24 |
|
#define NPTxyz_ENS 4 |
25 |
|
|
26 |
|
|
27 |
< |
#define FF_DUFF 0 |
28 |
< |
#define FF_LJ 1 |
29 |
< |
#define FF_EAM 2 |
27 |
> |
#define FF_DUFF 0 |
28 |
> |
#define FF_LJ 1 |
29 |
> |
#define FF_EAM 2 |
30 |
> |
#define FF_H2O 3 |
31 |
|
|
32 |
|
using namespace std; |
33 |
|
|
175 |
|
bend_set* theBends; |
176 |
|
torsion_set* theTorsions; |
177 |
|
|
177 |
– |
|
178 |
|
//init the forceField paramters |
179 |
|
|
180 |
|
the_ff->readParams(); |
182 |
|
|
183 |
|
// init the atoms |
184 |
|
|
185 |
+ |
double phi, theta, psi; |
186 |
+ |
double sux, suy, suz; |
187 |
+ |
double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz; |
188 |
|
double ux, uy, uz, u, uSqr; |
189 |
|
|
190 |
|
for (k = 0; k < nInfo; k++){ |
221 |
|
info[k].n_oriented++; |
222 |
|
molInfo.myAtoms[j] = dAtom; |
223 |
|
|
224 |
< |
ux = currentAtom->getOrntX(); |
225 |
< |
uy = currentAtom->getOrntY(); |
226 |
< |
uz = currentAtom->getOrntZ(); |
224 |
> |
// Directional Atoms have standard unit vectors which are oriented |
225 |
> |
// in space using the three Euler angles. We assume the standard |
226 |
> |
// unit vector was originally along the z axis below. |
227 |
|
|
228 |
+ |
phi = currentAtom->getEulerPhi() * M_PI / 180.0; |
229 |
+ |
theta = currentAtom->getEulerTheta() * M_PI / 180.0; |
230 |
+ |
psi = currentAtom->getEulerPsi()* M_PI / 180.0; |
231 |
+ |
|
232 |
+ |
Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
233 |
+ |
Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
234 |
+ |
Axz = sin(theta) * sin(psi); |
235 |
+ |
|
236 |
+ |
Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
237 |
+ |
Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
238 |
+ |
Ayz = sin(theta) * cos(psi); |
239 |
+ |
|
240 |
+ |
Azx = sin(phi) * sin(theta); |
241 |
+ |
Azy = -cos(phi) * sin(theta); |
242 |
+ |
Azz = cos(theta); |
243 |
+ |
|
244 |
+ |
sux = 0.0; |
245 |
+ |
suy = 0.0; |
246 |
+ |
suz = 1.0; |
247 |
+ |
|
248 |
+ |
ux = (Axx * sux) + (Ayx * suy) + (Azx * suz); |
249 |
+ |
uy = (Axy * sux) + (Ayy * suy) + (Azy * suz); |
250 |
+ |
uz = (Axz * sux) + (Ayz * suy) + (Azz * suz); |
251 |
+ |
|
252 |
|
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
253 |
|
|
254 |
|
u = sqrt(uSqr); |
636 |
|
else if (!strcasecmp(force_field, "EAM")){ |
637 |
|
ffCase = FF_EAM; |
638 |
|
} |
639 |
+ |
else if (!strcasecmp(force_field, "WATER")){ |
640 |
+ |
ffCase = FF_H2O; |
641 |
+ |
} |
642 |
|
else{ |
643 |
|
sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
644 |
|
force_field); |
667 |
|
} |
668 |
|
else{ |
669 |
|
sprintf(painCave.errMsg, |
670 |
< |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
671 |
< |
"reverting to NVE for this simulation.\n", |
670 |
> |
"SimSetup Warning. Unrecognized Ensemble -> %s \n" |
671 |
> |
"\treverting to NVE for this simulation.\n", |
672 |
|
ensemble); |
673 |
|
painCave.isFatal = 0; |
674 |
|
simError(); |
700 |
|
if (!the_components[i]->haveNMol()){ |
701 |
|
// we have a problem |
702 |
|
sprintf(painCave.errMsg, |
703 |
< |
"SimSetup Error. No global NMol or component NMol" |
704 |
< |
" given. Cannot calculate the number of atoms.\n"); |
703 |
> |
"SimSetup Error. No global NMol or component NMol given.\n" |
704 |
> |
"\tCannot calculate the number of atoms.\n"); |
705 |
|
painCave.isFatal = 1; |
706 |
|
simError(); |
707 |
|
} |
724 |
