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support for density, mass, temperature values

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This commit is contained in:
Steve Plimpton
2022-08-15 16:02:46 -06:00
parent 9750c72822
commit ce4ca06035
3 changed files with 306 additions and 45 deletions
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1
src/compute_chunk_atom.cpp
View File

@ -629,6 +629,7 @@ void ComputeChunkAtom::compute_peratom()
to return the number of chunks, we first need to make certain
that compute_peratom() has been called.
------------------------------------------------------------------------- */
double ComputeChunkAtom::compute_scalar()
{
if (invoked_peratom != update->ntimestep) compute_peratom();

341
src/fix_ave_grid.cpp
View File

@ -19,6 +19,7 @@
#include "compute.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "grid2d.h"
#include "grid3d.h"
#include "input.h"
@ -169,11 +170,14 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
// optional args
/*
normflag = ALL;
scaleflag = ATOM;
ave = ONE;
nwindow = 0;
biasflag = 0;
id_bias = nullptr;
adof = domain->dimension;
cdof = 0.0;
while (iarg < nargnew) {
if (strcmp(arg[iarg],"norm") == 0) {
@ -189,6 +193,7 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
scaleflag = NOSCALE;
} else error->all(FLERR,"Illegal fix ave/grid command");
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/grid command");
if (strcmp(arg[iarg+1],"one") == 0) ave = ONE;
@ -203,9 +208,26 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
iarg += 2;
if (ave == WINDOW) iarg++;
} else if (strcmp(arg[iarg],"bias") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/grid command");
biasflag = 1;
id_bias = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"adof") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/grid command");
adof = utils::numeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else if (strcmp(arg[iarg],"cdof") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix ave/grid command");
cdof = utils::numeric(FLERR,arg[iarg+1],false,lmp);
iarg += 2;
} else error->all(FLERR,"Illegal fix ave/grid command");
}
*/
// if wildcard expansion occurred, free earg memory from exapnd_args()
@ -229,6 +251,21 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
if (dimension == 2 && nzgrid != 1)
error->all(FLERR,"Fix ave/grid grid Nz must be 1 for 2d simulation");
if (biasflag) {
tbias = modify->get_compute_by_id(id_bias);
if (!tbias)
error->all(FLERR,"Could not find compute ID for temperature bias");
if (tbias->tempflag == 0)
error->all(FLERR,"Bias compute does not calculate temperature");
if (tbias->tempbias == 0)
error->all(FLERR,"Bias compute does not calculate a velocity bias");
}
if (normflag != ALL)
error->all(FLERR,"Fix ave/grid norm all is required for now");
if (normflag != ONE)
error->all(FLERR,"Fix ave/grid ave one is required for now");
// error checks for ATOM mode
if (modeatom) {
@ -517,6 +554,12 @@ int FixAveGrid::setmask()
void FixAveGrid::init()
{
if (biasflag) {
tbias = modify->get_compute_by_id(id_bias);
if (!tbias)
error->all(FLERR,"Could not find compute ID for temperature bias");
}
// set indices and check validity of all computes,fixes,variables
for (int m = 0; m < nvalues; m++) {
@ -579,6 +622,10 @@ void FixAveGrid::init()
}
}
// set triclinic flag
triclinic = domain->triclinic;
// need to reset nvalid if nvalid < ntimestep b/c minimize was performed
if (nvalid < update->ntimestep) {
@ -653,12 +700,33 @@ void FixAveGrid::end_of_step()
if (ngridout == 0) return;
// average the final results for the Nfreq output
// for ATOM mode, divide total values by total count
// for GRID mode, divide total values by # of samples
