forked from yyfdemajia/OCTP
/
fix_ordern.cpp
1162 lines (1103 loc) · 39 KB
/
fix_ordern.cpp
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/* ----------------------------------------------------------------------
fix ordern is a child class of "fix", developed based on two classes
of "fix ave/time" and "fix ave/correlate/long", provided by LAMMPS.
This command is distributed under the GNU General Public License.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <cstdlib>
#include <cstring>
#include <unistd.h>
#include "fix_ordern.h"
#include "update.h"
#include "force.h"
#include "modify.h"
#include "compute.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
#include "group.h"
#include "domain.h"
#include "atom.h"
#include "citeme.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{SCALAR,VECTOR};
enum{VISCOSITY,THERMCOND,DIFFUSIVITY};
#define INVOKED_VECTOR 2
static const char cite_fix_ordern[] =
"fix ave/ordern command:\n\n"
"@Article{Jamali2019,\n"
" author = {Jamali, Seyed Hossein and Wolf, Ludger and Becker, Tim M. and de Groen, Mariëtte and Ramdin, Mahinder and Hartkamp, Remco and Bardow, André and Vlugt, Thijs J. H. and Moultos, Othonas A.},\n"
" title = {OCTP: A Tool for On-the-Fly Calculation of Transport Properties of Fluids with the Order-n Algorithm in LAMMPS},\n"
" doi = {10.1021/acs.jcim.8b00939},\n"
" journal = {J. Chem. Inf. Model.},\n"
" year = {2019},\n"
" volume = {59},\n"
" pages = {1290-1294}\n "
"}\n\n";
/* ---------------------------------------------------------------------- */
FixOrderN::FixOrderN(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (lmp->citeme) lmp->citeme->add(cite_fix_ordern);
// At least 7 arguments are needed: [0-2], MODE, nevery, nwrite, value
if (narg < 7) error->all(FLERR,"Illegal fix ordern command");
MPI_Comm_rank(world,&me);
restart_global = 1;
// Initial values
restart_continue = 0;
startstep = 0;
flag_Dxyz = 0;
flag_TCconv = 0;
tnb = 10;
tnbe = 10;
fp1 = NULL;
fp2 = NULL;
title = NULL;
format_user = NULL;
format = (char *) " %g";
dynamic_group_allow = 0; // the groups should not be modified.
// SPECIFYING THE MAIN ARGUMENTS
// Define the type of transport property calculation
if (strcmp(arg[3],"diffusivity") == 0) {
mode = DIFFUSIVITY;
char filen1[] = "selfdiffusivity.dat";
filename1 = new char[strlen(filen1)+1];
strcpy(filename1,filen1);
char filen2[] = "onsagercoefficient.dat";
filename2 = new char[strlen(filen2)+1];
strcpy(filename2,filen2);
} else if (strcmp(arg[3],"viscosity") == 0) {
mode = VISCOSITY;
char filen1[] = "viscosity.dat";
filename1 = new char[strlen(filen1)+1];
strcpy(filename1,filen1);
filename2 = NULL;
} else if (strcmp(arg[3],"thermalconductivity") == 0) {
mode = THERMCOND;
char filen1[] = "thermconductivity.dat";
filename1 = new char[strlen(filen1)+1];
strcpy(filename1,filen1);
filename2 = NULL;
} else
error->all(FLERR,"Illegal fix ordern command");
// rate of sampling (end_of_step())
nevery = utils::inumeric(FLERR,arg[4],false,lmp);
// rate of writing files
nfreq = utils::inumeric(FLERR,arg[5],false,lmp);
global_freq = nevery;
// OBTAINING THE ID OF COMPUTE FOR THIS FIX
// number of input values (it must be only one compute)
nvalues = 0;
int iarg = 6;
while (iarg < narg) {
if ((strncmp(arg[iarg],"c_",2) == 0)) {
nvalues++;
iarg++;
} else break;
}
if (nvalues == 0) error->all(FLERR,"Incorrect number of inputs for fix ordern command");
if (nvalues > 1) error->all(FLERR,"Incorrect number of inputs for fix ordern command");
char *suffix = new char[strlen(arg[6])];
strcpy(suffix,&arg[6][2]);
char *ptr = strchr(suffix,'[');
