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#include <algorithm> |
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#include <cstdlib> |
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#include <stdlib.h> |
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#include <iostream> |
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#include <cmath> |
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#include <math.h> |
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#include <string> |
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#include <sprng.h> |
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|
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#include "SimSetup.hpp" |
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#include "ReadWrite.hpp" |
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#include "parse_me.h" |
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#define NVT_ENS 1 |
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#define NPTi_ENS 2 |
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#define NPTf_ENS 3 |
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#define NPTxyz_ENS 4 |
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|
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|
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#define FF_DUFF 0 |
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#define FF_LJ 1 |
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#define FF_EAM 2 |
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using namespace std; |
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|
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SimSetup::SimSetup(){ |
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|
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initSuspend = false; |
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isInfoArray = 0; |
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nInfo = 1; |
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|
55 |
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info = the_info; |
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nInfo = theNinfo; |
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isInfoArray = 1; |
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initSuspend = true; |
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} |
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|
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|
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#endif // is_mpi |
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|
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void SimSetup::createSim(void){ |
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int i, j, k, globalAtomIndex; |
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|
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// gather all of the information from the Bass file |
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|
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|
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// initialize the system coordinates |
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|
112 |
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if (!isInfoArray){ |
112 |
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if ( !initSuspend ){ |
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initSystemCoords(); |
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|
115 |
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if( !(globals->getUseInitTime()) ) |
116 |
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info[0].currentTime = 0.0; |
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} |
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|
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// make the output filenames |
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|
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|
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void SimSetup::makeMolecules(void){ |
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int k, l; |
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int k; |
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int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
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molInit molInfo; |
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DirectionalAtom* dAtom; |
557 |
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|
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|
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void SimSetup::gatherInfo(void){ |
560 |
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int i, j, k; |
560 |
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int i; |
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|
562 |
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ensembleCase = -1; |
563 |
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ffCase = -1; |
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else if (!strcasecmp(ensemble, "NPTf")){ |
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ensembleCase = NPTf_ENS; |
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} |
611 |
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else if (!strcasecmp(ensemble, "NPTxyz")){ |
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ensembleCase = NPTxyz_ENS; |
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} |
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else{ |
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sprintf(painCave.errMsg, |
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"SimSetup Warning. Unrecognized Ensemble -> %s, " |
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} |
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|
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// check for the temperature set flag |
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|
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|
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if (globals->haveTempSet()) |
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info[i].setTemp = globals->getTempSet(); |
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|
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// get some of the tricky things that may still be in the globals |
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// check for the extended State init |
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|
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double boxVector[3]; |
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if (globals->haveBox()){ |
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boxVector[0] = globals->getBox(); |
699 |
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boxVector[1] = globals->getBox(); |
700 |
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boxVector[2] = globals->getBox(); |
701 |
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|
702 |
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info[i].setBox(boxVector); |
703 |
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} |
704 |
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else if (globals->haveDensity()){ |
705 |
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double vol; |
706 |
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vol = (double) tot_nmol / globals->getDensity(); |
707 |
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boxVector[0] = pow(vol, (1.0 / 3.0)); |
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boxVector[1] = boxVector[0]; |
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boxVector[2] = boxVector[0]; |
