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import and adapt changes from jeff greathouse to support opls-aa

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This commit is contained in:
Axel Kohlmeyer
2013-08-02 13:13:01 +02:00
parent 5b2056130a
commit dbae00bfce
16 changed files with 618 additions and 53 deletions
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5
tools/msi2lmp/README
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@ -1,6 +1,11 @@
Stephanie Teich-McGoldrick (Sandai) is the current maintainer
of the msi2lmp tool. She can be contacted at steichm at sandia.gov
02 Aug 2013 Axel Kohlmeyer <akohlmey@gmail.com>
Added rudimentary support for OPLS-AA based on
input provided by jeff greathouse.
18 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
Added support for writing out image flags

236
tools/msi2lmp/biosym_frc_files/oplsaa.frc Normal file
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@ -0,0 +1,236 @@
!BIOSYM forcefield 1
! This is a modified version of msi2lmp for use specifically wtih the
! OPLS force field. No out-of-plane or cross-terms are included.
! Atom types from SPC water and CLAYFF are also included.
#atom_types cvff
> Masses from CRC 1973/74 pages B-250.
!Ver Ref Type Mass Element Connections Comment
!---- --- ---- ---------- ------- -----------------------------------------
1.0 1 HC 1.007970 H 1 H, RH, alkanes
1.0 1 HO 1.007970 H 1 H(O), ROH
1.0 1 HS 1.007970 H 1 H(S), RSH
1.0 1 HM 1.007970 H 1 H(C), CH3OH
1.0 1 CT 12.011150 C 4 Aliphatic C
1.0 1 OH 15.999400 O 2 O, ROH
1.0 1 SH 32.064000 S 2 S, RSH
1.0 1 S 32.064000 S 2 S, RSR
1.0 1 CG 12.011150 C 1 Graphite C
1.0 1 CL 35.453000 Cl 1 Cl, RCl
X.X X CC 12.011150 C 3 Carbonate ion C, AMBER
X.X X OC 15.035060 O 1 Carbonate ion O, AMBER
#equivalence cvff
> Equivalence table for any variant of cvff
! Equivalences
! -----------------------------------------
!Ver Ref Type NonB Bond Angle Torsion OOP
!---- --- ---- ---- ---- ----- ------- ----
1.0 1 h h h h h h
#quadratic_bond cvff
> E = K2 * (R - R0)^2
!Ver Ref I J R0 K2
!---- --- ---- ---- ------- --------
2.3 23 CT CT 1.529 268.0
2.3 23 CT HC 1.09 340.0
2.3 23 CT OH 1.410 320.0
2.3 23 CT SH 1.810 222.0
1.0 1 HO OH 0.96 553.0
1.0 1 HS SH 1.336 274.0
1.0 1 CT S 1.810 222.0
1.0 1 CT CL 1.781 245.0
X.X X CC OC 1.21 648.0
#quadratic_angle cvff
> E = K2 * (Theta - Theta0)^2
!Ver Ref I J K Theta0 K2
!---- --- ---- ---- ---- -------- -------
2.3 23 CT CT CT 112.7 58.35
2.3 23 CT CT HC 110.7 37.50
2.3 23 CT CT OH 109.5 50.00
2.3 23 HC CT HC 107.8 33.00
2.3 23 CT OH HO 108.5 55.00
2.3 23 HC CT OH 109.5 35.00
1.0 1 CT CT SH 108.6 50.00
1.0 1 CT SH HS 96.0 44.00
1.0 1 HC CT SH 109.5 35.00
1.0 1 CT CT S 114.7 50.00
1.0 1 CT S CT 98.9 62.00
1.0 1 HC CT S 109.5 35.00
1.0 1 CT CT CL 109.8 69.0
1.0 1 HC CT CL 107.6 51.0
X.X X OC CC OC 127.0 79.1
#bond-bond cvff
> E = K(b,b') * (R - R0) * (R' - R0')
!Ver Ref I J K K(b,b')
!---- --- ---- ---- ---- -------
1.0 1 c o c' 0.0000
#bond-angle cvff
> E = K * (R - R0) * (Theta - Theta0)
