1 |
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#include <algorithm> |
2 |
< |
#include <cstdlib> |
2 |
> |
#include <stdlib.h> |
3 |
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#include <iostream> |
4 |
< |
#include <cmath> |
4 |
> |
#include <math.h> |
5 |
|
#include <string> |
6 |
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#include <sprng.h> |
7 |
– |
|
7 |
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#include "SimSetup.hpp" |
8 |
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#include "ReadWrite.hpp" |
9 |
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#include "parse_me.h" |
21 |
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#define NVT_ENS 1 |
22 |
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#define NPTi_ENS 2 |
23 |
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#define NPTf_ENS 3 |
24 |
+ |
#define NPTxyz_ENS 4 |
25 |
|
|
26 |
– |
#define FF_DUFF 0 |
27 |
– |
#define FF_LJ 1 |
28 |
– |
#define FF_EAM 2 |
26 |
|
|
27 |
+ |
#define FF_DUFF 0 |
28 |
+ |
#define FF_LJ 1 |
29 |
+ |
#define FF_EAM 2 |
30 |
+ |
#define FF_H2O 3 |
31 |
+ |
|
32 |
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using namespace std; |
33 |
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|
34 |
+ |
/** |
35 |
+ |
* Check whether dividend is divisble by divisor or not |
36 |
+ |
*/ |
37 |
+ |
bool isDivisible(double dividend, double divisor){ |
38 |
+ |
double tolerance = 0.000001; |
39 |
+ |
double quotient; |
40 |
+ |
double diff; |
41 |
+ |
int intQuotient; |
42 |
+ |
|
43 |
+ |
quotient = dividend / divisor; |
44 |
+ |
|
45 |
+ |
if (quotient < 0) |
46 |
+ |
quotient = -quotient; |
47 |
+ |
|
48 |
+ |
intQuotient = int (quotient + tolerance); |
49 |
+ |
|
50 |
+ |
diff = fabs(fabs(dividend) - intQuotient * fabs(divisor)); |
51 |
+ |
|
52 |
+ |
if (diff <= tolerance) |
53 |
+ |
return true; |
54 |
+ |
else |
55 |
+ |
return false; |
56 |
+ |
} |
57 |
+ |
|
58 |
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SimSetup::SimSetup(){ |
59 |
+ |
|
60 |
+ |
initSuspend = false; |
61 |
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isInfoArray = 0; |
62 |
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nInfo = 1; |
63 |
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|
80 |
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info = the_info; |
81 |
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nInfo = theNinfo; |
82 |
|
isInfoArray = 1; |
83 |
+ |
initSuspend = true; |
84 |
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} |
85 |
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|
86 |
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|
119 |
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#endif // is_mpi |
120 |
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|
121 |
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void SimSetup::createSim(void){ |
93 |
– |
int i, j, k, globalAtomIndex; |
122 |
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|
123 |
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// gather all of the information from the Bass file |
124 |
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|
134 |
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|
135 |
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// initialize the system coordinates |
136 |
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|
137 |
< |
if (!isInfoArray){ |
137 |
> |
if ( !initSuspend ){ |
138 |
|
initSystemCoords(); |
139 |
+ |
|
140 |
+ |
if( !(globals->getUseInitTime()) ) |
141 |
+ |
info[0].currentTime = 0.0; |
142 |
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} |
143 |
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|
144 |
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// make the output filenames |
160 |
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|
161 |
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|
162 |
