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#include <cstdio>
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#include <cmath>
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#include <cstring>
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#include <vector>
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#include "CmdlineZsub.h"
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#include "SimInfo.hpp"
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#include "SimSetup.hpp"
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#include "ZConsReader.hpp"
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using namespace std;
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/**
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* @author: Teng Lin
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* @date: Feb 25, 2004
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* @version: 1.0
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* @email: tlin@nd.edu
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*
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* This program is a substitue of quickLate. It not only implemnets all of the functions in
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* quickLate, but also provides the functions of replacing atom types for z-constraint.
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* This implement is kind of wierd!!!
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*/
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vector<int> getAtomToZMol(SimInfo* info, vector<int>& zmolIndex);
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void replaceAtomType(SimInfo* info, vector<int>& zmolIndex, vector<double>& zmolPos,
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vector<int> atomToZMol,double zconsTol);
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void convertSSD(char* buffer, char* prefix, double pos[3], double RotMat[3][3], int dipole_given);
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void dumpToXYZ(SimInfo* info, ofstream* xyzStream, int repeatX, int repeatY, int repeatZ,
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int periodicBox_given, int dipole_given, int water_given);
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void matVecMul3(double a[3][3], double b[3]);
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int main(int argc, char* argv[]){
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gengetopt_args_info args_info;
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SimSetup startMe;
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SimInfo* info;
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string bassFileName;
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string dumpFileName;
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string xyzFileName;
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int nFrame;
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ZConsReader* zReader;
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DumpReader* dumpReader;
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ofstream* xyzStream;
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int nZmol;
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double zconsTol;
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vector<int> zmolIndex;
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vector<double> zmolPos;
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vector<int> atomToZMol;
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int havezcons;
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//parse the command line option
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if (cmdline_parser (argc, argv, &args_info) != 0)
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exit(1) ;
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//get the dumpfile name and bass file name
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if (args_info.input_given){
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dumpFileName = args_info.input_arg;
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}
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else{
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cerr << "Does not have input file name" << endl;
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exit(1);
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}
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bassFileName = dumpFileName;
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bassFileName = bassFileName.substr(0, bassFileName.rfind(".")) + ".bass";
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if (args_info.output_given){
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xyzFileName = args_info.output_arg;
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}
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else{
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xyzFileName = dumpFileName;
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xyzFileName = xyzFileName.substr(0, xyzFileName.rfind(".")) + ".xyz";
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}
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info = new SimInfo();
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startMe.setSimInfo(info );
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startMe.parseFile( bassFileName.c_str());
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startMe.createSim();
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dumpReader = new DumpReader(dumpFileName.c_str());
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nFrame = dumpReader->getNframes();
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if (args_info.replace_given && info->nZconstraints > 0){
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zReader = new ZConsReader(info);
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nZmol = zReader->getNumZMol();
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zmolIndex = zReader->getZConsIndex();
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zmolPos = zReader->getZConsPos();
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atomToZMol = getAtomToZMol(info, zmolIndex);
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//get tolerance
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GenericData* data;
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DoubleData* toleranceData;
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data = info->getProperty(ZCONSTOL_ID);
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if(!data) {
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cerr << "Zsub error: can not get tolerance \n" << endl;
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exit(1);
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}
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else{
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toleranceData = dynamic_cast<DoubleData*>(data);
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if(!toleranceData){
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cerr << "Zsub error: can not get tolerance \n" << endl;
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exit(1);
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}
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else{
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zconsTol = toleranceData->getData();
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}
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if (zReader->hasNextFrame())
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zReader->readNextFrame();
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}
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}
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xyzStream = new ofstream(xyzFileName.c_str());
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for (int i = 0; i < nFrame; i += args_info.frame_arg){
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dumpReader->readFrame(info, i);
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if (args_info.replace_given && info->nZconstraints > 0){
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while (zReader->getCurTime() < info->currentTime){
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// (zReader->hasNextFrame())
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zReader->readNextFrame();
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}
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zmolPos = zReader->getZConsPos();
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replaceAtomType(info, zmolIndex, zmolPos, atomToZMol, zconsTol);
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}
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dumpToXYZ(info, xyzStream,args_info.repeatX_arg,