!Ver Ref I J K K(b,theta) K(b',theta)
!---- --- ---- ---- ---- ---------- -----------
1.0 1 c o c' 57.0000 57.0000
#torsion_1 opls
> E = 0.5*K1*[1 + cos(Phi)] + 0.5*K2*[1 + cos(2*Phi)] + 0.5*K3*[1 + cos(3*Phi)] + 0.5*K4*[1 + cos(4*Phi)]
!Ver Ref I J K L K1 K2 K3 K4
!---- --- ---- ---- ---- ---- ------- ------ ------ -----
X.X XX HC CT CT HC 0.0 0.0 0.318 0.0
X.X XX HC CT CT CT 0.0 0.0 0.366 0.0
X.X XX HC CT OH HO 0.0 0.0 0.450 0.0
X.X XX CT CT OH HO -0.356 -0.174 0.492 0.0
X.X XX HC CT CT OH 0.0 0.0 0.468 0.0
X.X XX CT CT CT OH 1.711 -0.500 0.663 0.0
X.X XX HC CT SH HS 0.0 0.0 0.451 0.0
X.X XX CT CT SH HS -0.759 -0.282 0.603 0.0
X.X XX HC CT CT SH 0.0 0.0 0.452 0.0
X.X XX CT CT CT SH 1.876 0.0 0.0 0.0
X.X XX HC CT CT S 0.0 0.0 0.452 0.0
X.X XX CT CT S CT 0.925 -0.576 0.677 0.0
X.X XX HC CT S CT 0.0 0.0 0.647 0.0
X.X XX S CT CT CL 0.0 0.0 0.452 0.0
X.X XX CL CT CT CL 0.250 -0.250 0.0 0.0
X.X XX HC CT CT CL 0.0 0.0 0.400 0.0
#angle-angle-torsion_1 cvff
> E = K * (Theta - Theta0) * (Theta' - Theta0') * cos(Phi)
!Ver Ref I J K L K(Ang,Ang,Tor)
!---- --- ---- ---- ---- ---- --------------
1.0 1 * c c * -10.5000
#out_of_plane cvff
> E = Kchi * [ 1 + cos(n*Chi - Chi0) ]
!Ver Ref I J K L Kchi n Chi0
!---- --- ---- ---- ---- ---- ------- ------ -------
2.3 0 hn n c c' 10.0 2 180.0
X.X X OC CC OC OC 1.1 2 180.0
#out_of_plane-out_of_plane cvff
> E = Koo * Chi * Chi'
!Ver Ref I J K L Koo
!---- --- ---- ---- ---- ---- -------
1.0 1 c c' n o' 0.0100
#angle-angle cvff
> E = K * (Theta - Theta0) * (Theta' - Theta0')
! J' I' K'
!Ver Ref I J K K
!---- --- ---- ---- ---- ---- -------
1.0 1 c c c c -7.9000
#morse_bond cvff_auto
> E = D * (1 - exp(-ALPHA*(R - R0)))^2
!Ver Ref I J R0 D ALPHA
!---- --- ---- ---- ------- -------- -------
2.0 18 c3m_ c3m_ 1.5100 88.0000 1.9150
#quadratic_bond cvff_auto
> E = K2 * (R - R0)^2
!Ver Ref I J R0 K2
!---- --- ---- ---- ------- --------
2.0 18 c3m_ c3m_ 1.5100 322.7158
#quadratic_angle cvff_auto
> E = K2 * (Theta - Theta0)^2
!Ver Ref I J K Theta0 K2
!---- --- ---- ---- ---- -------- -------
2.0 18 c3m_ c3m_ c3m_ 60.0000 46.0000
#torsion_1 cvff_auto
> E = Kphi * [ 1 + cos(n*Phi - Phi0) ]
!Ver Ref I J K L Kphi n Phi0
!---- --- ---- ---- ---- ---- ------- ------ -------
2.0 18 * c_ n3n_ * 0.0500 3 0.
#out_of_plane cvff_auto
> E = Kchi * [ 1 + cos(n*Chi - Chi0) ]
!Ver Ref I J K L Kchi n Chi0
!---- --- ---- ---- ---- ---- ------- ------ -------
2.0 18 * c'_ * * 10.0000 2 180.0000
#nonbond(12-6) cvff
@type A-B
@combination geometric
> E = Aij/r^12 - Bij/r^6
> where Aij = sqrt( Ai * Aj )
> Bij = sqrt( Bi * Bj )
!Ver Ref I A B
!---- --- ---- ----------- -----------
1.0 1 HC 7152.557 29.297
1.0 1 HO 0.0 0.0
1.0 1 HS 0.0 0.0
1.8 14 HM 7152.557 29.297
1.0 1 CT 892114.214 485.302
1.0 1 OH 578580.831 627.244
2.3 25 SH 4006270.2 2001.567
2.3 25 S 4006270.2 2001.567
1.0 1 CG 531140.879 343.824
1.0 1 CL 2863704.82 1853.765299
X.X X CC 819971.66216 531.10286
XX X OC 379876.39852 564.88598
#bond_increments cvff
!Ver Ref I J DeltaIJ DeltaJI
!---- --- ---- ---- ------- -------
2.3 23 no o- 0.1684 -0.1684

