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mc_input.cc
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mc_input.cc
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#include <stdio.h>
#include <stdlib.h>
#include <fstream>
#include <sstream>
#include <iomanip>
#include "mc_confg.h"
#include "mc_setup.h"
#include "mc_input.h"
#include "mc_utils.h"
#include "mc_poten.h"
#include "mc_qworm.h"
//----- INPUT PARAMETERS----------------------------
// FILE NAMES
const char IO_MASTERDIR[] = "MASTERDIR";
const char IO_OUTPUTDIR[] = "OUTPUTDIR";
const char IO_FILENAMEPREFIX[] = "FILENAMEPREFIX";
// SYSTEM
const char IO_DIMENSION[] = "DIMENSION";
const char IO_RESTART[] = "RESTART";
const char IO_TEMPERATURE[] = "TEMPERATURE";
const char IO_ATOM[] = "ATOM";
const char IO_MOLECULE[] = "MOLECULE";
// Toby's value
const char IO_NONLINEAR[] = "NONLINEAR";
const char IO_DENSITY[] = "DENSITY";
const char IO_READMCCOORDS[] = "READMCCOORDS";
// MC
const char IO_NUMBEROFSLICES[] = "NUMBEROFSLICES";
const char IO_NUMBEROFPASSES[] = "NUMBEROFPASSES";
const char IO_NUMBEROFBLOCKS[] = "NUMBEROFBLOCKS";
const char IO_INITIALBLOCK[] = "INITIALBLOCK";
const char IO_REFLECTY[] = "REFLECTY";
const char IO_REFLECTX[] = "REFLECTX";
const char IO_REFLECTZ[] = "REFLECTZ";
const char IO_ROTSYM[] = "ROTSYM";
const char IO_ROTATION[] = "ROTATION";
const char IO_ROTDENSI[] = "ROTDENSI";
const char IO_WORM[] = "WORM";
const char IO_MINIMAGE[] = "MINIMAGE";
const char IO_CRYSTAL[] = "CRYSTAL";
const char IO_FCC[] = "FCC";
const char IO_HCP[] = "HCP";
const char IO_MCSKIP_RATIO[] = "MCSKIP_RATIO";
const char IO_MCSKIP_TOTAL[] = "MCSKIP_TOTAL";
const char IO_MCSKIP_AVERG[] = "MCSKIP_AVERG";
//------ MC STATUS----------------------------------
const char STATUS_STARTBLOCK[] = "STARTBLOCK";
//--------------------------------------------------
string MasterDir;
string OutputDir;
string FNPrefix;
string MCFileName; // mc output file name (no extension)
void IOReadParams(const char in_file[],int & mc_status)
// mc_status = 0 - new run, 1 - restart
{
const char *_proc_=__func__; // "MCReadInput()";
//-- Open file with input parameters ----------------
ifstream inf(in_file,ios::in);
if (!inf.good())
_io_error(_proc_,IO_ERR_FOPEN,in_file);
//-- Read input parameters --------------------------
int numb = 0; // total number of particles in the system
int type = 0; // total number of atom types
IMPURITY = false;
WORM = false;
MINIMAGE = false;
CRYSTAL = false;
ROTATION = false;
NUMB_ATOMS = 0; // number of atoms (structureless particles)
NUMB_MOLCS = 0; // number of molecules (rotational degrees of freedom)
NUMB_ATOMTYPES = 0; // number of atoms types
NUMB_MOLCTYPES = 0; // number of molecules types
mc_status = 0; // 0 - new run, 1 - restart
int _wtypes = 0; // number of atom's types to apply the worm algorithm
int _rtypes = 0; // number of molecule's types to sample rot degrees of freedom
double _rot_step; // step for sampling the rotational degrees of freedom