if (ptr) error->all(FLERR,"All components of the vector are required for fix ordern command");
idcompute = new char[strlen(suffix) + 1];
strcpy(idcompute,suffix);
delete [] suffix;
icompute = modify->find_compute(idcompute); // id of the compute (int)
nrows = modify->compute[icompute]->size_vector; // get the number of rows (int)
Compute *compute = modify->compute[icompute]; // the whole compute class
// PARSING OPTIONAL ARGUMENTS
iarg = 7;
while (iarg < narg) {
// add more file options for mode == visocisty/diffusion/thermcond
if (strcmp(arg[iarg],"file") == 0) {
if (mode == DIFFUSIVITY) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix ordern command");
delete [] filename1;
filename1 = new char[strlen(arg[iarg+1])+1];
strcpy(filename1,arg[iarg+1]);
delete [] filename2;
filename2 = new char[strlen(arg[iarg+2])+1];
strcpy(filename2,arg[iarg+2]);
iarg += 3;
} else if (mode == THERMCOND || mode == VISCOSITY) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ordern command");
delete [] filename1;
filename1 = new char[strlen(arg[iarg+1])+1];
strcpy(filename1,arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix ordern command");
} else if (strcmp(arg[iarg],"start") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ordern command");
startstep = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"nb") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ordern command");
tnb = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"nbe") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ordern command");
tnbe = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"format") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ordern command");
delete [] format_user;
int n = strlen(arg[iarg+1]) + 2;
format_user = new char[n];
sprintf(format_user," %s",arg[iarg+1]);
format = format_user;
iarg += 2;
} else if (strcmp(arg[iarg],"title") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ordern command");
delete [] title;
int n = strlen(arg[iarg+1]) + 1;
title = new char[n];
strcpy(title,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"Dxyz") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ordern command");
if (strcmp(arg[iarg+1],"no") == 0) flag_Dxyz = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) flag_Dxyz = 1;
else error->all(FLERR,"Illegal fix ordern command");
iarg += 2;
} else if (strcmp(arg[iarg],"TCconvective") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ordern command");
if (strcmp(arg[iarg+1],"no") == 0) flag_TCconv = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) flag_TCconv = 1;
else error->all(FLERR,"Illegal fix ordern command");
iarg += 2;
} else error->all(FLERR,"Illegal fix ordern command");
}
// SETUP & ERROR CHECK
// for fix inputs, check that fix frequency is acceptable
// set variable_length if any compute is variable length
if (nevery <= 0 || nfreq <= 0 || startstep < 0)
error->all(FLERR,"Illegal fix ordern command: illegal numbers for fix ordern command");
if ( (nfreq % (2*nevery)) && ( (mode == VISCOSITY) || (mode == THERMCOND) ) )
error->all(FLERR,"Illegal fix ordern command: nevery is not a factor of nfreq");
if (startstep % (nevery) )
error->all(FLERR,"Illegal fix ordern command: nevery is not a factor of start");
if (icompute < 0)
error->all(FLERR,"No compute ID for fix ordern command");
if (modify->compute[icompute]->vector_flag == 0)
error->all(FLERR,"No global compute vector is computed for fix ordern command");
if (modify->compute[icompute]->size_vector_variable)
error->all(FLERR,"Input vector for fix ordern command has variable size");
// DEFINING THE PARAMETERS AND VARILABLES
count = -1; // the number of samp
cnb = 1;
boltz = force->boltz;