10
tools/msi2lmp/src/GetParameters.c
View File

@ -77,7 +77,7 @@ void GetParameters()
printf(" Unable to find vdw data for %s\n",atomtypes[i].potential);
condexit(11);
} else {
if (forcefield & FF_TYPE_CLASS1) {
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
if((ff_vdw.data[k].ff_param[0] != 0.0 ) &&
(ff_vdw.data[k].ff_param[1] != 0.0)) {
atomtypes[i].params[0] =
@ -132,7 +132,7 @@ void GetParameters()
potential_types[0],potential_types[1]);
condexit(12);
} else {
if (forcefield & FF_TYPE_CLASS1) {
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
bondtypes[i].params[0] = ff_bond.data[k].ff_param[1];
bondtypes[i].params[1] = ff_bond.data[k].ff_param[0];
}
@ -189,7 +189,7 @@ void GetParameters()
potential_types[0],potential_types[1],potential_types[2]);
condexit(13);
} else {
if (forcefield & FF_TYPE_CLASS1) {
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
angletypes[i].params[0] = ff_ang.data[k].ff_param[1];
angletypes[i].params[1] = ff_ang.data[k].ff_param[0];
}
@ -341,6 +341,10 @@ void GetParameters()
}
dihedraltypes[i].params[2] = ff_tor.data[k].ff_param[1];
}
if (forcefield & FF_TYPE_OPLSAA) {
for (j=0; j < 4; j++)
dihedraltypes[i].params[j] = ff_tor.data[k].ff_param[j];
}
if (forcefield & FF_TYPE_CLASS2) {
for (j=0; j < 6; j++)
dihedraltypes[i].params[j] = ff_tor.data[k].ff_param[j];

8
tools/msi2lmp/src/InitializeItems.c
View File

@ -31,7 +31,7 @@ void InitializeItems(void)
/* BOND */
ff_bond.number_of_members = 2;
if (forcefield & FF_TYPE_CLASS1) {
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
strcpy(ff_bond.keyword,"#quadratic_bond");
ff_bond.number_of_parameters = 2;
}
@ -52,7 +52,7 @@ void InitializeItems(void)
/* ANGLE */
ff_ang.number_of_members = 3;
if (forcefield & FF_TYPE_CLASS1) {
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
strcpy(ff_ang.keyword,"#quadratic_angle");
ff_ang.number_of_parameters = 2;
}
@ -65,7 +65,7 @@ void InitializeItems(void)
/* TORSION */
ff_tor.number_of_members = 4;
if (forcefield & FF_TYPE_CLASS1) {
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
strcpy(ff_tor.keyword,"#torsion_1");
ff_tor.number_of_parameters = 3;
}
@ -78,7 +78,7 @@ void InitializeItems(void)
/* OOP */
ff_oop.number_of_members = 4;
if (forcefield & FF_TYPE_CLASS1) {
if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA)) {
strcpy(ff_oop.keyword,"#out_of_plane");
ff_oop.number_of_parameters = 3;
}