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void SimSetup::makeMolecules(void){ |
163 |
< |
int k, l; |
163 |
> |
int k; |
164 |
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int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
165 |
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molInit molInfo; |
166 |
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DirectionalAtom* dAtom; |
174 |
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bond_pair* theBonds; |
175 |
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bend_set* theBends; |
176 |
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torsion_set* theTorsions; |
146 |
– |
|
177 |
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|
178 |
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//init the forceField paramters |
179 |
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|
182 |
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|
183 |
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// init the atoms |
184 |
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|
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 |
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|
190 |
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for (k = 0; k < nInfo; k++){ |
221 |
|
info[k].n_oriented++; |
222 |
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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 |
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|
252 |
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uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
253 |
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|
608 |
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|
609 |
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|
610 |
|
void SimSetup::gatherInfo(void){ |
611 |
< |
int i, j, k; |
611 |
> |
int i; |
612 |
|
|
613 |
|
ensembleCase = -1; |
614 |
|
ffCase = -1; |
635 |
|
} |
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", |
662 |
|
else if (!strcasecmp(ensemble, "NPTf")){ |
663 |
|
ensembleCase = NPTf_ENS; |
664 |
|
} |
665 |
+ |
else if (!strcasecmp(ensemble, "NPTxyz")){ |
666 |
+ |
ensembleCase = NPTxyz_ENS; |
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 |
|
} |
721 |
|
simError(); |
722 |
|
} |
723 |
|
|
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" |
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" |
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" |
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" |
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 |
+ |
} |
764 |
+ |
|
765 |
|
// set the status, sample, and thermal kick times |
766 |
|
|
767 |
|
for (i = 0; i < nInfo; i++){ |
791 |
|
} |
792 |
|
|
793 |
|
// check for the temperature set flag |
794 |
< |
|
794 |
> |
|
795 |
|
if (globals->haveTempSet()) |
796 |
|
info[i].setTemp = globals->getTempSet(); |
797 |
|
|
798 |
< |
// get some of the tricky things that may still be in the globals |
798 |
> |
// check for the extended State init |
799 |
|
|
800 |
< |
double boxVector[3]; |
801 |
< |
if (globals->haveBox()){ |
802 |
< |
boxVector[0] = globals->getBox(); |
699 |
< |
boxVector[1] = globals->getBox(); |
700 |
< |
boxVector[2] = globals->getBox(); |
701 |
< |
|
702 |
< |
info[i].setBox(boxVector); |
703 |
< |
} |
704 |
< |
else if (globals->haveDensity()){ |
705 |
< |
double vol; |
706 |
< |
vol = (double) tot_nmol / globals->getDensity(); |
707 |
< |
boxVector[0] = pow(vol, (1.0 / 3.0)); |
708 |
< |
boxVector[1] = boxVector[0]; |
709 |
< |
boxVector[2] = boxVector[0]; |
710 |
< |
|
711 |
< |
info[i].setBox(boxVector); |
712 |
< |
} |
713 |
< |
else{ |
714 |
< |
if (!globals->haveBoxX()){ |
715 |
< |
sprintf(painCave.errMsg, |
716 |
< |
"SimSetup error, no periodic BoxX size given.\n"); |
717 |
< |
painCave.isFatal = 1; |
718 |
< |
simError(); |
719 |
< |
} |
720 |
< |
boxVector[0] = globals->getBoxX(); |
721 |
< |
|
722 |
< |
if (!globals->haveBoxY()){ |
723 |
< |
sprintf(painCave.errMsg, |