nktv2p = force->nktv2p;
// Specific variables for each mode
if (mode == DIFFUSIVITY) {
deltat = (double) (nevery)*(update->dt);
tngroup = group->ngroup ; // the size of the arrays (group "all" included)
ngroup = 0; // WILL BE OVERWRITTEN at count = 0 (# of groups for diffusion)
tnatom = atom->natoms; // Total # of atoms in the system (nrows = 5*tnatom)
vecsize = 0; // WILL BE OVERWRITTEN at count = 0 (# of atoms in groups)
} else if (mode == VISCOSITY) {
deltat = (double) (2.0*nevery)*(update->dt);
vecsize = 7;
sampsize = 8;
sumP = 0;
numP = 0;
} else if (mode == THERMCOND) {
deltat = (double) (2.0*nevery)*(update->dt);
vecsize = 6;
sampsize = 6;
}
// Order-n algorithm-specific parameters
if ( (mode == VISCOSITY) || (mode == THERMCOND) )
{
memory->create(data,vecsize,"fix/ordern:data");
memory->create(simpf0,vecsize,"fix/ordern:simpf0");
memory->create(simpf1,vecsize,"fix/ordern:simpf1");
memory->create(samp,tnb,tnbe,sampsize,"fix/ordern:samp");
memory->create(oldint,tnb,tnbe,vecsize,"fix/ordern:oldint");
memory->create(rint,vecsize,"fix/ordern:rint");
} else if ( mode == DIFFUSIVITY)
{
memory->create(PosC_ii,tnb,tnbe,tngroup,"fix/ordern:PosC_ii");
memory->create(PosC_iix,tnb,tnbe,tngroup,"fix/ordern:PosC_iix");
memory->create(PosC_iiy,tnb,tnbe,tngroup,"fix/ordern:PosC_iiy");
memory->create(PosC_iiz,tnb,tnbe,tngroup,"fix/ordern:PosC_iiz");
memory->create(PosC_ij,tnb,tnbe,tngroup,tngroup,"fix/ordern:PosC_ij");
memory->create(PosC_ijx,tnb,tnbe,tngroup,tngroup,"fix/ordern:PosC_ijx");
memory->create(PosC_ijy,tnb,tnbe,tngroup,tngroup,"fix/ordern:PosC_ijy");
memory->create(PosC_ijz,tnb,tnbe,tngroup,tngroup,"fix/ordern:PosC_ijz");
memory->create(PosCorrSum,tnb,tnbe,tngroup,3,"fix/ordern:PosCorrSum");
memory->create(atomingroup,tnatom,2,"fix/ordern:atomingroup");
memory->create(groupinfo,tngroup,2,"fix/ordern:groupinfo");
// NOTE: "oldint" and "rint" will be made at count = 0 in "invoke_scalar"
}
memory->create(recdata,nrows,"fix/ordern:recdata"); // data passed from compute
memory->create(nsamp,tnb,tnbe,"fix/ordern:nsamp");
memory->create(nbe,tnb,"fix/ordern:nbe");
for (int i = 0; i < tnb; i++) nbe[i]=1;
// this fix produces a global scalar
// intensive/extensive flags set by compute that produces value
// This fix produces only a SCALAR value (The timestep)
scalar_flag = 1;
vector_flag = 0;
extscalar = 0;
// nvalid = next step on which end_of_step does something
// add nvalid to all computes that store invocation times
// since don't know a priori which are invoked by this fix
// once in end_of_step() can set timestep for ones actually invoked
nvalid_last = -1;
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
// Opening new data files to output data
if (me == 0) {
if (mode == DIFFUSIVITY) {
fp1 = fopen(filename1,"w");
fp2 = fopen(filename2,"w");
if (fp1 == NULL || fp2 == NULL) {
error->all(FLERR,"Cannot open fix ordern files");
}
} else if (mode == THERMCOND || mode == VISCOSITY) {
fp1 = fopen(filename1,"w");
if (fp1 == NULL) {
error->all(FLERR,"Cannot open fix ordern files");
}
}
}
// Writing the header lines to files
if (fp1 && me == 0) {
clearerr(fp1);
if (title) fprintf(fp1,"%s\n",title);
if (mode == DIFFUSIVITY) {
fprintf(fp1,"#NOTE: MSDs should be divided by ");
fprintf(fp1,"the number of molecules of species i (N_i).\n");
fprintf(fp1,"#NOTE: MSDs have been divided by ");
fprintf(fp1,"the factor 6 (or 2, i.e., MSD_x, MSD_y, and MSD_z).\n");
} else if (mode == VISCOSITY) {
fprintf(fp1,"#NOTE: MSDs should be divided by the temperature.\n");
fprintf(fp1,"#NOTE: MSDs have been divided by ");
fprintf(fp1,"2 or 10 (i.e., the viscosity computed from all components).\n");