2
tools/msi2lmp/src/ReadCarFile.c
View File

@ -188,7 +188,7 @@ void ReadCarFile(void)
atoms[k].molecule = m;
atoms[k].no = k;
fscanf(CarF,"%s %lf %lf %lf %*s %d %s %s %f",
fscanf(CarF,"%s %lf %lf %lf %*s %d %s %s %lf",
atoms[k].name,
&(atoms[k].x[0]),
&(atoms[k].x[1]),

5
tools/msi2lmp/src/ReadFrcFile.c
View File

@ -57,8 +57,9 @@ void ReadFrcFile(void)
ff_vdw.keyword,ff_vdw.entries);
fprintf(stderr," Item %s has %d entries\n",
ff_bond.keyword,ff_bond.entries);
fprintf(stderr," Item %s has %d entries\n",
ff_morse.keyword,ff_morse.entries);
if (forcefield & FF_TYPE_CLASS1)
fprintf(stderr," Item %s has %d entries\n",
ff_morse.keyword,ff_morse.entries);
fprintf(stderr," Item %s has %d entries\n",
ff_ang.keyword,ff_ang.entries);
if (forcefield & FF_TYPE_CLASS2) {

2
tools/msi2lmp/src/SearchAndFill.c
View File

@ -41,7 +41,7 @@ void SearchAndFill(struct FrcFieldItem *item)
while (got_it == 0) {
status = fgets( line, MAX_LINE_LENGTH, FrcF );
if (status == NULL) {
fprintf(stderr," Unable to find forcefield keyword %s\n",item->keyword);
fprintf(stderr," Unable to find keyword '%s'\n",item->keyword);
fprintf(stderr," Check consistency of forcefield name and class \n");
fprintf(stderr," Exiting....\n");
exit(1);

24
tools/msi2lmp/src/WriteDataFile.c
View File

@ -94,6 +94,7 @@ void WriteDataFile(char *nameroot)
if (no_bond_types > 0) {
m = 0;
if (forcefield & FF_TYPE_CLASS1) m = 2;
if (forcefield & FF_TYPE_OPLSAA) m = 2;
if (forcefield & FF_TYPE_CLASS2) m = 4;
fprintf(DatF,"Bond Coeffs\n\n");
@ -109,6 +110,7 @@ void WriteDataFile(char *nameroot)
if (no_angle_types > 0) {
m = 0;
if (forcefield & FF_TYPE_CLASS1) m = 2;
if (forcefield & FF_TYPE_OPLSAA) m = 2;
if (forcefield & FF_TYPE_CLASS2) m = 4;
fprintf(DatF,"Angle Coeffs\n\n");
@ -134,6 +136,17 @@ void WriteDataFile(char *nameroot)
(int) dihedraltypes[i].params[1],
(int) dihedraltypes[i].params[2]);
} else if (forcefield & FF_TYPE_OPLSAA) {
fprintf(DatF,"Dihedral Coeffs\n\n");
for (i=0; i < no_dihedral_types; i++) {
fprintf(DatF, "%3i",i+1);
for ( j = 0; j < 4; j++)
fprintf(DatF, " %10.4f",dihedraltypes[i].params[j]);
fputs("\n",DatF);
}
} else if (forcefield & FF_TYPE_CLASS2) {
fprintf(DatF,"Dihedral Coeffs\n\n");
@ -160,6 +173,17 @@ void WriteDataFile(char *nameroot)
}
fputs("\n",DatF);
}
} else if (forcefield & FF_TYPE_OPLSAA) {
if (no_oop_types > 0) {
/* opls improper coeffs are like cvff: type K0 d(=-1) n(=2) */
fprintf(DatF,"Improper Coeffs\n\n");
for (i=0; i < no_oop_types; i++) {
fprintf(DatF,"%5i %10.4f %3i %3i\n",i+1,
ooptypes[i].params[0], (int) ooptypes[i].params[1],
(int) ooptypes[i].params[2]);
}
fputs("\n",DatF);
}
} else if (forcefield & FF_TYPE_CLASS2) {
if ((no_oop_types + no_angleangle_types) > 0) {
fprintf(DatF,"Improper Coeffs\n\n");