724 |
< |
"SimSetup error, no periodic BoxY size given.\n"); |
725 |
< |
painCave.isFatal = 1; |
726 |
< |
simError(); |
727 |
< |
} |
728 |
< |
boxVector[1] = globals->getBoxY(); |
729 |
< |
|
730 |
< |
if (!globals->haveBoxZ()){ |
731 |
< |
sprintf(painCave.errMsg, |
732 |
< |
"SimSetup error, no periodic BoxZ size given.\n"); |
733 |
< |
painCave.isFatal = 1; |
734 |
< |
simError(); |
735 |
< |
} |
736 |
< |
boxVector[2] = globals->getBoxZ(); |
737 |
< |
|
738 |
< |
info[i].setBox(boxVector); |
739 |
< |
} |
800 |
> |
info[i].useInitXSstate = globals->getUseInitXSstate(); |
801 |
> |
info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
802 |
> |
|
803 |
|
} |
804 |
< |
|
804 |
> |
|
805 |
|
//setup seed for random number generator |
806 |
|
int seedValue; |
807 |
|
|
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 1/2 the smallest " |
880 |
< |
"box length for the electrostaticCutoffRadius.\n" |
881 |
< |
"I hope you have a very fast processor!\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 |
< |
double smallest; |
822 |
< |
smallest = info[i].boxL[0]; |
823 |
< |
if (info[i].boxL[1] <= smallest) |
824 |
< |
smallest = info[i].boxL[1]; |
825 |
< |
if (info[i].boxL[2] <= smallest) |
826 |
< |
smallest = info[i].boxL[2]; |
827 |
< |
theEcr = 0.5 * smallest; |
884 |
> |
theEcr = 15.0; |
885 |
|
} |
886 |
|
else{ |
887 |
|
theEcr = globals->getECR(); |
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; |
901 |
|
theEst = globals->getEST(); |
902 |
|
} |
903 |
|
|
904 |
< |
info[i].setEcr(theEcr, theEst); |
904 |
> |
info[i].setDefaultEcr(theEcr, theEst); |
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 1/2 the smallest " |
921 |
< |
"box length for the electrostaticCutoffRadius.\n" |
922 |
< |
"I hope you have a very fast processor!\n"); |
923 |
< |
painCave.isFatal = 0; |
924 |
< |
simError(); |
925 |
< |
double smallest; |
866 |
< |
smallest = info[i].boxL[0]; |
867 |
< |
if (info[i].boxL[1] <= smallest) |
868 |
< |
smallest = info[i].boxL[1]; |
869 |
< |
if (info[i].boxL[2] <= smallest) |
870 |
< |
smallest = info[i].boxL[2]; |
871 |
< |
theEcr = 0.5 * smallest; |
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; |
926 |
|
} |
927 |
|
else{ |
928 |
|
theEcr = globals->getECR(); |
929 |
|
} |
930 |
< |
|
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; |
941 |
|
else{ |
942 |
|
theEst = globals->getEST(); |
943 |
|
} |
944 |
< |
|
945 |
< |
info[i].setEcr(theEcr, theEst); |
944 |
> |
|
945 |
> |
info[i].setDefaultEcr(theEcr, theEst); |
946 |
|
} |
947 |
|
} |
948 |
|
} |
894 |
– |
|
949 |
|
#ifdef IS_MPI |
950 |
|
strcpy(checkPointMsg, "post processing checks out"); |
951 |
|
MPIcheckPoint(); |
952 |
|
#endif // is_mpi |
953 |
|
} |
954 |
< |
|
954 |
> |
|
955 |
|
void SimSetup::initSystemCoords(void){ |
956 |
|
int i; |
957 |
|
|
968 |
|
if (worldRank == 0){ |
969 |
|
#endif //is_mpi |
970 |
|
inName = globals->getInitialConfig(); |
917 |
– |
double* tempDouble = new double[1000000]; |
971 |
|
fileInit = new InitializeFromFile(inName); |
972 |
|
#ifdef IS_MPI |
973 |
|
} |
979 |
|
delete fileInit; |
980 |
|
} |
981 |
|
else{ |
982 |
< |
#ifdef IS_MPI |
930 |
< |
|
982 |
> |
|
983 |
|
// no init from bass |
984 |
< |
|
984 |
> |
|
985 |
|
sprintf(painCave.errMsg, |
986 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n"); |
987 |
< |
painCave.isFatal; |
986 |
> |
"Cannot intialize a simulation without an initial configuration file.\n"); |
987 |
> |
painCave.isFatal = 1;; |
988 |
|
simError(); |
989 |
< |
|
938 |
< |
#else |
939 |
< |
|
940 |
< |
initFromBass(); |
941 |
< |
|
942 |
< |
|
943 |
< |
#endif |
989 |
> |
|
990 |
|
} |
991 |
|
|
992 |
|
#ifdef IS_MPI |
1138 |
|
|
1139 |
|
case FF_EAM: |
1140 |
|
the_ff = new EAM_FF(); |
1141 |
+ |
break; |
1142 |
+ |
|
1143 |
+ |
case FF_H2O: |
1144 |
+ |
the_ff = new WATER(); |
1145 |
|
break; |
1146 |
|
|
1147 |
|
default: |
1208 |
|
} |
1209 |
|
|
1210 |
|
void SimSetup::calcSysValues(void){ |
1211 |
< |