string _srot_type; // the molecule type to sample the rotational degrees of freedom
string _srot_dens; // the file name with the rotational density matrix
string crytype; // type of crystal (FCC or HCP)
InitMCCoords = 0;
MCStartBlock = 0;
string params;
while (inf>>params)
{
if (params==IO_RESTART)
{
mc_status = 1; // restart
}
else
if (params==IO_MASTERDIR)
{
inf>>MasterDir;
}
else
if (params==IO_OUTPUTDIR)
{
inf>>OutputDir;
}
else
if (params==IO_FILENAMEPREFIX)
{
inf>>FNPrefix;
}
else
if (params==IO_TEMPERATURE)
{
inf>>Temperature;
}
else
if (params==IO_DENSITY)
{
inf>>Density;
}
else
if ((params==IO_ATOM)||(params==IO_MOLECULE)||(params==IO_NONLINEAR))
{
inf>>MCAtom[type].type; // [1]
inf>>MCAtom[type].numb; // [2]
if(MCAtom[type].numb < 0)
{
ISPHER = 1;
MCAtom[type].numb = -MCAtom[type].numb;
}
string sstat;
int stat;
inf>>sstat; // [3]
if (sstat == STATISTICS[BOSE ]) stat = BOSE;
else if (sstat == STATISTICS[BOLT ]) stat = BOLT;
// else if (sstat == STATISTICS[FERMI]) stat = FERMI;
else
nrerror(_proc_,"Unknown statistics");
MCAtom[type].stat = stat;
inf>>MCAtom[type].mcstep; // [4]
inf>>MCAtom[type].levels; // [5]
inf>>MCAtom[type].fpot; // [6]
string smod; // model of interaction
int pmod;
inf>>smod; // [7]
if (smod == PMODEL[PRIMITIVE]) pmod = PRIMITIVE;
else if (smod == PMODEL[EFFECTIVE]) pmod = EFFECTIVE;
else
nrerror(_proc_,"Unknown model of interaction");
MCAtom[type].pmod = pmod;
// ------- set atom/molecule flag -------------------------
MCAtom[type].molecule = 0; // atom
if (params == IO_MOLECULE)
MCAtom[type].molecule = 1; // molecular impurity
else if (params == IO_NONLINEAR)
MCAtom[type].molecule = 2;
else // atom
if (IMPURITY) nrerror(_proc_,"Molecules should follow atoms in input file");
// the latter is important, for example, for the density estimators
if (MCAtom[type].numb > 0) // ignore this atom/molecule type if N <= 0
{
if ((MCAtom[type].molecule == 1)||(MCAtom[type].molecule == 2))
{
IMPURITY = true;
NUMB_MOLCS += MCAtom[type].numb;
NUMB_MOLCTYPES ++;
}
else
{
NUMB_ATOMS += MCAtom[type].numb;
NUMB_ATOMTYPES ++;
}
numb += MCAtom[type].numb;
type++; // SHOULD BE THE LAST LINE IN THIS SECTION
}
}
else
if (params==IO_NUMBEROFSLICES)
{
inf>>NumbTimes;
}
else
if (params==IO_NUMBEROFPASSES)
{
inf>>NumberOfMCPasses;
}
else
if (params==IO_NUMBEROFBLOCKS)
{
inf>>NumberOfMCBlocks>>NumberOfEQBlocks;
}
else
if (params==IO_INITIALBLOCK)
{
inf>>MCStartBlock;
}
else
if (params==IO_REFLECTY)
{
inf>>IREFLY;
}
else
if (params==IO_REFLECTX)
{
inf>>IREFLX;
}
if (params==IO_REFLECTZ)
{
inf>>IREFLZ;
}
else
if (params==IO_ROTSYM)
{
IROTSYM=1;
inf>>NFOLD_ROT;
}
else
if (params==IO_DIMENSION)
{
inf>>NDIM;
}
else
if (params==IO_ROTATION)
{
inf>>_srot_type; // [1] the molecule type for rotational sampling
inf>>_rot_step; // [2] the rotational MC step(s)
// inf>>_srot_dens; // [3] the file name with the rotational density
inf>> NumbRotTimes;// [3] number of rotational time slices
ROTATION = true;
_rtypes ++;
}
else
if (params==IO_ROTDENSI)
{
inf>>RotDenType;
inf>>RotOdEvn;
inf>>RotEoff;