fprintf(fp1,"#Time\tMSD_xx\tMSD_yy\tMSD_zz\tMSD_xy\tMSD_xz\tMSD_yz\t");
fprintf(fp1,"MSD_off\tMSD_all\tMSD_bulkvisc\n");
} else if (mode == THERMCOND) {
fprintf(fp1,"#NOTE: MSDs should be divided by (temperature^2).\n");
fprintf(fp1,"#NOTE: MSDs have been divided by 2.\n");
fprintf(fp1,"#Time\tMSD_x\tMSD_y\tMSD_z\tMSD_all");
if (flag_TCconv)
fprintf(fp1,"\tMSDconvect_x\tMSDconvect_y\tMSDconvect_z\tMSDconvect_all");
fprintf(fp1,"\n");
}
if (ferror(fp1)) error->one(FLERR,"Error in writing file header for fix ordern command");
filepos1 = platform::ftell(fp1);
}
if (fp2 && me == 0) {
clearerr(fp2);
if (title) fprintf(fp2,"%s\n",title);
if (mode == DIFFUSIVITY) {
fprintf(fp2,"#NOTE: MSDs should be divided by ");
fprintf(fp2,"the total number of molecules (N).\n");
fprintf(fp1,"#NOTE: MSDs have been divided by ");
fprintf(fp1,"the factor 6 (or 2, i.e., MSD_x, MSD_y, and MSD_z).\n");
}
if (ferror(fp2)) error->one(FLERR,"Error in writing file header for fix ordern command");
filepos2 = platform::ftell(fp2);
}
delete [] title;
}
/* ---------------------------------------------------------------------- */
FixOrderN::~FixOrderN()
{
delete [] format_user;
if (fp1 && me == 0)
{
fclose(fp1);
delete [] filename1;
}
if (fp2 && me == 0)
{
fclose(fp2);
delete [] filename2;
}
if ( (mode == VISCOSITY) || (mode == THERMCOND) )
{
memory->destroy(data);
memory->destroy(simpf0);
memory->destroy(simpf1);
memory->destroy(samp);
} else if ( mode == DIFFUSIVITY)
{
memory->destroy(PosC_ii);
memory->destroy(PosC_iix);
memory->destroy(PosC_iiy);
memory->destroy(PosC_iiz);
memory->destroy(PosC_ij);
memory->destroy(PosC_ijx);
memory->destroy(PosC_ijy);
memory->destroy(PosC_ijz);
memory->destroy(PosCorrSum);
memory->destroy(atomingroup);
memory->destroy(groupinfo);
}
memory->destroy(recdata);
memory->destroy(nsamp);
memory->destroy(oldint);
memory->destroy(rint);
memory->destroy(nbe);
}
/* ----------------------------------------------------------------------
defines when fix can be called (at the end of step)
------------------------------------------------------------------------- */
int FixOrderN::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ----------------------------------------------------------------------
Initializing the whole fix in Modify::init()
------------------------------------------------------------------------- */
void FixOrderN::init()
{
// set current indices for all computes,fixes,variables
int icompute_new = modify->find_compute(idcompute);
if (icompute < 0 || icompute_new != icompute)
error->all(FLERR,"No compute ID for fix ordern command");
// need to reset nvalid if nvalid < ntimestep b/c minimize was performed
if (nvalid < update->ntimestep) {
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
}
/* ----------------------------------------------------------------------
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
void FixOrderN::setup(int /*vflag*/)
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixOrderN::end_of_step()
{
// skip if not step which requires doing something
// error check if timestep was reset in an invalid manner
bigint ntimestep = update->ntimestep;
if (ntimestep < nvalid_last || ntimestep > nvalid)
error->all(FLERR,"Invalid timestep reset for fix order");
if (ntimestep != nvalid) return;
nvalid_last = nvalid;
invoke_scalar(ntimestep);
}
void FixOrderN::invoke_scalar(bigint ntimestep)
{
int i,j,k,l;
double scalar = ntimestep;
// update the next timestep to call end_of_step()
modify->addstep_compute(ntimestep+nevery);
// invoke compute vector if not previously invoked
// get the data from compute_vector and store it in recdata