30
tools/msi2lmp/src/msi2lmp.c
View File

@ -1,6 +1,8 @@
/*
*
* msi2lmp.exe V3.8
* msi2lmp.exe V3.9
*
* v3.9 AK - Rudimentary support for OPLS-AA
*
* v3.6 KLA - Changes to output to either lammps 2001 (F90 version) or to
* lammps 2005 (C++ version)
@ -317,15 +319,23 @@ int main (int argc, char *argv[])
printf(" Forcefield file name: %s\n",FrcFileName);
}
if (((forcefield & FF_TYPE_CLASS1) && (strstr(FrcFileName,"cff") != NULL)) ||
((forcefield & FF_TYPE_CLASS2) &&
! ((strstr(FrcFileName,"cvff") == NULL)
|| (strstr(FrcFileName,"clayff") == NULL)
|| (strstr(FrcFileName,"compass") == NULL))) ||
((forcefield & FF_TYPE_OPLSAA) &&
! (strstr(FrcFileName,"opls") == NULL))) {
fprintf(stderr," WARNING - forcefield name and class appear to\n");
fprintf(stderr," be inconsistent - Errors may result\n\n");
n = 0;
if (forcefield & FF_TYPE_CLASS1) {
if (strstr(FrcFileName,"cvff") != NULL) ++n;
if (strstr(FrcFileName,"clayff") != NULL) ++n;
} else if (forcefield & FF_TYPE_OPLSAA) {
if (strstr(FrcFileName,"oplsaa") != NULL) ++n;
} else if (forcefield & FF_TYPE_CLASS2) {
if (strstr(FrcFileName,"pcff") != NULL) ++n;
if (strstr(FrcFileName,"cff91") != NULL) ++n;
if (strstr(FrcFileName,"compass") != NULL) ++n;
}
if (n == 0) {
if (iflag > 0) fputs(" WARNING",stderr);
else fputs(" Error ",stderr);
fputs("- forcefield name and class appear to be inconsistent\n\n",stderr);
if (iflag == 0) return 7;
}