inf>>X_Rot;
inf>>Y_Rot;
inf>>Z_Rot;
inf>>RNratio;
}
else
if (params==IO_WORM)
{
inf>>Worm.stype; // [1]
inf>>Worm.c; // [2]
inf>>Worm.m; // [3]
WORM = true;
_wtypes ++;
}
else
if (params==IO_MINIMAGE)
{
MINIMAGE = true;
}
else
if (params==IO_CRYSTAL)
{
CRYSTAL = true;
if (NDIM != 3)
nrerror(_proc_,"Crystal must be in 3 dimensions");
inf >> crytype;
if (crytype==IO_FCC)
FCC = 1;
else if (crytype==IO_HCP)
HCP = 1;
else
nrerror(_proc_,"Unknown crystal type");
inf >> N1d[0] >> N1d[1] >> N1d[2];
if (NUMB_ATOMS != (N1d[0]*N1d[1]*N1d[2]*4))
nrerror(_proc_,"NUMB_ATOMS = N1d1*N1d2*N1d3*4 with CRYSTAL");
}
else
if (params==IO_READMCCOORDS)
{
InitMCCoords = 1;
}
else
if (params==IO_MCSKIP_RATIO)
{
inf >> MCSKIP_RATIO;
}
else
if (params==IO_MCSKIP_TOTAL)
{
inf >> MCSKIP_TOTAL;
}
else
if (params==IO_MCSKIP_AVERG)
{
inf >> MCSKIP_AVERG;
}
else
{}
getline(inf,params,'\n'); // skip comments at the end of the line
}
inf.close();
// POST READ INITIALIZATION
NumbAtoms = numb; // the total number of atoms/molecules
NumbTypes = type; // the total number of atoms/molecules types
int gatom = 0; // offset = NumbTimes*gatom
for (int type=0;type<NumbTypes;type++)
{
MCAtom[type].gatom = gatom; // the other parts of the code relies on this
MCAtom[type].offset = gatom*NumbTimes; // MCCoords[][offset+NumbTimes*atom+it]
gatom += MCAtom[type].numb;
}
MaxnTimes = gatom*NumbTimes; // (NumbTimes*NumbAtoms)
MCAtom[NumbTypes].offset = MaxnTimes; // used to define MCatom[type+1]
MCFileName = (OutputDir+FNPrefix);
if (ROTATION)
{
if (_rtypes != 1)
nrerror(_proc_,"Rotational degrees of freedom for one molecule's type only");
bool found = false;
for (int type=0;type<NumbTypes;type++)
if (_srot_type == MCAtom[type].type)
{
if (MCAtom[type].molecule == 0)
nrerror(_proc_,"Rotational degrees of freedom for molecules only");
MCAtom[type].rtstep = _rot_step;
// strcpy(MCAtom[type].rdens,_srot_dens.c_str());
found = true;
break;
}
if (!found)
nrerror(_proc_,"Can't find a particle type to sample rotational degrees of freedom");
}
if (Worm.m >=NumbTimes)
{
nrerror(_proc_,"Worm algorithm: m should be smaller then M");
}
if ((NUMB_ATOMTYPES >1 ) || (NUMB_MOLCTYPES > 1 ))
nrerror(_proc_,"No more then one atom/molecule type: densities and potential energy");
if (WORM && (_wtypes != 1))
nrerror(_proc_,"Worm algorithm only for one atom type");
#ifdef HOSC_TEST
if (NumbTypes !=1)
nrerror(_proc_,"HOSC_TEST: only one atom type");
#endif
// begin DUMP -----------------------------------------
cout << endl;
cout << "MasterDir " <<MasterDir<<endl;
cout << "OutPut " <<OutputDir<<endl;
cout << "File Name Prefix "<<FNPrefix<<endl;
cout << "Temperature "<<Temperature<<endl;
cout << "Density " <<Density<<endl;
cout << "DIM = " <<NDIM<<endl;
int w = 6;
for (int type=0;type<NumbTypes;type++)
{
cout << setw(w) << MCAtom[type].type << BLANK;
cout << setw(w) << MCAtom[type].numb << BLANK;
cout << setw(10) << STATISTICS[MCAtom[type].stat] << BLANK;
cout << setw(w) << MCAtom[type].mcstep << BLANK;