|
//check whether sample time, status time, thermal time and reset time are divisble by dt |
725 |
|
if (!isDivisible(globals->getSampleTime(), globals->getDt())){ |
726 |
|
sprintf(painCave.errMsg, |
727 |
< |
"Sample time is not divisible by dt \n"); |
727 |
> |
"Sample time is not divisible by dt.\n" |
728 |
> |
"\tThis will result in samples that are not uniformly\n" |
729 |
> |
"\tdistributed in time. If this is a problem, change\n" |
730 |
> |
"\tyour sampleTime variable.\n"); |
731 |
|
painCave.isFatal = 0; |
732 |
|
simError(); |
733 |
|
} |
734 |
|
|
735 |
|
if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
736 |
|
sprintf(painCave.errMsg, |
737 |
< |
"Status time is not divisible by dt\n"); |
737 |
> |
"Status time is not divisible by dt.\n" |
738 |
> |
"\tThis will result in status reports that are not uniformly\n" |
739 |
> |
"\tdistributed in time. If this is a problem, change \n" |
740 |
> |
"\tyour statusTime variable.\n"); |
741 |
|
painCave.isFatal = 0; |
742 |
|
simError(); |
743 |
|
} |
744 |
|
|
745 |
|
if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){ |
746 |
|
sprintf(painCave.errMsg, |
747 |
< |
"Thermal time is not divisible by dt\n"); |
747 |
> |
"Thermal time is not divisible by dt.\n" |
748 |
> |
"\tThis will result in thermalizations that are not uniformly\n" |
749 |
> |
"\tdistributed in time. If this is a problem, change \n" |
750 |
> |
"\tyour thermalTime variable.\n"); |
751 |
|
painCave.isFatal = 0; |
752 |
|
simError(); |
753 |
|
} |
754 |
|
|
755 |
|
if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){ |
756 |
|
sprintf(painCave.errMsg, |
757 |
< |
"Reset time is not divisible by dt\n"); |
757 |
> |
"Reset time is not divisible by dt.\n" |
758 |
> |
"\tThis will result in integrator resets that are not uniformly\n" |
759 |
> |
"\tdistributed in time. If this is a problem, change\n" |
760 |
> |
"\tyour resetTime variable.\n"); |
761 |
|
painCave.isFatal = 0; |
762 |
|
simError(); |
763 |
|
} |
843 |
|
} |
844 |
|
|
845 |
|
#ifdef IS_MPI |
846 |
< |
strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n"); |
846 |
> |
strcpy(checkPointMsg, "Successfully gathered all information from Bass\n"); |
847 |
|
MPIcheckPoint(); |
848 |
|
#endif // is_mpi |
849 |
|
} |
876 |
|
|
877 |
|
if (!globals->haveECR()){ |
878 |
|
sprintf(painCave.errMsg, |
879 |
< |
"SimSetup Warning: using default value of 15.0 angstroms" |
880 |
< |
"box length for the electrostaticCutoffRadius.\n"); |
879 |
> |
"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
880 |
> |
"\tOOPSE will use a default value of 15.0 angstroms" |
881 |
> |
"\tfor the electrostaticCutoffRadius.\n"); |
882 |
|
painCave.isFatal = 0; |
883 |
|
simError(); |
884 |
|
theEcr = 15.0; |
889 |
|
|
890 |
|
if (!globals->haveEST()){ |
891 |
|
sprintf(painCave.errMsg, |
892 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
893 |
< |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n"); |
892 |
> |
"SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
893 |
> |
"\tOOPSE will use a default value of\n" |
894 |
> |
"\t0.05 * electrostaticCutoffRadius\n" |
895 |
> |
"\tfor the electrostaticSkinThickness\n"); |
896 |
|
painCave.isFatal = 0; |
897 |
|
simError(); |
898 |
|
theEst = 0.05 * theEcr; |
905 |
|
|
906 |
|
if (!globals->haveDielectric()){ |
907 |
|
sprintf(painCave.errMsg, |