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args_info.repeatY_arg, args_info.repeatZ_arg,
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args_info.periodicBox_given, args_info.dipole_given,
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args_info.water_given);
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}
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delete xyzStream;
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delete zReader;
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delete dumpReader;
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}
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void replaceAtomType(SimInfo* info, vector<int>& zmolIndex, vector<double>& zmolPos,
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vector<int> atomToZMol,double zconsTol){
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vector<int> zconsStatus;
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Molecule* mols;
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Atom** atoms;
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double com[3];
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size_t curIndex;
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char newAtomType[2000];
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int molIndex;
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mols = info->molecules;
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atoms = info->atoms;
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curIndex = 0;
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//determine the status of zconstraint molecules
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for(int i = 0; i< info->n_mol && curIndex < zmolIndex.size(); i++){
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if (mols[i].getGlobalIndex() == zmolIndex[curIndex]){
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mols[i].getCOM(com);
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if (fabs(com[2] - zmolPos[curIndex]) < zconsTol)
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zconsStatus.push_back(1);
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else
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zconsStatus.push_back(0);
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curIndex++;
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}
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}
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for(int j = 0; j < info->n_atoms; j++){
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molIndex = atomToZMol[j];
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if (molIndex >= 0){
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switch(zconsStatus[molIndex]){
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case 1 :
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strcpy(newAtomType, "ZF");
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break;
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case 0 :
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strcpy(newAtomType, "ZM");
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break;
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default:
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cerr << "error in zconsStatus" <<endl;
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}
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strcat(newAtomType, atoms[j]->getType());
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atoms[j]->setType(newAtomType);
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}
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}
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}
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void dumpToXYZ(SimInfo* info, ofstream* xyzStream, int repeatX, int repeatY, int repeatZ,
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int periodicBox_given, int dipole_given, int water_given) {
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char buffer[2000];
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int newN;
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Atom** atoms;
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double pos[3];
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char* atomType;
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double HMat[3][3];
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int numNonSSD;
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int numSSD;
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numSSD = 0;
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numNonSSD = 0;
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atoms = info->atoms;
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//Determine the number of SSD molecules and Non-SSD molecules
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for (int i = 0; i < info->n_atoms; i++){
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atomType = atoms[i]->getType();
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if (!strcmp(atomType, "SSD") || !strcmp(atomType+2, "SSD"))
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numSSD++;
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else
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numNonSSD++;
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}
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if(water_given)
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newN = numNonSSD + numSSD * 4;
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else
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newN = numNonSSD;
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newN = newN * (repeatX + 1) * (repeatY + 1) * (repeatZ + 1);
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sprintf(buffer, "%d\n%lf;\t%lf\t%lf\t%lf;\t%lf\t%lf\t%lf;\t%lf\t%lf\t%lf;\n",
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newN, info->getTime(),
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info->Hmat[0][0], info->Hmat[1][0],info->Hmat[2][0],
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info->Hmat[0][1], info->Hmat[1][1],info->Hmat[2][1],
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info->Hmat[0][2], info->Hmat[1][2], info->Hmat[2][2] );
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(*xyzStream) << buffer;
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for(int i = 0; i < repeatX+1; i++){
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for(int j = 0; j < repeatY+1; j++){
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for(int k = 0; k < repeatY+1; k++){
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info->getBoxM(HMat);
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for (int l = 0; l < info->n_atoms; l++){
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atoms[l]->getPos(pos);
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atomType = atoms[l]->getType();
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if (periodicBox_given)
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info->wrapVector(pos);
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for(int m = 0; m < 3; m++) {
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pos[m] += i * HMat[m][0] + j * HMat[m][1] + k * HMat[m][2];
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}
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if (atoms[l]->isDirectional()){
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double RotMat[3][3];
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DirectionalAtom* dAtom;
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dAtom = (DirectionalAtom*) atoms[l];
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dAtom->getA(RotMat);
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if (strcmp(atomType, "SSD") == 0){
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if (water_given)
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convertSSD(buffer, "",pos, RotMat, dipole_given);
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else
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continue;
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}
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else if (strcmp(atomType+2, "SSD") == 0){
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if (water_given){
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//just a hard code here
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char prefix[3];
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prefix[0] = atomType[0];
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prefix[1] = atomType[1];
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prefix[2] = '\0';
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convertSSD(buffer, prefix,pos, RotMat, dipole_given);