cout << setw(w) << MCAtom[type].levels << BLANK;
cout << setw(w) << MCAtom[type].fpot << BLANK;
cout << setw(w) << PMODEL[MCAtom[type].pmod] << BLANK;
cout << endl;
}
cout << "Total number of atoms " << NumbAtoms << endl;
cout << "Total number of types " << NumbTypes << endl;
if (WORM)
{
cout << "WORM" << BLANK << Worm.stype;
cout << setw(w) << Worm.c << BLANK;
cout << setw(w) << Worm.m << BLANK;
cout << endl;
}
if (ROTATION)
{
cout << endl;
cout << "ROTATION" <<endl;
cout << "Rotational step: " << _rot_step << endl;
// cout << "Rotational density matrix: " << _srot_dens << endl;
cout << "Number of Rotational Slices = " << NumbRotTimes << endl;
cout << "Rotational Density Type = " << RotDenType << endl;
cout << "RotOdEvn = "<< RotOdEvn <<endl;
cout << "Rotational Energy Estimator offset = "<< RotEoff <<"CM-1"<<endl;
cout << "Rotational Constants (CM-1) :"<<X_Rot<<" "<<Y_Rot<<" "<<Z_Rot<<endl;
cout << "RS / Noya: "<<RNratio<<endl;
cout << endl;
}
if(ROTATION && ISPHER == 1)
nrerror(_proc_,"ISPHER = 1 is not compatible with ROTATION");
cout << "NONLINEAR DOPANT SPHERICAL TREATMENT: "<<ISPHER<<endl;
if(CRYSTAL)
{
cout<<"Crystal type: "<<crytype<<endl;
cout<<"Number of unit cells along each side: "<<N1d[0]<<" "<<N1d[1]<<" "<<N1d[2]<<endl;
}
cout << "Number of Slices = " << NumbTimes << endl;
cout << "Number of Passes = " << NumberOfMCPasses << endl;
cout << "Number of Blocks = " << NumberOfMCBlocks << BLANK << NumberOfEQBlocks << endl;
cout << "Initial Block No.= " << MCStartBlock<<endl;
cout << endl;
cout << endl;
cout << "Number of steps to skip to save ACCEPT RATIO" << BLANK << MCSKIP_RATIO << endl;
cout << "Number of steps to skip to save ACCUML AVERG" << BLANK << MCSKIP_TOTAL << endl;
cout << "Number of steps to skip to evaluate AVERAGES" << BLANK << MCSKIP_AVERG << endl;
cout << endl;
cout << endl;
if(IREFLY == 1)
cout <<"REFLECT WITH RESPECT TO XZ PLANE OF DOPANT WHEN EVALUATING PROPERTIES"<<endl;
if(IREFLX == 1)
cout <<"REFLECT WITH RESPECT TO YZ PLANE OF DOPANT WHEN EVALUATING PROPERTIES"<<endl;
if(IREFLZ == 1)
cout <<"REFLECT WITH RESPECT TO XY PLANE OF DOPANT WHEN EVALUATING PROPERTIES"<<endl;
if(IROTSYM ==1)
cout <<"ROTATIONAL SYMMETRY OF THE DOPANT WITH NFOLD="<<NFOLD_ROT<<endl;
#ifdef HOSC_TEST
cout << " <<<<<< Harmonic oscillator test [HOSC_TEST 1] >>>>>>> " << endl;
#endif
#ifdef ROTS_TEST
cout << " <<<<<< Free rotor test [ROTS_TEST 1] >>>>>>> " << endl;
#endif
cout << endl;
cout << endl;
// end DUMP -----------------------------------------
// return mc_status;
}
void StatusIO(int tstatus, const char file_name[])
// read/wrire status of MC run
{
const char *_proc_=__func__; // "MCStatus()";
ios::openmode mode;
switch (tstatus)
{
case IOWrite: mode=ios::out; break;
case IORead : mode=ios::in; break;
default :
nrerror (_proc_,IO_ERR_WMODE); break;
}
fstream fid(file_name,mode);
if (!fid.good())
_io_error(_proc_,IO_ERR_FOPEN,file_name);
string status;
switch (tstatus)
{
case IOWrite:
fid<<STATUS_STARTBLOCK<<" "<<MCStartBlock<<endl;
break;
case IORead:
while (fid>>status)