908 |
< |
"SimSetup Error: You are trying to use Reaction Field without" |
909 |
< |
"setting a dielectric constant!\n"); |
908 |
> |
"SimSetup Error: No Dielectric constant was set.\n" |
909 |
> |
"\tYou are trying to use Reaction Field without" |
910 |
> |
"\tsetting a dielectric constant!\n"); |
911 |
|
painCave.isFatal = 1; |
912 |
|
simError(); |
913 |
|
} |
917 |
|
if (usesDipoles){ |
918 |
|
if (!globals->haveECR()){ |
919 |
|
sprintf(painCave.errMsg, |
920 |
< |
"SimSetup Warning: using default value of 15.0 angstroms" |
921 |
< |
"box length for the electrostaticCutoffRadius.\n"); |
920 |
> |
"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n" |
921 |
> |
"\tOOPSE will use a default value of 15.0 angstroms" |
922 |
> |
"\tfor the electrostaticCutoffRadius.\n"); |
923 |
|
painCave.isFatal = 0; |
924 |
|
simError(); |
925 |
|
theEcr = 15.0; |
930 |
|
|
931 |
|
if (!globals->haveEST()){ |
932 |
|
sprintf(painCave.errMsg, |
933 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
934 |
< |
"electrostaticCutoffRadius for the " |
935 |
< |
"electrostaticSkinThickness\n"); |
933 |
> |
"SimSetup Warning: No value was set for electrostaticSkinThickness.\n" |
934 |
> |
"\tOOPSE will use a default value of\n" |
935 |
> |
"\t0.05 * electrostaticCutoffRadius\n" |
936 |
> |
"\tfor the electrostaticSkinThickness\n"); |
937 |
|
painCave.isFatal = 0; |
938 |
|
simError(); |
939 |
|
theEst = 0.05 * theEcr; |
1140 |
|
the_ff = new EAM_FF(); |
1141 |
|
break; |
1142 |
|
|
1143 |
+ |
case FF_H2O: |
1144 |
+ |
the_ff = new WATER(); |
1145 |
+ |
break; |
1146 |
+ |
|
1147 |
|
default: |
1148 |
|
sprintf(painCave.errMsg, |
1149 |
|
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1286 |
|
|
1287 |
|
if (local_atoms != info[0].n_atoms){ |
1288 |
|
sprintf(painCave.errMsg, |
1289 |
< |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1290 |
< |
" localAtom (%d) are not equal.\n", |
1289 |
> |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n" |
1290 |
> |
"\tlocalAtom (%d) are not equal.\n", |
1291 |
|
info[0].n_atoms, local_atoms); |
1292 |
|
painCave.isFatal = 1; |
1293 |
|
simError(); |
1429 |
|
else{ |
1430 |
|
sprintf(painCave.errMsg, |
1431 |
|
"SimSetup error: If you use the NVT\n" |
1432 |
< |
" ensemble, you must set tauThermostat.\n"); |
1432 |
> |
"\tensemble, you must set tauThermostat.\n"); |
1433 |
|
painCave.isFatal = 1; |
1434 |
|
simError(); |
1435 |
|
} |
1452 |
|
else{ |
1453 |
|
sprintf(painCave.errMsg, |
1454 |
|
"SimSetup error: If you use a constant pressure\n" |
1455 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1455 |
> |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1456 |
|
painCave.isFatal = 1; |
1457 |
|
simError(); |
1458 |
|
} |
1462 |
|
else{ |
1463 |
|
sprintf(painCave.errMsg, |
1464 |
|
"SimSetup error: If you use an NPT\n" |
1465 |
< |
" ensemble, you must set tauThermostat.\n"); |
1465 |
> |
"\tensemble, you must set tauThermostat.\n"); |
1466 |
|
painCave.isFatal = 1; |
1467 |
|
simError(); |
1468 |
|
} |
1472 |
|
else{ |
1473 |
|
sprintf(painCave.errMsg, |
1474 |
|
"SimSetup error: If you use an NPT\n" |
1475 |
< |
" ensemble, you must set tauBarostat.\n"); |
1475 |
> |
"\tensemble, you must set tauBarostat.\n"); |
1476 |
|
painCave.isFatal = 1; |
1477 |
|
simError(); |
1478 |
|
} |
1495 |
|
else{ |
1496 |
|
sprintf(painCave.errMsg, |