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|
711 |
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info[i].setBox(boxVector); |
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} |
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else{ |
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if (!globals->haveBoxX()){ |
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sprintf(painCave.errMsg, |
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"SimSetup error, no periodic BoxX size given.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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boxVector[0] = globals->getBoxX(); |
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|
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if (!globals->haveBoxY()){ |
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sprintf(painCave.errMsg, |
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"SimSetup error, no periodic BoxY size given.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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boxVector[1] = globals->getBoxY(); |
729 |
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|
730 |
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if (!globals->haveBoxZ()){ |
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sprintf(painCave.errMsg, |
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"SimSetup error, no periodic BoxZ size given.\n"); |
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painCave.isFatal = 1; |
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simError(); |
735 |
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} |
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boxVector[2] = globals->getBoxZ(); |
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|
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info[i].setBox(boxVector); |
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} |
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info[i].useInitXSstate = globals->getUseInitXSstate(); |
706 |
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info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
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|
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} |
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|
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|
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//setup seed for random number generator |
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int seedValue; |
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|
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|
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if (!globals->haveECR()){ |
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sprintf(painCave.errMsg, |
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"SimSetup Warning: using default value of 1/2 the smallest " |
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"box length for the electrostaticCutoffRadius.\n" |
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"I hope you have a very fast processor!\n"); |
784 |
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"SimSetup Warning: using default value of 15.0 angstroms" |
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"box length for the electrostaticCutoffRadius.\n"); |
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painCave.isFatal = 0; |
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simError(); |
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double smallest; |
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smallest = info[i].boxL[0]; |
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if (info[i].boxL[1] <= smallest) |
824 |
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smallest = info[i].boxL[1]; |
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if (info[i].boxL[2] <= smallest) |
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smallest = info[i].boxL[2]; |
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theEcr = 0.5 * smallest; |
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theEcr = 15.0; |
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} |
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else{ |
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theEcr = globals->getECR(); |
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theEst = globals->getEST(); |
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} |
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|
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info[i].setEcr(theEcr, theEst); |
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info[i].setDefaultEcr(theEcr, theEst); |
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|
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if (!globals->haveDielectric()){ |
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sprintf(painCave.errMsg, |
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if (usesDipoles){ |
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if (!globals->haveECR()){ |
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sprintf(painCave.errMsg, |
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"SimSetup Warning: using default value of 1/2 the smallest " |
822 |
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"box length for the electrostaticCutoffRadius.\n" |
823 |
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"I hope you have a very fast processor!\n"); |
824 |
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painCave.isFatal = 0; |
825 |
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simError(); |
865 |
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double smallest; |
866 |
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smallest = info[i].boxL[0]; |
867 |
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if (info[i].boxL[1] <= smallest) |
868 |
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smallest = info[i].boxL[1]; |
869 |
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if (info[i].boxL[2] <= smallest) |
870 |
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smallest = info[i].boxL[2]; |
871 |
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theEcr = 0.5 * smallest; |
821 |
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"SimSetup Warning: using default value of 15.0 angstroms" |
822 |
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"box length for the electrostaticCutoffRadius.\n"); |
823 |
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painCave.isFatal = 0; |
824 |
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simError(); |
825 |
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theEcr = 15.0; |
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} |
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else{ |
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theEcr = globals->getECR(); |
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} |
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|
830 |
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|
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if (!globals->haveEST()){ |
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sprintf(painCave.errMsg, |
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"SimSetup Warning: using default value of 0.05 * the " |
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else{ |
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theEst = globals->getEST(); |
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} |
843 |
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|
844 |
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info[i].setEcr(theEcr, theEst); |