// average the final results across Nrepeat samples
// for ATOM mode, result = total_value / total_count
// exception is DENSITY_NUMBER:
// result = value / (current binvol * Nrepeat)
// exception is DENSITY_MASS:
// result = (value * mv2d) / (current binvol * Nrepeat)
// exception is TEMPERATURE:
// result = (value * mvv2e) / (Nrepeat*cdof + adof*count) * boltz)
// for GRID mode, final is total value / Nrepeat
if (modeatom) {
double count,invcount;
double mvv2e = force->mvv2e;
double mv2d = force->mv2d;
double boltz = force->boltz;
double count,invcount,norm;
double repeat = nrepeat;
double invrepeat = 1.0/nrepeat;
double *prd = domain->prd;
double dx = prd[0]/nxgrid;
double dy = prd[1]/nygrid;
double dz = prd[2]/nzgrid;
double binvol;
if (dimension == 2) binvol = dx*dy;
else binvol = dx*dy*dz;
if (dimension == 2) {
if (nvalues == 1) {
@ -666,8 +734,16 @@ void FixAveGrid::end_of_step()
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
count = count2d[iy][ix];
if (count) {
vec2d[iy][ix] /= count;
count2d[iy][iz] /= nrepeat;
if (which[0] == ArgInfo::DENSITY_NUMBER)
norm = 1.0 / (binvol * repeat);
else if (which[0] == ArgInfo::DENSITY_MASS)
norm = mv2d / (binvol * nrepeat);
else if (which[0] == ArgInfo::TEMPERATURE)
norm = mvv2e /((repeat*cdof + adof*count) * boltz);
else
norm = 1.0/count;
vec2d[iy][ix] *= norm;
count2d[iy][iz] *= invrepeat;
}
}
} else {
@ -676,9 +752,18 @@ void FixAveGrid::end_of_step()
count = count2d[iy][ix];
if (count) {
invcount = 1.0/count;
for (m = 0; m <= nvalues; m++)
array2d[iy][ix][m] *= invcount;
count2d[iy][iz] /= nrepeat;
for (m = 0; m <= nvalues; m++) {
if (which[m] == ArgInfo::DENSITY_NUMBER)
norm = 1.0 / (binvol * repeat);
else if (which[m] == ArgInfo::DENSITY_MASS)
norm = mv2d / (binvol * nrepeat);
else if (which[m] == ArgInfo::TEMPERATURE)
norm = mvv2e /((repeat*cdof + adof*count) * boltz);
else
norm = 1.0/count;
array2d[iy][ix][m] *= norm;
}
count2d[iy][iz] *= invrepeat;
}
}
}
@ -689,8 +774,16 @@ void FixAveGrid::end_of_step()
for (ix = nxlo_in; ix <= nxhi_in; ix++) {
count = count3d[iz][iy][ix];
if (count) {
vec3d[iz][iy][ix] /= count;
count3d[iz][iy][iz] /= nrepeat;
if (which[0] == ArgInfo::DENSITY_NUMBER)
norm = 1.0 / (binvol * repeat);
else if (which[0] == ArgInfo::DENSITY_MASS)
norm = mv2d / (binvol * nrepeat);
else if (which[0] == ArgInfo::TEMPERATURE)
norm = mvv2e /((repeat*cdof + adof*count) * boltz);
else
norm = 1.0/count;
vec3d[iz][iy][ix] *= norm;
count3d[iz][iy][iz] *= invrepeat;
}
}
} else {
@ -700,9 +793,18 @@ void FixAveGrid::end_of_step()
count = count3d[iz][iy][ix];
if (count) {
invcount = 1.0/count;
for (m = 0; m <= nvalues; m++)
array3d[iz][iy][ix][m] *= invcount;
count3d[iz][iy][iz] /= nrepeat;
for (m = 0; m <= nvalues; m++) {
if (which[m] == ArgInfo::DENSITY_NUMBER)
norm = 1.0 / (binvol * repeat);
else if (which[m] == ArgInfo::DENSITY_MASS)
norm = mv2d / (binvol * nrepeat);
else if (which[m] == ArgInfo::TEMPERATURE)
norm = mvv2e /((repeat*cdof + adof*count) * boltz);
else
norm = 1.0/count;
array3d[iz][iy][ix][m] *= norm;
}
count3d[iz][iy][iz] *= invrepeat;
}
}
}
@ -755,10 +857,20 @@ void FixAveGrid::atom2grid()
// also count atoms contributing to each bin
// check if any atom is out of bounds for my local grid
double *boxlo = domain->boxlo;
double dxinv = nxgrid/domain->xprd;
double dyinv = nygrid/domain->yprd;
double dzinv = nzgrid/domain->zprd;
double *boxlo,*prd;
int *periodicity = domain->periodicity;
if (triclinic) {
boxlo = domain->boxlo_lamda;
prd = domain->prd_lamda;
} else {
boxlo = domain->boxlo;
prd = domain->prd;
}
double dxinv = nxgrid/prd[0];
double dyinv = nygrid/prd[1];
double dzinv = nzgrid/prd[2];
double **x = atom->x;
int *mask = atom->mask;