// the size of recdata is nrows
modify->clearstep_compute();
Compute *compute = modify->compute[icompute]; // the whole compute class
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
double *cvector = compute->vector;
for (i = 0; i < nrows; i++)
recdata[i] = cvector[i];
// update the next timestep to call end_of_step()
nvalid += nevery;
modify->addstep_compute(nvalid);
// Check if this timestep has not been sampled during restarting
if (restart_continue)
{
restart_continue = 0;
return;
}
if (count < 0)
{
count = 0;
icount = 0;
} else {
icount++;
if ( (mode == DIFFUSIVITY) || (icount%2 == 0) )
count++;
}
// From now, everything is computed only on the main core
if (me != 0) return;
// Preliminary calculations for each transport property
// Fill in the vector "data" accordingly
if (mode == DIFFUSIVITY) // DIFFUSION
{
if (count == 0) // only run during the first time step
{
natom = 0;
// Finding corresponding groups to each atom at the first time
for (sortID = 0; sortID < tnatom; sortID++)
{
ID = (int) (recdata[5*sortID+3]+0.1);
atommask = (int) recdata[5*sortID+4]+0.1;
int groupfound = 0;
if (ngroup > 0 ) // First try to match with available groups
{
for (j = 1; j <= ngroup; j++)
{
if ( atommask & groupinfo[j][1] )
{
atomingroup[ID][0] = natom; // ID starts from 0
atomingroup[ID][1] = j; // groupID starts from 1
natom++;
groupfound = 1;
break;
}
}
}
if (groupfound == 0) // If no match, try to find a new group
{
for (k = 1 ; k < tngroup; k++)
{
if ( atommask & group->bitmask[k] )
{
ngroup++;
groupinfo[ngroup][0] = k;
groupinfo[ngroup][1] = group->bitmask[k];
atomingroup[ID][0] = natom; // ID starts from 0
atomingroup[ID][1] = ngroup; // groupID starts from 1
natom++;
groupfound = 1;
break;
}
}
}
// if this atom doesn't belong to any group
if (groupfound == 0)
atomingroup[ID][0] = atomingroup[ID][1] = -1;
}
vecsize = 3*natom;
// NOTE: "oldint" and "rint" are constructed hear at count = 0
memory->create(oldint,tnb,tnbe,vecsize,"fix/ordern:oldint");
memory->create(rint,vecsize,"fix/ordern:rint");
// initializing the arrays
for(sortID = 0; sortID < tnatom ; sortID++)
{
ID = (int) (recdata[5*sortID+3]+0.1);
if (atomingroup[ID][0] < 0)
continue;
atomID = atomingroup[ID][0];
for( i = 0; i < tnb; i++)
{
oldint[i][tnbe-1][3*atomID] = recdata[5*sortID];
oldint[i][tnbe-1][3*atomID+1] = recdata[5*sortID+1];
oldint[i][tnbe-1][3*atomID+2] = recdata[5*sortID+2];
for ( j = 0; j < tnbe; j++)
{
nsamp[i][j] = 0.0;
for ( k = 0; k < tngroup; k++)
{
PosC_ii[i][j][k] = 0.0;
PosC_iix[i][j][k] = 0.0;
PosC_iiy[i][j][k] = 0.0;
PosC_iiz[i][j][k] = 0.0;
for ( l = 0; l < tngroup ; l++)
{
PosC_ij[i][j][k][l] = 0.0;
PosC_ijx[i][j][k][l] = 0.0;
PosC_ijy[i][j][k][l] = 0.0;
PosC_ijz[i][j][k][l] = 0.0;
}
}
}
}
}
}
if (count == 0) return; // nothing to do at this timestep
for(sortID = 0; sortID < tnatom ; sortID++)
{
ID = (int) (recdata[5*sortID+3]+0.1);
if (atomingroup[ID][0] < 0)
continue;
atomID = atomingroup[ID][0];
rint[3*atomID] = recdata[5*sortID];
rint[3*atomID+1] = recdata[5*sortID+1];
rint[3*atomID+2] = recdata[5*sortID+2];
}
} else if (mode == VISCOSITY) // VISCOSITY
{
if (count == 0) {
for ( i = 0; i<tnb; i++ )
for ( j = 0; j < tnbe; j++ ) {
nsamp[i][j] = 0.0;
for (int k = 0; k < vecsize; k++) {
oldint[i][j][k] = 0.0;
samp[i][j][k] = 0.0;
}
samp[i][j][vecsize] = 0.0;
}
}
data[6] = (recdata[0]+recdata[1]+recdata[2])/3.0;
for (i = 0; i < 3; i++) data[i] = (recdata[i] - data[6]);
for (i = 3; i < 6; i++) data[i] = recdata[i];
sumP += data[6];
numP += 1.0;
} else if (mode == THERMCOND) // THERMAL CONDUCTIVITY
{
if (count == 0) {
for ( i = 0; i<tnb; i++ )
