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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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#include "SimSetup.hpp" |
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#include "ReadWrite.hpp" |
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#include "parse_me.h" |
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using namespace std; |
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SimSetup::SimSetup(){ |
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initSuspend = false; |
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isInfoArray = 0; |
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nInfo = 1; |
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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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// creation of complex system objects |
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sysObjectsCreation(); |
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// check on the post processing info |
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finalInfoCheck(); |
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// initialize the system coordinates |
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if (!isInfoArray){ |
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if ( !initSuspend ){ |
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initSystemCoords(); |
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if( !(globals->getUseInitTime()) ) |
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info[0].currentTime = 0.0; |
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} |
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// check on the post processing info |
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finalInfoCheck(); |
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// make the output filenames |
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makeOutNames(); |
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} |
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// check for the temperature set flag |
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if (globals->haveTempSet()) |
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info[i].setTemp = globals->getTempSet(); |
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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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double boxVector[3]; |
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if (globals->haveBox()){ |
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boxVector[0] = globals->getBox(); |
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boxVector[1] = globals->getBox(); |
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boxVector[2] = globals->getBox(); |
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info[i].setBox(boxVector); |
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} |
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else if (globals->haveDensity()){ |
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double vol; |
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vol = (double) tot_nmol / globals->getDensity(); |
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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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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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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(); |
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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(); |
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} |
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boxVector[2] = globals->getBoxZ(); |
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info[i].setBox(boxVector); |
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} |
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info[i].useInitXSstate = globals->getUseInitXSstate(); |
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info[i].orthoTolerance = globals->getOrthoBoxTolerance(); |
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} |
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//setup seed for random number generator |
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int seedValue; |
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theEst = globals->getEST(); |
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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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if (!globals->haveDielectric()){ |
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sprintf(painCave.errMsg, |
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theEst = globals->getEST(); |
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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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} |
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if( !initSuspend ) |
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info[i].checkCutOffs(); |
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} |
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#ifdef IS_MPI |
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if (globals->haveTauThermostat()) |
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myNPTf->setTauThermostat(globals->getTauThermostat()); |
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else{ |
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sprintf(painCave.errMsg, |
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"SimSetup error: If you use an NPT\n" |
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if (globals->haveTauBarostat()) |
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myNPTf->setTauBarostat(globals->getTauBarostat()); |
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else{ |
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sprintf(painCave.errMsg, |
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"SimSetup error: If you use an NPT\n" |