@ -766,42 +878,69 @@ void FixAveGrid::atom2grid()
if (nlocal > maxatom) {
memory->destroy(bin);
memory->destroy(skip);
maxatom = atom->nmax;
memory->create(bin,maxatom,dimension,"ave/grid:bin");
memory->create(skip,maxatom,"ave/grid:skip");
}
if (triclinic) domain->x2lamda(nlocal);
int flag = 0;
if (dimension == 2) {
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
ix = static_cast<int> ((x[i][0]-boxlo[0])*dxinv + shift) - OFFSET;
iy = static_cast<int> ((x[i][1]-boxlo[1])*dyinv + shift) - OFFSET;
if (ix < nxlo_out || ix > nxhi_out ||
iy < nylo_out || iy > nyhi_out) {
flag = 1;
if (!(mask[i] & groupbit)) {
skip[i] = 1;
continue;
}
ix = static_cast<int> ((x[i][0]-boxlo[0])*dxinv + shift) - OFFSET;
iy = static_cast<int> ((x[i][1]-boxlo[1])*dyinv + shift) - OFFSET;
if (ix < nxlo_out || ix > nxhi_out) {
if (periodicity[0]) flag = 1;
else skip[i] = 1;
continue;
}
if (iy < nylo_out || iy > nyhi_out) {
if (periodicity[1]) flag = 1;
else skip[i] = 1;
continue;
}
skip[i] = 0;
count2d[iy][ix] += 1.0;
bin[i][0] = iy;
bin[i][1] = ix;
}
} else {
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
if (!(mask[i] & groupbit)) {
skip[i] = 1;
continue;
}
ix = static_cast<int> ((x[i][0]-boxlo[0])*dxinv + shift) - OFFSET;
iy = static_cast<int> ((x[i][1]-boxlo[1])*dyinv + shift) - OFFSET;
iz = static_cast<int> ((x[i][2]-boxlo[2])*dzinv + shift) - OFFSET;
if (ix < nxlo_out || ix > nxhi_out ||
iy < nylo_out || iy > nyhi_out ||
iz < nzlo_out || iz > nzhi_out) {
flag = 1;
if (ix < nxlo_out || ix > nxhi_out) {
if (periodicity[0]) flag = 1;
else skip[i] = 1;
continue;
}
if (iy < nylo_out || iy > nyhi_out) {
if (periodicity[1]) flag = 1;
else skip[i] = 1;
continue;
}
if (iz < nzlo_out || iz > nyhi_out) {
if (periodicity[2]) flag = 1;
else skip[i] = 1;
continue;
}
skip[i] = 0;
count3d[iz][iy][ix] += 1.0;
bin[i][0] = iz;
bin[i][1] = iy;
@ -810,6 +949,7 @@ void FixAveGrid::atom2grid()
}
if (flag) error->one(FLERR,"Out of range fix ave/grid atoms");
if (triclinic) domain->lamda2x(nlocal);
// loop over user-specified values
@ -817,8 +957,11 @@ void FixAveGrid::atom2grid()
n = value2index[m];
j = argindex[m];
// X,V,F adds coord,velocity,force to value
if (which[m] == ArgInfo::X || which[m] == ArgInfo::V ||
which[m] == ArgInfo::F) {
double **attribute;
if (which[m] == ArgInfo::X) attribute = atom->x;
else if (which[m] == ArgInfo::V) attribute = atom->v;
@ -827,27 +970,137 @@ void FixAveGrid::atom2grid()
if (dimension == 2) {
if (nvalues == 1) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
if (!skip[i])
vec2d[bin[i][0]][bin[i][1]] += attribute[i][j];
}
} else
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
if (skip[i])
array2d[bin[i][0]][bin[i][1]][m] += attribute[i][j];
}
} else {
if (nvalues == 1) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
if (!skip[i])
vec3d[bin[i][0]][bin[i][1]][bin[i][2]] += attribute[i][j];
}
} else
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
if (!skip[i])
array3d[bin[i][0]][bin[i][1]][bin[i][2]][m] += attribute[i][j];
}
}
// DENSITY_NUMBER adds 1 to value
// DENSITY_MASS or MASS adds mass to value
} else if ((which[m] == ArgInfo::DENSITY_NUMBER) ||
(which[m] == ArgInfo::DENSITY_MASS) ||
(which[m] == ArgInfo::MASS)) {
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
double one;
if (dimension == 2) {
if (nvalues == 1) {
for (i = 0; i < nlocal; i++) {
if (!skip[i]) {
if (which[m] == ArgInfo::DENSITY_NUMBER) one = 1.0;
else if (rmass) one = rmass[i];
else one = mass[type[i]];
vec2d[bin[i][0]][bin[i][1]] += one;
}
}
} else
for (i = 0; i < nlocal; i++) {
if (skip[i]) {
if (which[m] == ArgInfo::DENSITY_NUMBER) one = 1.0;
else if (rmass) one = rmass[i];
else one = mass[type[i]];