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}
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else
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continue;
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}
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else{
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if (dipole_given){
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double u[3] = {0, 0, 1};
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matVecMul3(RotMat, u);
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sprintf(buffer,"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
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atomType, pos[0], pos [1], pos[2], u[0], u[1], u[2] );
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}
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else
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sprintf(buffer,"%s\t%lf\t%lf\t%lf\n",
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atomType,pos[0], pos [1], pos[2]);
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}
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}
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else{
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if (dipole_given)
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sprintf(buffer,"%s\t%lf\t%lf\t%lf\t0.0\t0.0\t0.0\n",
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atomType,pos[0], pos [1], pos[2]);
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else
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sprintf(buffer,"%s\t%lf\t%lf\t%lf\n",
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atomType,pos[0], pos [1], pos[2]);
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}//end if atoms[i]->isDirectional()
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(*xyzStream) << buffer;
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}//end for int l = 0
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}//end for int k =0
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}// end for int j = 0
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}//end for int i = 0
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}
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void convertSSD(char* buffer, char* prefix, double pos[3], double RotMat[3][3], int dipole_given){
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double h1[3] = {0.0, -0.75695, 0.5206};
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double h2[3] = {0.0, 0.75695, 0.5206};
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double ox[3] = {0.0, 0.0, -0.0654};
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double u[3] = {0, 0, 1};
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matVecMul3(RotMat, u);
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matVecMul3(RotMat, h1);
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matVecMul3(RotMat, h2);
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matVecMul3(RotMat, ox);
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if (dipole_given){
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sprintf(buffer, "%sX\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
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prefix,
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pos[0], pos[1], pos[2],
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u[0], u[1], u[2]);
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sprintf(buffer+strlen(buffer), "%sO\t%lf\t%lf\t%lf\t0.0\t0.0\t0.0\n",
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prefix,
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pos[0] + ox[0],
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pos[1] + ox[1],
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pos[2] + ox[2] );
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sprintf(buffer+strlen(buffer), "%sH\t%lf\t%lf\t%lf\t0.0\t0.0\t0.0\n",
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prefix,
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pos[0] + h1[0],
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pos[1] + h1[1],
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pos[2] + h1[2] );
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sprintf(buffer+strlen(buffer), "%sH\t%lf\t%lf\t%lf\t0.0\t0.0\t0.0\n",
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prefix,
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pos[0] + h2[0],
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pos[1] + h2[1],
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pos[2] + h2[2] );
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}
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else{
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sprintf(buffer, "%sX\t%lf\t%lf\t%lf\n",
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prefix,
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pos[0], pos[1], pos[2]);
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sprintf(buffer+strlen(buffer), "%sO\t%lf\t%lf\t%lf\n",
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prefix,
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pos[0] + ox[0],
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pos[1] + ox[1],
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pos[2] + ox[2] );
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sprintf(buffer+strlen(buffer), "%sH\t%lf\t%lf\t%lf\n",
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prefix,
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pos[0] + h1[0],
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pos[1] + h1[1],
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pos[2] + h1[2] );
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sprintf(buffer+strlen(buffer), "%sH\t%lf\t%lf\t%lf\n",
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prefix,
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pos[0] + h2[0],
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pos[1] + h2[1],
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pos[2] + h2[2] );
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}
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}
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| 376 |
vector<int> getAtomToZMol(SimInfo* info, vector<int>& zmolIndex){
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| 377 |
Molecule* mols;
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| 378 |
Atom** atoms;
|
| 379 |
int nmol;
|
| 380 |
int natom;
|
| 381 |
vector<int> atomToZMol;
|
| 382 |
int isZmol;
|
| 383 |
size_t curIndex;
|
| 384 |
|
| 385 |
atomToZMol.resize(info->n_atoms);
|
| 386 |
mols = info->molecules;
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| 387 |
nmol = info->n_mol;
|
| 388 |
curIndex = 0;
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| 389 |
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| 390 |
for(int i = 0; i < nmol; i++){
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| 391 |
atoms =mols[i].getMyAtoms();
|
| 392 |
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| 393 |
if (curIndex >= zmolIndex.size()){
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| 394 |
isZmol = -1;
|
| 395 |
}
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| 396 |
else{
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| 397 |
if(mols[i].getGlobalIndex() == zmolIndex[curIndex]){
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| 398 |
isZmol = curIndex;
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| 399 |
curIndex ++;
|
| 400 |
}
|
| 401 |
else
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| 402 |
isZmol = -1;
|
| 403 |
}
|
| 404 |
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| 405 |
|
| 406 |
|
| 407 |
natom = mols[i].getNAtoms();
|
| 408 |
for(int j = 0; j < natom; j++)
|
| 409 |
#ifndef IS_MPI
|
| 410 |
atomToZMol[atoms[j]->getIndex()] = isZmol;
|
| 411 |
#else
|
| 412 |
atomToZMol[atoms[j]->getGlobalIndex()] = isZmol;
|
| 413 |
#endif
|
| 414 |
}
|
| 415 |
|
| 416 |
return atomToZMol;
|
| 417 |
}
|
| 418 |
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| 419 |
void matVecMul3(double a[3][3], double b[3]){
|
| 420 |
double inVect[3];
|
| 421 |
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| 422 |
inVect[0] = b[0];
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| 423 |
inVect[1] = b[1];
|
| 424 |
inVect[2] = b[2];
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| 425 |
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| 426 |
b[0] = a[0][0]*inVect[0] + a[0][1]*inVect[1] + a[0][2]*inVect[2];
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| 427 |
b[1] = a[1][0]*inVect[0] + a[1][1]*inVect[1] + a[1][2]*inVect[2];
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| 428 |
b[2] = a[2][0]*inVect[0] + a[2][1]*inVect[1] + a[2][2]*inVect[2];
|
| 429 |
}
|
