.000000000 5.000000000 TIP3 1 htip H 0.417 9 | end 10 | end 11 | -------------------------------------------------------------------------------- /msi2lmp/test/water-class1.mdf: -------------------------------------------------------------------------------- 1 | !BIOSYM molecular_data 4 2 | 3 | !Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file 4 | 5 | #topology 6 | 7 | @column 1 element 8 | @column 2 atom_type 9 | @column 3 charge_group 10 | @column 4 isotope 11 | @column 5 formal_charge 12 | @column 6 charge 13 | @column 7 switching_atom 14 | @column 8 oop_flag 15 | @column 9 chirality_flag 16 | @column 10 occupancy 17 | @column 11 xray_temp_factor 18 | @column 12 connections 19 | 20 | @molecule tip3p-water 21 | 22 | TIP3_1:O1 O otip 1 0 0 -0.8340 0 0 8 1.0000 0.0000 H2 H3 23 | TIP3_1:H2 H htip 1 0 0 0.4170 0 0 8 1.0000 0.0000 O1 24 | TIP3_1:H3 H htip 1 0 0 0.4170 0 0 8 1.0000 0.0000 O1 25 | 26 | ! 27 | #symmetry 28 | @periodicity 3 xyz 29 | @group (P1) 30 | 31 | #end 32 | -------------------------------------------------------------------------------- /msi2lmp/test/water-class2b.car: -------------------------------------------------------------------------------- 1 | !BIOSYM archive 3 2 | PBC=ON 3 | Materials Studio Generated CAR File 4 | !DATE Tue Jul 02 12:42:22 2013 5 | PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1) 6 | O1 5.000000000 5.000000000 5.000000000 TIP3 1 o* O -0.834 7 | H2 4.000000000 5.000000000 5.000000000 TIP3 1 h* H 0.417 8 | H3 5.000000000 4.000000000 5.000000000 TIP3 1 h* H 0.417 9 | end 10 | end 11 | -------------------------------------------------------------------------------- /msi2lmp/test/water-class2b.mdf: -------------------------------------------------------------------------------- 1 | !BIOSYM molecular_data 4 2 | 3 | !Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file 4 | 5 | #topology 6 | 7 | @column 1 element 8 | @column 2 atom_type 9 | @column 3 charge_group 10 | @column 4 isotope 11 | @column 5 formal_charge 12 | @column 6 charge 13 | @column 7 switching_atom 14 | @column 8 oop_flag 15 | @column 9 chirality_flag 16 | @column 10 occupancy 17 | @column 11 xray_temp_factor 18 | @column 12 connections 19 | 20 | @molecule cff91-water 21 | 22 | TIP3_1:O1 O o* 1 0 0 -0.8340 0 0 8 1.0000 0.0000 H2 H3 23 | TIP3_1:H2 H h* 1 0 0 0.4170 0 0 8 1.0000 0.0000 O1 24 | TIP3_1:H3 H h* 1 0 0 0.4170 0 0 8 1.0000 0.0000 O1 25 | 26 | ! 27 | #symmetry 28 | @periodicity 3 xyz 29 | @group (P1) 30 | 31 | #end 32 | --------------------------------------------------------------------------------