{
if (status==STATUS_STARTBLOCK)
fid>>MCStartBlock;
getline(fid,status,'\n'); // skip comments
}
break;
default :
nrerror (_proc_,IO_ERR_WMODE);
break;
}
fid.close();
}
void ConfigIO(int tstatus, const char file_name[])
// read/wrire initial configuration
{
const char *_proc_=__func__; // "MCStatus()";
ios::openmode mode;
switch (tstatus)
{
case IOWrite: mode = ios::out; break;
case IORead : mode = ios::in; break;
default :
nrerror (_proc_,IO_ERR_WMODE); break;
}
fstream fid(file_name,mode);
// fstream fid(file_name,mode | ios::binary);
if (!fid.good())
_io_error(_proc_,IO_ERR_FOPEN,file_name);
io_setout(fid); //added by Hui Li
streamsize size;
switch (tstatus)
{
case IOWrite:
size=sizeof(double)*NumbAtoms*NumbTimes;
fid.write((char *)&size,sizeof(streamsize));
fid.write((char *)MCCoords[0],size);
fid.write((char *)MCCosine[0],size);
// Toby replaces the above line by
// fid.write((char *)MCAngles[0],size);
// to store the three Euler angles
break;
case IORead:
fid.read((char *)&size,sizeof(streamsize));
fid.read((char *)MCCoords[0],size);
fid.read((char *)MCCosine[0],size);
// Toby replaces the above line by
// fid.read((char *)MCAngles[0],size);
// to read the three Euler angles
break;
default :
nrerror (_proc_,IO_ERR_WMODE);
break;
}
fid.close();
}
void TablesIO(int tstatus, const char file_name[])
// read/wrire permutation tables
{
const char *_proc_=__func__; // "TablesIO";
ios::openmode mode;
switch (tstatus)
{
case IOWrite: mode = ios::out; break;
case IORead : mode = ios::in; break;
default :
nrerror (_proc_,IO_ERR_WMODE); break;
}
fstream fid(file_name,mode | ios::binary);
if (!fid.good())
_io_error(_proc_,IO_ERR_FOPEN,file_name);
streamsize size;
switch (tstatus)
{
case IOWrite:
size=sizeof(int)*NumbAtoms;
fid.write((char *)&size,sizeof(streamsize));
fid.write((char *)PIndex,size);
fid.write((char *)RIndex,size);
break;
case IORead:
fid.read((char *)&size,sizeof(streamsize));
fid.read((char *)PIndex,size);
fid.read((char *)RIndex,size);
break;
default :
nrerror (_proc_,IO_ERR_WMODE);
break;
}
fid.close();
}
void QWormsIO(int tstatus, const char file_name[])
// read/write a status of the worm
{
const char *_proc_=__func__; // "QWormsIO()";
ios::openmode mode;
switch (tstatus)
{
case IOWrite: mode = ios::out; break;
case IORead : mode = ios::in; break;
default :
nrerror (_proc_,IO_ERR_WMODE); break;
}
fstream fid(file_name,mode | ios::binary);
if (!fid.good())
_io_error(_proc_,IO_ERR_FOPEN,file_name);
// streamsize size;
switch (tstatus)
{
case IOWrite:
fid.write((char *)&Worm,sizeof(TPathWorm));
break;
case IORead:
fid.read((char *)&Worm,sizeof(TPathWorm));
break;
default :
nrerror (_proc_,IO_ERR_WMODE);
break;
}
fid.close();
}
void IOxyz(int tstatus, const char file_name[])
{
const char *_proc_=__func__; // "IOxyz";
//---------------- Open ------------
ios::openmode mode;
switch (tstatus)
{
case IOWrite: mode = ios::out; break;
case IORead : mode = ios::in; break;
default :
nrerror (_proc_,IO_ERR_WMODE); break;
}
fstream fid(file_name,mode);