for ( j = 0; j < tnbe; j++ ) {
nsamp[i][j] = 0.0;
for (int k = 0; k < vecsize; k++) {
oldint[i][j][k] = 0.0;
samp[i][j][k] = 0.0;
}
}
}
for (i = 0; i < vecsize; i++) data[i] = recdata[i];
}
// INTEGRATION according to Simpson's rule
if (mode == VISCOSITY || mode == THERMCOND)
{
integrate();
if ((icount % 2) == 1) return; // return for odd timesteps
}
// ORDER-N ALGORITHM
// Assign the number of active blocks
i = count/(pow(tnbe,cnb));
while (i != 0)
{
cnb++;
i /= tnbe;
}
for(i = 0; i < cnb; i++) // loop over all active blocks
{
if ((count)%((int)pow(tnbe,i))==0)
{
cnbe = MIN(nbe[i],tnbe);
for (j=tnbe-1; j>=tnbe-cnbe; j--) // loop over all active block elements
{
nsamp[i][j] += 1.0;
if ( (mode == VISCOSITY) || (mode == THERMCOND) )
{
for ( k = 0; k < vecsize; k++)
{
dist = rint[k]-oldint[i][j][k];
// Add the coefficient later
samp[i][j][k] += (dist*dist);
if ( (mode == VISCOSITY) && (k == vecsize-1) )
{
samp[i][j][vecsize] += (dist);
}
}
} else if (mode == DIFFUSIVITY)
{
for( k = 1 ; k <= ngroup ; k++ )
{
PosCorrSum[i][j][k][0] = 0;
PosCorrSum[i][j][k][1] = 0;
PosCorrSum[i][j][k][2] = 0;
}
double distx, disty, distz;
double distx2, disty2, distz2;
for (ID = 0; ID < tnatom ; ID++)
{
if (atomingroup[ID][0] < 0)
continue;
atomID = atomingroup[ID][0];
atomgroup = atomingroup[ID][1];
distx = oldint[i][j][3*atomID] - rint[3*atomID];
disty = oldint[i][j][3*atomID+1] - rint[3*atomID+1];
distz = oldint[i][j][3*atomID+2] - rint[3*atomID+2];
distx2 = distx*distx;
disty2 = disty*disty;
distz2 = distz*distz;
// Add coefficients (2.0 and 6.0) later
PosC_iix[i][j][atomgroup] += distx2;
PosC_iiy[i][j][atomgroup] += disty2;
PosC_iiz[i][j][atomgroup] += distz2;
PosC_ii[i][j][atomgroup] += (distx2 + disty2 + distz2);
PosCorrSum[i][j][atomgroup][0] += distx;
PosCorrSum[i][j][atomgroup][1] += disty;
PosCorrSum[i][j][atomgroup][2] += distz;
}
for ( k = 1 ; k <= ngroup ; k++)
{
for ( l = 1 ; l <= ngroup ; l++)
{
distx2 = PosCorrSum[i][j][k][0] * PosCorrSum[i][j][l][0];
disty2 = PosCorrSum[i][j][k][1] * PosCorrSum[i][j][l][1];
distz2 = PosCorrSum[i][j][k][2] * PosCorrSum[i][j][l][2];
// Add coefficients (2.0 and 6.0) later
PosC_ijx[i][j][k][l] += distx2;
PosC_ijy[i][j][k][l] += disty2;
PosC_ijz[i][j][k][l] += distz2;
PosC_ij[i][j][k][l] += ( distx2 + disty2 + distz2 );
}
}
}
}
//increase the current blocklength
nbe[i]++;
//shift to the left, set last index to the correlation value
if ( (mode == VISCOSITY) || (mode == THERMCOND) )
{
for (int k=0; k < vecsize; k++)
{
for (int j=1; j < tnbe; j++)
oldint[i][j-1][k] = oldint[i][j][k] ;
oldint[i][tnbe-1][k] = rint[k];
}
} else if (mode == DIFFUSIVITY)
{
for (ID = 0; ID < tnatom ; ID++)
{
if (atomingroup[ID][0] < 0)
continue;
atomID = atomingroup[ID][0];
for(j = 1 ; j < tnbe ; j++)
{
oldint[i][j-1][3*atomID] = oldint[i][j][3*atomID];
oldint[i][j-1][3*atomID+1] = oldint[i][j][3*atomID+1];
oldint[i][j-1][3*atomID+2] = oldint[i][j][3*atomID+2];
}
oldint[i][tnbe-1][3*atomID] = rint[3*atomID];
oldint[i][tnbe-1][3*atomID+1] = rint[3*atomID+1];
oldint[i][tnbe-1][3*atomID+2] = rint[3*atomID+2];
}
}
}
}
// Output results to files (fp1 and fp2) if time == nfreq
if (ntimestep % nfreq) return;
if (mode == DIFFUSIVITY)
write_diffusivity();
else if (mode == VISCOSITY)
write_viscosity();
else if (mode == THERMCOND)
write_thermcond();
}
/* ----------------------------------------------------------------------
calculate nvalid = next step on which end_of_step does something
lower bound is the smallest multiple of nevery larger than startstep
used only in the initialization
------------------------------------------------------------------------- */