64
tools/msi2lmp/test/data-compare.pl
View File

@ -826,6 +826,38 @@ sub syscompare {
die "Number of ",$i," types does not match: $a vs $b" unless ($a == $b);
}
topocompare($d1,$d2,'bond',2);
topocompare($d1,$d2,'angle',3);
topocompare($d1,$d2,'dihedral',4);
topocompare($d1,$d2,'improper',4);
coeffcompare($d1,$d2,'pair','atom');
coeffcompare($d1,$d2,'bond','bond');
coeffcompare($d1,$d2,'angle','angle');
coeffcompare($d1,$d2,'bondbond','angle');
coeffcompare($d1,$d2,'bondangle','angle');
coeffcompare($d1,$d2,'dihedral','dihedral');
coeffcompare($d1,$d2,'angleangletorsion','dihedral');
coeffcompare($d1,$d2,'bondbond13','dihedral');
coeffcompare($d1,$d2,'endbondtorsion','dihedral');
coeffcompare($d1,$d2,'middlebondtorsion','dihedral');
coeffcompare($d1,$d2,'improper','improper');
coeffcompare($d1,$d2,'angleangle','improper');
for ($i=0; $i < $d1->{natomtypes}; ++$i) {
$j = $i+1;
if (exists $d1->{mass}[$i]) {
$a = $d1->{mass}[$i];
} else {
die "No mass for atom type $j in data file 1";
}
if (exists $d2->{mass}[$i]) {
$a = $d2->{mass}[$i];
} else {
die "No mass for atom type $j in data file 2";
}
}
# check box information
die "Inconsistent box shape" if ($d1->{triclinic} != $d2->{triclinic});
@ -868,38 +900,6 @@ sub syscompare {
}
}
for ($i=0; $i < $d1->{natomtypes}; ++$i) {
$j = $i+1;
if (exists $d1->{mass}[$i]) {
$a = $d1->{mass}[$i];
} else {
die "No mass for atom type $j in data file 1";
}
if (exists $d2->{mass}[$i]) {
$a = $d2->{mass}[$i];
} else {
die "No mass for atom type $j in data file 2";
}
}
topocompare($d1,$d2,'bond',2);
topocompare($d1,$d2,'angle',3);
topocompare($d1,$d2,'dihedral',4);
topocompare($d1,$d2,'improper',4);
coeffcompare($d1,$d2,'pair','atom');
coeffcompare($d1,$d2,'bond','bond');
coeffcompare($d1,$d2,'angle','angle');
coeffcompare($d1,$d2,'bondbond','angle');
coeffcompare($d1,$d2,'bondangle','angle');
coeffcompare($d1,$d2,'dihedral','dihedral');
coeffcompare($d1,$d2,'angleangletorsion','dihedral');
coeffcompare($d1,$d2,'bondbond13','dihedral');
coeffcompare($d1,$d2,'endbondtorsion','dihedral');
coeffcompare($d1,$d2,'middlebondtorsion','dihedral');
coeffcompare($d1,$d2,'improper','improper');
coeffcompare($d1,$d2,'angleangle','improper');
}
########################################################################

15
tools/msi2lmp/test/ethane-oplsaa.car Normal file
View File

@ -0,0 +1,15 @@
!BIOSYM archive 3
PBC=ON
Materials Studio Generated CAR File
!DATE Tue Jul 02 12:42:22 2013
PBC 10.0000 10.0000 10.0000 90.0000 90.0000 90.0000 (P1)
C1 4.462910000 5.148330000 -5.000410000 XXXX 1 CT C -0.180
C2 5.965490000 5.079930000 -4.999750000 XXXX 1 CT C -0.180
H3 4.099550000 6.054480000 -5.502500000 XXXX 1 HC H 0.060
H4 4.020330000 4.288350000 -5.519840000 XXXX 1 HC H 0.060
H5 4.057610000 5.156680000 -3.980190000 XXXX 1 HC H 0.060
H6 6.409980000 5.944880000 -4.490510000 XXXX 1 HC H 0.060
H7 6.329880000 4.179410000 -4.488110000 XXXX 1 HC H 0.060
H8 6.370610000 5.061380000 -6.019850000 XXXX 1 HC H 0.060
end
end

36
tools/msi2lmp/test/ethane-oplsaa.mdf Normal file
View File

@ -0,0 +1,36 @@
!BIOSYM molecular_data 4
!Date: Tue Jul 02 12:42:23 2013 Materials Studio Generated MDF file
#topology
@column 1 element
@column 2 atom_type
@column 3 charge_group
@column 4 isotope
@column 5 formal_charge
@column 6 charge
@column 7 switching_atom
@column 8 oop_flag
@column 9 chirality_flag
@column 10 occupancy
@column 11 xray_temp_factor
@column 12 connections
@molecule ethane
XXXX_1:C1 C CT 1 0 0 -0.1800 0 0 8 1.0000 0.0000 C2 H3 H4 H5
XXXX_1:C2 C CT 1 0 0 -0.1800 0 0 8 1.0000 0.0000 C1 H6 H7 H8
XXXX_1:H3 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C1
XXXX_1:H4 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C1
XXXX_1:H5 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C1
XXXX_1:H6 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C2
XXXX_1:H7 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C2
XXXX_1:H8 H HC 1 0 0 0.0600 0 0 8 1.0000 0.0000 C2
!
#symmetry
@periodicity 3 xyz
@group (P1)
#end