if (!fid.good())
_io_error(_proc_,IO_ERR_FOPEN,file_name);
io_setout(fid);
//---------------- Read/Write ------------
stringstream stype;
string sbuff;
int offset;
int type = 0;
int atom = 0; // first atom # will be 1, NOT 0
switch (tstatus)
{
case IOWrite:
fid<<MaxnTimes<<endl; // total number of "atoms"
fid<<COMMENTS<<BLANK<<IO_COM_XYZ<<endl; // comments
for (int it=0;it<MaxnTimes;it++)
{
if (it==MCAtom[type+1].offset) {type++; atom=0;} // new atom type
if ((it-MCAtom[type].offset)%NumbTimes==0) atom++; // new atom
stype.str(""); stype<<MCAtom[type].type<<atom; // atom label
fid<<setw(5)<<stype.str()<<BLANK;
for (int id=0;id<NDIM;id++)
{
fid<<setw(IO_WIDTH)<<MCCoords[id][it]<<BLANK;
fid<<setw(IO_WIDTH)<<MCCosine[id][it]<<BLANK;
// Toby replaces the above line by
// fid<<setw(IO_WIDTH)<<MCAngles[id][it]<<BLANK;
// by doing that, Toby stores the three Euler angles, not the unit vector of the two angles orientation
}
fid<<endl;
}
/* the same as above, but explicit sum over atoms and types
for (int type=0;type<NumbTypes;type++)
for (int atom=0;atom<MCAtom[type].numb;atom++)
for (int it=0;it<NumbTimes;it++)
{
stype.str(""); stype<<MCAtom[type].type<<atom; // atom label
fid<<setw(5)<<stype.str()<<BLANK;
offset=MCAtom[type].offset+NumbTimes*atom;
for (int id=0;id<NDIM;id++)
fid<<MCCoords[id][offset+it]<<BLANK;
fid<<endl;
}
*/
break;
case IORead:
fid>>MaxnTimes;
getline(fid,sbuff); // skip a comment line
for (int type=0;type<NumbTypes;type++)
for (int atom=0;atom<MCAtom[type].numb;atom++)
for (int it=0;it<NumbTimes;it++)
{
fid>>sbuff; // skip an atom type
offset=MCAtom[type].offset+NumbTimes*atom;
for (int id=0;id<NDIM;id++)
{
fid>>MCCoords[id][offset+it];
fid>>MCCosine[id][offset+it];
// Toby replaces the above line by
// fid>>MCAngles[id][offset+it];
// by doing that, Toby reads the three Euler angles, not the unit vector of the two angle orientation
}
}
break;
default :
nrerror (_proc_,IO_ERR_WMODE);
break;
}
fid.close();
}
void IOFileBackUp(const char file_name[])
{
#ifdef DEBUG_PIMC
const char *_proc_=__func__;
#endif
string cmd="cp";
if (FileExist(file_name))
{
cmd += " " + (string)file_name;
cmd += " " + (string)file_name+(string)FBACKUP_EXTENSION;
int status = system(cmd.c_str());
#ifdef DEBUG_PIMC
if (status < 0)
nrerror(_proc_,IO_ERR_SCALL);
#endif
}
}
void IOFileDelete(const char file_name[])
{
#ifdef DEBUG_PIMC
const char *_proc_=__func__;
#endif
string cmd="rm";
if (FileExist(file_name))
{
cmd += " " + (string)file_name;
int status = system(cmd.c_str());
#ifdef DEBUG_PIMC
if (status < 0)
nrerror(_proc_,IO_ERR_SCALL);
#endif
}
}
int FileExist (const char fileName [])
{
FILE *infile = fopen (fileName, "r");
// ifstream infile(fileName,ios::in);
int ret_code=0;
if (infile == NULL)
ret_code = 0; // file doesn't exist
else
{
ret_code = 1; // file exists
fclose (infile);
}
return (ret_code);
}
void io_setout(fstream &out, int set_precision)
{
out<<setprecision(set_precision);
out<<setiosflags (ios::scientific);
// out<<setiosflags (ios::right);
}