1497 |
|
"SimSetup error: If you use a constant pressure\n" |
1498 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1498 |
> |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1499 |
|
painCave.isFatal = 1; |
1500 |
|
simError(); |
1501 |
|
} |
1506 |
|
else{ |
1507 |
|
sprintf(painCave.errMsg, |
1508 |
|
"SimSetup error: If you use an NPT\n" |
1509 |
< |
" ensemble, you must set tauThermostat.\n"); |
1509 |
> |
"\tensemble, you must set tauThermostat.\n"); |
1510 |
|
painCave.isFatal = 1; |
1511 |
|
simError(); |
1512 |
|
} |
1517 |
|
else{ |
1518 |
|
sprintf(painCave.errMsg, |
1519 |
|
"SimSetup error: If you use an NPT\n" |
1520 |
< |
" ensemble, you must set tauBarostat.\n"); |
1520 |
> |
"\tensemble, you must set tauBarostat.\n"); |
1521 |
|
painCave.isFatal = 1; |
1522 |
|
simError(); |
1523 |
|
} |
1540 |
|
else{ |
1541 |
|
sprintf(painCave.errMsg, |
1542 |
|
"SimSetup error: If you use a constant pressure\n" |
1543 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1543 |
> |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1544 |
|
painCave.isFatal = 1; |
1545 |
|
simError(); |
1546 |
|
} |
1550 |
|
else{ |
1551 |
|
sprintf(painCave.errMsg, |
1552 |
|
"SimSetup error: If you use an NPT\n" |
1553 |
< |
" ensemble, you must set tauThermostat.\n"); |
1553 |
> |
"\tensemble, you must set tauThermostat.\n"); |
1554 |
|
painCave.isFatal = 1; |
1555 |
|
simError(); |
1556 |
|
} |
1560 |
|
else{ |
1561 |
|
sprintf(painCave.errMsg, |
1562 |
|
"SimSetup error: If you use an NPT\n" |
1563 |
< |
" ensemble, you must set tauBarostat.\n"); |
1563 |
> |
"\tensemble, you must set tauBarostat.\n"); |
1564 |
|
painCave.isFatal = 1; |
1565 |
|
simError(); |
1566 |
|
} |
1613 |
|
} |
1614 |
|
else{ |
1615 |
|
sprintf(painCave.errMsg, |
1616 |
< |
"ZConstraint error: If you use an ZConstraint\n" |
1617 |
< |
" , you must set sample time.\n"); |
1616 |
> |
"ZConstraint error: If you use a ZConstraint,\n" |
1617 |
> |
"\tyou must set zconsTime.\n"); |
1618 |
|
painCave.isFatal = 1; |
1619 |
|
simError(); |
1620 |
|
} |
1629 |
|
else{ |
1630 |
|
double defaultZConsTol = 0.01; |
1631 |
|
sprintf(painCave.errMsg, |
1632 |
< |
"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1633 |
< |
" , default value %f is used.\n", |
1632 |
> |
"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
1633 |
> |
"\tOOPSE will use a default value of %f.\n" |
1634 |
> |
"\tTo set the tolerance, use the zconsTol variable.\n", |
1635 |
|
defaultZConsTol); |
1636 |
|
painCave.isFatal = 0; |
1637 |
|
simError(); |
1649 |
|
} |
1650 |
|
else{ |
1651 |
|
sprintf(painCave.errMsg, |
1652 |
< |
"ZConstraint Warning: User does not set force Subtraction policy, " |
1653 |
< |
"PolicyByMass is used\n"); |
1652 |
> |
"ZConstraint Warning: No force subtraction policy was set.\n" |
1653 |
> |
"\tOOPSE will use PolicyByMass.\n" |
1654 |
> |
"\tTo set the policy, use the zconsForcePolicy variable.\n"); |
1655 |
|
painCave.isFatal = 0; |
1656 |
|
simError(); |
1657 |
|
zconsForcePolicy->setData("BYMASS"); |
1695 |
|
//check the uniqueness of index |
1696 |
|
if(!zconsParaData->isIndexUnique()){ |
1697 |
|
sprintf(painCave.errMsg, |
1698 |
< |
"ZConstraint Error: molIndex is not unique\n"); |
1698 |
> |
"ZConstraint Error: molIndex is not unique!\n"); |
1699 |
|
painCave.isFatal = 1; |
1700 |
|
simError(); |
1701 |
|
} |