bigint FixOrderN::nextvalid()
{
bigint nvalid = update->ntimestep;
if (startstep > nvalid) nvalid = startstep;
if (nvalid % nevery) nvalid = (nvalid/nevery)*nevery+nevery;
return nvalid;
}
/*-------------------------------------------------------------------------
Integrating Dynamical Variables According to the Simpson's Rule
------------------------------------------------------------------------- */
void FixOrderN::integrate()
{
if (icount == 0) {
for (int i = 0; i < vecsize; i++)
{
rint[i] = 0.0;
simpf0[i] = data[i];
}
} else if ((icount % 2) == 1) {
for (int i = 0; i < vecsize; i++)
simpf1[i] = data[i];
} else {
for (int i = 0; i < vecsize; i++)
{
// delta = dt*(f0+4f1+f2)/6
rint[i] += deltat*(simpf0[i]+4*simpf1[i]+data[i])/6.0;
simpf0[i] = data[i];
simpf1[i] = 0.0;
}
}
return;
}
/*-------------------------------------------------------------------------
Writing Order-n Results for Diffusivity into a File
------------------------------------------------------------------------- */
void FixOrderN::write_diffusivity()
{
fseek(fp1,filepos1,SEEK_SET);
fseek(fp2,filepos2,SEEK_SET);
int i, j, k, l, xyz;
// Writing the header
fprintf(fp1,"#Time\t");
fprintf(fp2,"#Time\t");
for ( k = 1; k <= ngroup; k++)
{
if (flag_Dxyz)
{
fprintf(fp1,"MSD__%s_x\t",group->names[groupinfo[k][0]]);
fprintf(fp1,"MSD__%s_y\t",group->names[groupinfo[k][0]]);
fprintf(fp1,"MSD__%s_z\t",group->names[groupinfo[k][0]]);
}
fprintf(fp1,"MSD__%s\t",group->names[groupinfo[k][0]]);
for ( l = k; l <= ngroup; l++)
{
if (flag_Dxyz)
{
fprintf(fp2,"MSD__%s_%s_x\t",
group->names[groupinfo[k][0]],group->names[groupinfo[l][0]]);
fprintf(fp2,"MSD__%s_%s_y\t",
group->names[groupinfo[k][0]],group->names[groupinfo[l][0]]);
fprintf(fp2,"MSD__%s_%s_z\t",
group->names[groupinfo[k][0]],group->names[groupinfo[l][0]]);
}
fprintf(fp2,"MSD__%s_%s\t",
group->names[groupinfo[k][0]],group->names[groupinfo[l][0]]);
}
}
fprintf(fp1,"\n");
fprintf(fp2,"\n");
for( i = 0;i < MIN(tnb,cnb); i++ )
{
cnbe = MIN(nbe[i],tnbe);
if (i == MIN(tnb,cnb)-1)
cnbe = cnbe-1;
for( j = 1; j <= cnbe; j++ )
{
time = (double) ((1.0*j)*(deltat)*pow(tnbe,i));
fprintf(fp1,format,time);
fprintf(fp2,format,time);
for( k = 1; k <= ngroup; k++ )
{
if (flag_Dxyz)
{
fprintf(fp1,format,PosC_iix[i][tnbe-j][k]/nsamp[i][tnbe-j]/2.0);
fprintf(fp1,format,PosC_iiy[i][tnbe-j][k]/nsamp[i][tnbe-j]/2.0);
fprintf(fp1,format,PosC_iiz[i][tnbe-j][k]/nsamp[i][tnbe-j]/2.0);
}
fprintf(fp1,format,PosC_ii[i][tnbe-j][k]/nsamp[i][tnbe-j]/6.0);
for( l = k; l <= ngroup; l++ )
{
if (flag_Dxyz)
{
fprintf(fp2,format,PosC_ijx[i][tnbe-j][k][l]/nsamp[i][tnbe-j]/2.0);
fprintf(fp2,format,PosC_ijy[i][tnbe-j][k][l]/nsamp[i][tnbe-j]/2.0);
fprintf(fp2,format,PosC_ijz[i][tnbe-j][k][l]/nsamp[i][tnbe-j]/2.0);
}
fprintf(fp2,format,PosC_ij[i][tnbe-j][k][l]/nsamp[i][tnbe-j]/6.0);
}
}
fprintf(fp1,"\n");
fprintf(fp2,"\n");
}
}
fflush(fp1);
fflush(fp2);
// delete all unnecessary text from the output file
long fileend1 = platform::ftell(fp1);
if (fileend1 > 0) platform::ftruncate(fp1,fileend1);
long fileend2 = platform::ftell(fp2);
if (fileend2 > 0) platform::ftruncate(fp2,fileend2);
}
/*-------------------------------------------------------------------------
Writing Order-n Results for Viscosity into a File
------------------------------------------------------------------------- */
void FixOrderN::write_viscosity()
{
fseek(fp1,filepos1,SEEK_SET);
int i, j, k;
double totalall;
double totaloff;
double stresscomp;
double volume = (domain->xprd * domain->yprd * domain->zprd);
double coef = (volume/2.0/boltz)*(1.0/nktv2p);
avgP = sumP / numP;
for (i=0; i<MIN(tnb,cnb); i++)
{
cnbe = MIN(nbe[i],tnbe);