int i, j, k; |
1211 |
> |
int i; |
1212 |
|
|
1213 |
|
int* molMembershipArray; |
1214 |
|
|
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(); |
1307 |
|
|
1308 |
|
|
1309 |
|
void SimSetup::makeSysArrays(void){ |
1310 |
< |
int i, j, k, l; |
1310 |
> |
|
1311 |
> |
#ifndef IS_MPI |
1312 |
> |
int k, j; |
1313 |
> |
#endif // is_mpi |
1314 |
> |
int i, l; |
1315 |
|
|
1316 |
|
Atom** the_atoms; |
1317 |
|
Molecule* the_molecules; |
1394 |
|
void SimSetup::makeIntegrator(void){ |
1395 |
|
int k; |
1396 |
|
|
1397 |
+ |
NVE<RealIntegrator>* myNVE = NULL; |
1398 |
|
NVT<RealIntegrator>* myNVT = NULL; |
1399 |
|
NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1400 |
|
NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1401 |
+ |
NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1402 |
|
|
1403 |
|
for (k = 0; k < nInfo; k++){ |
1404 |
|
switch (ensembleCase){ |
1405 |
|
case NVE_ENS: |
1406 |
|
if (globals->haveZconstraints()){ |
1407 |
|
setupZConstraint(info[k]); |
1408 |
< |
new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1408 |
> |
myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1409 |
|
} |
1410 |
< |
else |
1411 |
< |
new NVE<RealIntegrator>(&(info[k]), the_ff); |
1410 |
> |
else{ |
1411 |
> |
myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1412 |
> |
} |
1413 |
> |
|
1414 |
> |
info->the_integrator = myNVE; |
1415 |
|
break; |
1416 |
|
|
1417 |
|
case NVT_ENS: |
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 |
|
} |
1436 |
+ |
|
1437 |
+ |
info->the_integrator = myNVT; |
1438 |
|
break; |
1439 |
|
|
1440 |
|
case NPTi_ENS: |
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 |
|
} |
1479 |
+ |
|
1480 |
+ |
info->the_integrator = myNPTi; |
1481 |
|
break; |
1482 |
|
|
1483 |
|
case NPTf_ENS: |
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 |
|
} |
1502 |
|
|
1503 |
|
if (globals->haveTauThermostat()) |
1504 |
|
myNPTf->setTauThermostat(globals->getTauThermostat()); |
1505 |
+ |
|
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 |
|
} |
1513 |
|
|
1514 |
|
if (globals->haveTauBarostat()) |
1515 |
|
myNPTf->setTauBarostat(globals->getTauBarostat()); |
1516 |
+ |
|
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 |
> |
} |
1524 |
> |
|
1525 |
> |
info->the_integrator = myNPTf; |
1526 |
> |
break; |
1527 |
> |
|
1528 |
> |
case NPTxyz_ENS: |
1529 |
> |
if (globals->haveZconstraints()){ |
1530 |
> |
setupZConstraint(info[k]); |
1531 |
> |
myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1532 |
> |
} |
1533 |
> |
else |
1534 |
> |
myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1535 |
> |
|
1536 |
> |
myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1537 |
> |
|
1538 |
> |
if (globals->haveTargetPressure()) |
1539 |
> |
myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1540 |
> |
else{ |
1541 |
> |
sprintf(painCave.errMsg, |
1542 |
> |
"SimSetup error: If you use a constant pressure\n" |
1543 |
> |
"\tensemble, you must set targetPressure in the BASS file.\n"); |
1544 |
|
painCave.isFatal = 1; |
1545 |
|
simError(); |
1546 |
+ |
} |
1547 |
+ |
|
1548 |
+ |
if (globals->haveTauThermostat()) |
1549 |
+ |
myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1550 |
+ |
else{ |
1551 |
+ |
sprintf(painCave.errMsg, |
1552 |
+ |
"SimSetup error: If you use an NPT\n" |
1553 |
+ |
"\tensemble, you must set tauThermostat.\n"); |
1554 |
+ |
painCave.isFatal = 1; |
1555 |
+ |
simError(); |
1556 |
|
} |
1557 |
+ |
|
1558 |
+ |
if (globals->haveTauBarostat()) |
1559 |
+ |
myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1560 |
+ |
else{ |
1561 |
+ |
sprintf(painCave.errMsg, |
1562 |
+ |
"SimSetup error: If you use an NPT\n" |
1563 |
+ |
"\tensemble, you must set tauBarostat.\n"); |
1564 |
+ |
painCave.isFatal = 1; |
1565 |
+ |
simError(); |
1566 |
+ |
} |
1567 |
+ |
|
1568 |
+ |
info->the_integrator = myNPTxyz; |
1569 |
|
break; |
1570 |
|
|
1571 |
|
default: |
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 |
|
} |