14
tools/msi2lmp/test/in.ethane-oplsaa Normal file
View File

@ -0,0 +1,14 @@
log log.ethane-oplsaa
units real
atom_style full
pair_style lj/cut/coul/cut 15.0
bond_style harmonic
angle_style harmonic
dihedral_style opls
read_data ethane-oplsaa.data
thermo_style multi
minimize 0.0 0.0 100 1000
write_data ethane-oplsaa.data2

89
tools/msi2lmp/test/reference/ethane-oplsaa.data Normal file
View File

@ -0,0 +1,89 @@
LAMMPS data file from msi2lmp v3.8 for ethane-oplsaa
8 atoms
7 bonds
12 angles
9 dihedrals
0 impropers
2 atom types
2 bond types
2 angle types
1 dihedral types
-5.000000000 5.000000000 xlo xhi
-5.000000000 5.000000000 ylo yhi
-5.000000000 5.000000000 zlo zhi
Masses
1 12.011150
2 1.007970
Pair Coeffs
1 0.0659999660 3.5000001502
2 0.0300002576 2.4999982005
Bond Coeffs
1 268.0000 1.5290
2 340.0000 1.0900
Angle Coeffs
1 37.5000 110.7000
2 33.0000 107.8000
Dihedral Coeffs
1 0.0000 0.0000 0.3180 0.0000
Atoms
1 1 1 -0.180000 4.462910000 -4.851670000 4.999590000 0 1 -1
2 1 1 -0.180000 -4.034510000 -4.920070000 -4.999750000 1 1 0
3 1 2 0.060000 4.099550000 -3.945520000 4.497500000 0 1 -1
4 1 2 0.060000 4.020330000 4.288350000 4.480160000 0 0 -1
5 1 2 0.060000 4.057610000 -4.843320000 -3.980190000 0 1 0
6 1 2 0.060000 -3.590020000 -4.055120000 -4.490510000 1 1 0
7 1 2 0.060000 -3.670120000 4.179410000 -4.488110000 1 0 0
8 1 2 0.060000 -3.629390000 -4.938620000 3.980150000 1 1 -1
Bonds
1 1 1 2
2 2 1 3
3 2 1 4
4 2 1 5
5 2 2 6
6 2 2 7
7 2 2 8
Angles
1 1 2 1 3
2 1 2 1 4
3 1 2 1 5
4 2 3 1 4
5 2 3 1 5
6 2 4 1 5
7 1 1 2 6
8 1 1 2 7
9 1 1 2 8
10 2 6 2 7
11 2 6 2 8
12 2 7 2 8
Dihedrals
1 1 3 1 2 6
2 1 3 1 2 7
3 1 3 1 2 8
4 1 4 1 2 6
5 1 4 1 2 7
6 1 4 1 2 8
7 1 5 1 2 6
8 1 5 1 2 7
9 1 5 1 2 8