if (i == MIN(tnb,cnb)-1)
cnbe = cnbe-1;
for (j = 1; j <= cnbe; j++) // Just neglect the first data on the right (k=2)
{
time = (double) ((1.0*j)*(deltat)*pow(tnbe,i));
fprintf(fp1,format,time);
// SHEAR VISCOSITY
totalall = 0.0;
totaloff = 0.0;
for (k = 0; k < 6; k++)
{
stresscomp = coef*samp[i][tnbe-j][k]/nsamp[i][tnbe-j];
if (k<3)
{
// implicit 4/3 contribution from diagonal
fprintf(fp1,format,stresscomp*3.0/4.0);
totalall += 1.0*1.0*stresscomp/10.0;
}
else
{
fprintf(fp1,format,stresscomp);
totalall += 2.0*1.0*stresscomp/10.0;
totaloff += stresscomp/3.0;
}
}
fprintf(fp1,format,totaloff);
fprintf(fp1,format,totalall);
// BULK VISCOSITY
double intp2 = samp[i][tnbe-j][vecsize-1]/nsamp[i][tnbe-j];
double intp = samp[i][tnbe-j][vecsize]/nsamp[i][tnbe-j];
double bulkvis = coef*(intp2 - 2.0*intp*(avgP*time) + (avgP*time)*(avgP*time));
fprintf(fp1,format,bulkvis);
fprintf(fp1,"\n");
}
}
fflush(fp1);
// delete all unnecessary text from the output file
long fileend1 = platform::ftell(fp1);
if (fileend1 > 0) platform::ftruncate(fp1,fileend1);
}
/*-------------------------------------------------------------------------
Writing Order-n Results for Thermal Conductivity into a File
------------------------------------------------------------------------- */
void FixOrderN::write_thermcond()
{
fseek(fp1,filepos1,SEEK_SET);
int i, j, k;
double totalcond;
double totalconvcond;
double fluxcomp;
double volume = (domain->xprd * domain->yprd * domain->zprd);
double coef = (1.0/volume/2.0/boltz);
for (i=0; i<MIN(tnb,cnb); i++)
{
cnbe = MIN(nbe[i],tnbe);
if (i == MIN(tnb,cnb)-1)
cnbe = cnbe-1;
for (j = 1; j <= cnbe; j++) // Just neglect the first data on the right (k=2)
{
time = (double) ((1.0*j)*(deltat)*pow(tnbe,i));
fprintf(fp1,format,time);
totalcond = 0.0;
totalconvcond = 0.0;
for (k = 0; k < 3; k++)
{
fluxcomp = coef*samp[i][tnbe-j][k]/nsamp[i][tnbe-j];
fprintf(fp1,format,fluxcomp);
totalcond += fluxcomp/3.0;
}
fprintf(fp1,format,totalcond);
if (flag_TCconv) // convective terms of the heat flux
{
for (k = 3; k < 6; k++)
{
fluxcomp = coef*samp[i][tnbe-j][k]/nsamp[i][tnbe-j];
fprintf(fp1,format,fluxcomp);
totalconvcond += fluxcomp/3.0;
}
fprintf(fp1,format,totalconvcond);
}
fprintf(fp1,"\n");
}
}
fflush(fp1);
// delete all unnecessary text from the output file
long fileend1 = platform::ftell(fp1);
if (fileend1 > 0) platform::ftruncate(fp1,fileend1);
}
/* ----------------------------------------------------------------------
Write Restart data to restart file
this is based on the command fix ave/correlate/long
------------------------------------------------------------------------- */
void FixOrderN::write_restart(FILE *fp)
{
if (me == 0)
{
int i, j, k, l;
int nsize = 1 + 6 + 4; // initial + general + specific variables
nsize += (tnb + tnb*tnbe + tnb*tnbe*vecsize + vecsize); // nbe,nsamp,oldint,rint
if ( (mode == VISCOSITY) || (mode == THERMCOND) ) {
nsize += (tnb*tnbe*sampsize + vecsize*3); // samp, simpf0, simpf1, data
} else if (mode == DIFFUSIVITY) {
nsize += (tnb*tnbe*tngroup*(4 + 5*tngroup)); // 4*PosC_ii,4*PosC_ij,PosCorrSum
nsize += (2*tngroup + 2*tnatom); // groupinfo, atomingroup
}
int n = 0; // the counter over all components of the array
double *list; // the array written to the restart file
memory->create(list,nsize,"fix/ordern:list");
// Parameters of the simulation //
list[n++] = mode;
list[n++] = tnb;
list[n++] = tnbe;
list[n++] = vecsize;
list[n++] = count;
list[n++] = cnb;
if ( (mode == VISCOSITY) || (mode == THERMCOND) ) {
list[n++] = sampsize;
list[n++] = icount;
list[n++] = sumP;
list[n++] = numP;
} else if (mode == DIFFUSIVITY) {
list[n++] = ngroup;