array2d[bin[i][0]][bin[i][1]][m] += one;
}
}
} else {
if (nvalues == 1) {
for (i = 0; i < nlocal; i++) {
if (!skip[i]) {
if (which[m] == ArgInfo::DENSITY_NUMBER) one = 1.0;
else if (rmass) one = rmass[i];
else one = mass[type[i]];
vec3d[bin[i][0]][bin[i][1]][bin[i][2]] += one;
}
}
} else
for (i = 0; i < nlocal; i++) {
if (!skip[i]) {
if (which[m] == ArgInfo::DENSITY_NUMBER) one = 1.0;
else if (rmass) one = rmass[i];
else one = mass[type[i]];
array3d[bin[i][0]][bin[i][1]][bin[i][2]][m] += one;
}
}
}
// TEMPERATURE adds KE to values
// subtract and restore velocity bias if requested
} else if (which[m] == ArgInfo::TEMPERATURE) {
if (biasflag) {
if (tbias->invoked_scalar != update->ntimestep) tbias->compute_scalar();
tbias->remove_bias_all();
}
double **v = atom->v;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
double vsq,one;
if (dimension == 2) {
if (nvalues == 1) {
for (i = 0; i < nlocal; i++) {
if (!skip[i]) {
vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
if (rmass) one = rmass[i];
else one = mass[type[i]];
vec2d[bin[i][0]][bin[i][1]] += one*vsq;
}
}
} else
for (i = 0; i < nlocal; i++) {
if (skip[i]) {
vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
if (rmass) one = rmass[i];
else one = mass[type[i]];
array2d[bin[i][0]][bin[i][1]][m] += one*vsq;;
}
}
} else {
if (nvalues == 1) {
for (i = 0; i < nlocal; i++) {
if (!skip[i]) {
vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
if (rmass) one = rmass[i];
else one = mass[type[i]];
vec3d[bin[i][0]][bin[i][1]][bin[i][2]] += one*vsq;
}
}
} else
for (i = 0; i < nlocal; i++) {
if (!skip[i]) {
vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
if (rmass) one = rmass[i];
else one = mass[type[i]];
array3d[bin[i][0]][bin[i][1]][bin[i][2]][m] += one*vsq;
}
}
}
if (biasflag) tbias->restore_bias_all();
// per-atom compute or fix or variable
// invoke compute if not previously invoked
// evaluate atom-style variable
@ -883,26 +1136,26 @@ void FixAveGrid::atom2grid()
if (nvalues == 1) {
if (j == 0) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
if (!skip[i])
vec2d[bin[i][0]][bin[i][1]] += ovector[i];
}
} else {
int jm1 = j = 1;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
if (!skip[i])
vec2d[bin[i][0]][bin[i][1]] += oarray[i][jm1];
}
}
} else {
if (j == 0) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
if (!skip[i])
array2d[bin[i][0]][bin[i][1]][m] += ovector[i];
}
} else {
int jm1 = j - 1;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
if (!skip[i])
array2d[bin[i][0]][bin[i][1]][m] += oarray[i][jm1];
}
}
@ -912,26 +1165,26 @@ void FixAveGrid::atom2grid()
if (nvalues == 1) {
if (j == 0) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
if (!skip[i])
vec3d[bin[i][0]][bin[i][1]][bin[i][2]] += ovector[i];
}
} else {
int jm1 = j - 1;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
if (!skip[i])
vec3d[bin[i][0]][bin[i][1]][bin[i][2]] += oarray[i][jm1];
}
}
} else {
if (j == 0) {
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
if (!skip[i])
array3d[bin[i][0]][bin[i][1]][bin[i][2]][m] += ovector[i];
}
} else {
int jm1 = j - 1;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit)
if (!skip[i])
array3d[bin[i][0]][bin[i][1]][bin[i][2]][m] += oarray[i][jm1];
}
}

9
src/fix_ave_grid.h
View File

@ -52,7 +52,13 @@ class FixAveGrid : public Fix {
bigint nvalid, nvalid_last;
int modeatom,modegrid;
int normflag,scaleflag,ave,nwindow;
int dimension;
int biasflag;
char *id_bias;
class Compute *tbias; // ptr to additional bias compute
double adof,cdof;
int dimension,triclinic;
int *which, *argindex;
char **ids;
@ -73,6 +79,7 @@ class FixAveGrid : public Fix {
double **count2d,***count3d;
int **bin;
int *skip;
int maxatom;
double *vresult;