97
tools/msi2lmp/test/reference/ethane-oplsaa.data2 Normal file
View File

@ -0,0 +1,97 @@
LAMMPS data file via write_data, version 14 Aug 2013-ICMS, timestep = 38
8 atoms
2 atom types
7 bonds
2 bond types
12 angles
2 angle types
9 dihedrals
1 dihedral types
-5.0000000000000000e+00 5.0000000000000000e+00 xlo xhi
-5.0000000000000000e+00 5.0000000000000000e+00 ylo yhi
-5.0000000000000000e+00 5.0000000000000000e+00 zlo zhi
Masses
1 12.0112
2 1.00797
Pair Coeffs
1 0.066 3.5
2 0.0300003 2.5
Bond Coeffs
1 268 1.529
2 340 1.09
Angle Coeffs
1 37.5 110.7
2 33 107.8
Dihedral Coeffs
1 0 0 0.318 0
Atoms
1 1 1 -1.7999999999999999e-01 4.4513654787991950e+00 -4.8452952225235171e+00 4.9978618185413897e+00 0 1 -1
2 1 1 -1.7999999999999999e-01 -4.0223413274230113e+00 -4.9265327783543249e+00 -4.9984426635205530e+00 1 1 0
3 1 2 5.9999999999999998e-02 4.1118234494897825e+00 -3.9519955907798003e+00 4.4733619774254318e+00 0 1 -1
4 1 2 5.9999999999999998e-02 4.0174988470475572e+00 4.2860576171223572e+00 4.5022469929383719e+00 0 0 -1
5 1 2 5.9999999999999998e-02 4.0630111196035328e+00 -4.8077899330369602e+00 -3.9842586979365473e+00 0 1 0
6 1 2 5.9999999999999998e-02 -3.5902683367048773e+00 -4.0732209849776302e+00 -4.4754195169139814e+00 1 1 0
7 1 2 5.9999999999999998e-02 -3.6834327143496224e+00 4.1648625434843920e+00 -4.5005239377702599e+00 1 0 0
8 1 2 5.9999999999999998e-02 -3.6312965164625557e+00 -4.9326456509345169e+00 3.9840140272361455e+00 1 1 -1
Velocities
1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
2 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
3 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
4 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
5 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
6 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
7 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
8 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
Bonds
1 1 1 2
2 2 1 3
3 2 1 4
4 2 1 5
5 2 2 6
6 2 2 7
7 2 2 8
Angles
1 1 2 1 3
2 1 2 1 4
3 1 2 1 5
4 2 3 1 4
5 2 3 1 5
6 2 4 1 5
7 1 1 2 6
8 1 1 2 7
9 1 1 2 8
10 2 6 2 7
11 2 6 2 8
12 2 7 2 8
Dihedrals
1 1 3 1 2 6
2 1 3 1 2 7
3 1 3 1 2 8
4 1 4 1 2 6
5 1 4 1 2 7
6 1 4 1 2 8
7 1 5 1 2 6
8 1 5 1 2 7
9 1 5 1 2 8

34
tools/msi2lmp/test/runtests.sh
View File

@ -5,6 +5,24 @@ MSI2LMP=../src/msi2lmp.exe
LAMMPS=../../../src/lmp_serial
CHECKDATA=./data-compare.pl
if [ ! -x $MSI2LMP ]
then
echo "No executable $MSI2LMP"
exit 1
fi
if [ ! -d $BIOSYM_LIBRARY ]
then
echo "No directory $BIOSYM_LIBRARY"
exit 1
fi
if [ ! -x $LAMMPS ]
then
echo "No executable $LAMMPS"
exit 1
fi
verbose=1
counter=0
errors=0
@ -41,6 +59,22 @@ do \
counter=$(expr $counter + 4)
done
# OPLS-AA tests
for m in ethane
do \
before=$errors
${MSI2LMP} ${m}-oplsaa -c 0 -p ${verbose} -f oplsaa -n \
|| errors=$(expr $errors + 1)
${LAMMPS} -log none -screen none -in in.${m}-oplsaa \
|| errors=$(expr $errors + 1)
${CHECKDATA} ${m}-oplsaa.data reference/${m}-oplsaa.data \
|| errors=$(expr $errors + 1)
${CHECKDATA} ${m}-oplsaa.data2 reference/${m}-oplsaa.data2 \
|| errors=$(expr $errors + 1)
[ $before -eq $errors ] && rm ${m}-oplsaa.data ${m}-oplsaa.data2 log.${m}-oplsaa
counter=$(expr $counter + 4)
done
# Class2 tests with compass
for m in hydrogen ethane benzene naphthalene
do \