843 |
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|
844 |
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info[i].setDefaultEcr(theEcr, theEst); |
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} |
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} |
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} |
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|
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#ifdef IS_MPI |
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strcpy(checkPointMsg, "post processing checks out"); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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} |
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|
853 |
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|
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void SimSetup::initSystemCoords(void){ |
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int i; |
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|
867 |
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if (worldRank == 0){ |
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#endif //is_mpi |
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inName = globals->getInitialConfig(); |
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double* tempDouble = new double[1000000]; |
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fileInit = new InitializeFromFile(inName); |
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#ifdef IS_MPI |
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} |
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delete fileInit; |
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} |
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else{ |
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#ifdef IS_MPI |
930 |
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|
881 |
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|
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// no init from bass |
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|
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|
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sprintf(painCave.errMsg, |
885 |
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"Cannot intialize a parallel simulation without an initial configuration file.\n"); |
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painCave.isFatal; |
885 |
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"Cannot intialize a simulation without an initial configuration file.\n"); |
886 |
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painCave.isFatal = 1;; |
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simError(); |
888 |
< |
|
938 |
< |
#else |
939 |
< |
|
940 |
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initFromBass(); |
941 |
< |
|
942 |
< |
|
943 |
< |
#endif |
888 |
> |
|
889 |
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} |
890 |
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|
891 |
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#ifdef IS_MPI |
1103 |
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} |
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|
1105 |
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void SimSetup::calcSysValues(void){ |
1106 |
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int i, j, k; |
1106 |
> |
int i; |
1107 |
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|
1108 |
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int* molMembershipArray; |
1109 |
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|
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|
1203 |
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|
1204 |
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void SimSetup::makeSysArrays(void){ |
1205 |
< |
int i, j, k, l; |
1205 |
> |
|
1206 |
> |
#ifndef IS_MPI |
1207 |
> |
int k, j; |
1208 |
> |
#endif // is_mpi |
1209 |
> |
int i, l; |
1210 |
|
|
1211 |
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Atom** the_atoms; |
1212 |
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Molecule* the_molecules; |
1293 |
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NVT<RealIntegrator>* myNVT = NULL; |
1294 |
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NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1295 |
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NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1296 |
+ |
NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1297 |
|
|
1298 |
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for (k = 0; k < nInfo; k++){ |
1299 |
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switch (ensembleCase){ |
1397 |
|
|
1398 |
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if (globals->haveTauThermostat()) |
1399 |
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myNPTf->setTauThermostat(globals->getTauThermostat()); |
1400 |
+ |
|
1401 |
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else{ |
1402 |
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sprintf(painCave.errMsg, |
1403 |
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"SimSetup error: If you use an NPT\n" |
1408 |
|
|
1409 |
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if (globals->haveTauBarostat()) |
1410 |
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myNPTf->setTauBarostat(globals->getTauBarostat()); |
1411 |
+ |
|
1412 |
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else{ |
1413 |
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sprintf(painCave.errMsg, |
1414 |
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"SimSetup error: If you use an NPT\n" |
1420 |
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info->the_integrator = myNPTf; |
1421 |
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break; |
1422 |
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|
1423 |
+ |
case NPTxyz_ENS: |
1424 |
+ |
if (globals->haveZconstraints()){ |
1425 |
+ |
setupZConstraint(info[k]); |
1426 |
+ |
myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1427 |
+ |
} |
1428 |
+ |
else |
1429 |
+ |
myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1430 |
+ |
|
1431 |
+ |
myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1432 |
+ |
|
1433 |
+ |
if (globals->haveTargetPressure()) |
1434 |
+ |
myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1435 |
+ |
else{ |
1436 |
+ |
sprintf(painCave.errMsg, |
1437 |
+ |
"SimSetup error: If you use a constant pressure\n" |
1438 |
+ |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1439 |
+ |
painCave.isFatal = 1; |
1440 |
+ |
simError(); |
1441 |
+ |
} |
1442 |
+ |
|
1443 |
+ |
if (globals->haveTauThermostat()) |
1444 |
+ |
myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1445 |
+ |
else{ |
1446 |
+ |
sprintf(painCave.errMsg, |
1447 |
+ |
"SimSetup error: If you use an NPT\n" |
1448 |
+ |
" ensemble, you must set tauThermostat.\n"); |
1449 |
+ |
painCave.isFatal = 1; |
1450 |
+ |
simError(); |
1451 |
+ |
} |
1452 |
+ |
|
1453 |
+ |
if (globals->haveTauBarostat()) |
1454 |
+ |
myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1455 |
+ |
else{ |
1456 |
+ |
sprintf(painCave.errMsg, |
1457 |
+ |
"SimSetup error: If you use an NPT\n" |
1458 |
+ |
" ensemble, you must set tauBarostat.\n"); |
1459 |
+ |
painCave.isFatal = 1; |
1460 |
+ |
simError(); |
1461 |
+ |
} |
1462 |
+ |
|
1463 |
+ |
info->the_integrator = myNPTxyz; |
1464 |
+ |
break; |
1465 |
+ |
|
1466 |
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default: |
1467 |
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sprintf(painCave.errMsg, |
1468 |
|
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |