more normalization
This commit is contained in:
Steve Plimpton
@ -646,7 +646,7 @@ void FixAveGrid::end_of_step()
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// for ATOM mode, perform ghost to owned grid communication
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// done every sample for norm = SAMPLE, else once per Nfreq epoch
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// nvalues + 1 for atom count
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// nvalues+1 includes atom count
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if (modeatom) {
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if (dimension == 2)
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@ -658,15 +658,11 @@ void FixAveGrid::end_of_step()
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}
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// for norm = SAMPLE, sum per-sample values and count to per-epoch
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// for ATOM mode, also need to normalize per-sample values
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// for ATOM mode, also need to normalize for single sample
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// then return if irepeat < nrepeat
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if (normflag == SAMPLE) {
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if (modeatom) normalize_atom(1);
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sum_sample_to_epoch();
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if (irepeat < nrepeat && (normflag == ALL || normflag == NONORM)) {
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@ -686,149 +682,24 @@ void FixAveGrid::end_of_step()
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if (ngridout == 0) return;
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// average the final results across Nrepeat samples
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// for ATOM mode, result = total_value / total_count
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// exception is DENSITY_NUMBER:
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// result = value / (current binvol * Nrepeat)
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// exception is DENSITY_MASS:
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// result = (value * mv2d) / (current binvol * Nrepeat)
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// exception is TEMPERATURE:
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// result = (value * mvv2e) / (Nrepeat*cdof + adof*count) * boltz)
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// for GRID mode, final is total value / Nrepeat
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// average the final results for the entire epoch
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// for norm = ALL, normalize values_sample by Nrepeat and counts
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// for norm = SAMPLE, normalize values_epoch by Nrepeat
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if (modeatom) {
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double mvv2e = force->mvv2e;
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double mv2d = force->mv2d;
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double boltz = force->boltz;
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double count,norm;
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double repeat = nrepeat;
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double invrepeat = 1.0/nrepeat;
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double *prd = domain->prd;
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double dx = prd[0]/nxgrid;
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double dy = prd[1]/nygrid;
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double dz = prd[2]/nzgrid;
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double binvol;
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if (dimension == 2) binvol = dx*dy;
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else binvol = dx*dy*dz;
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if (dimension == 2) {
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if (nvalues == 1) {
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for (iy = nylo_in; iy <= nyhi_in; iy++)
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for (ix = nxlo_in; ix <= nxhi_in; ix++) {
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count = count2d[iy][ix];
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if (count) {
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if (which[0] == ArgInfo::DENSITY_NUMBER)
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norm = 1.0 / (binvol * repeat);
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else if (which[0] == ArgInfo::DENSITY_MASS)
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norm = mv2d / (binvol * nrepeat);
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else if (which[0] == ArgInfo::TEMPERATURE)
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norm = mvv2e /((repeat*cdof + adof*count) * boltz);
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else
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norm = 1.0/count;
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vec2d[iy][ix] *= norm;
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count2d[iy][ix] *= invrepeat;
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}
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}
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} else {
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for (iy = nylo_in; iy <= nyhi_in; iy++)
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for (ix = nxlo_in; ix <= nxhi_in; ix++) {
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count = count2d[iy][ix];
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if (count) {
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for (m = 0; m <= nvalues; m++) {
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if (which[m] == ArgInfo::DENSITY_NUMBER)
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norm = 1.0 / (binvol * repeat);
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else if (which[m] == ArgInfo::DENSITY_MASS)
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norm = mv2d / (binvol * nrepeat);
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else if (which[m] == ArgInfo::TEMPERATURE)
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norm = mvv2e /((repeat*cdof + adof*count) * boltz);
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else
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norm = 1.0/count;
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array2d[iy][ix][m] *= norm;
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}
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count2d[iy][ix] *= invrepeat;
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}
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}
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}
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} else {
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if (nvalues == 1) {
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for (iz = nzlo_in; iz <= nzhi_in; iz++)
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for (iy = nylo_in; iy <= nyhi_in; iy++)
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for (ix = nxlo_in; ix <= nxhi_in; ix++) {
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count = count3d[iz][iy][ix];
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if (count) {
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if (which[0] == ArgInfo::DENSITY_NUMBER)
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norm = 1.0 / (binvol * repeat);
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else if (which[0] == ArgInfo::DENSITY_MASS)
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norm = mv2d / (binvol * nrepeat);
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else if (which[0] == ArgInfo::TEMPERATURE)
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norm = mvv2e /((repeat*cdof + adof*count) * boltz);
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else
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norm = 1.0/count;
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vec3d[iz][iy][ix] *= norm;
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count3d[iz][iy][ix] *= invrepeat;
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}
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}
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} else {
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for (iz = nzlo_in; iz <= nzhi_in; iz++)
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for (iy = nylo_in; iy <= nyhi_in; iy++)
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for (ix = nxlo_in; ix <= nxhi_in; ix++) {
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count = count3d[iz][iy][ix];
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if (count) {
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for (m = 0; m <= nvalues; m++) {
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if (which[m] == ArgInfo::DENSITY_NUMBER)
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norm = 1.0 / (binvol * repeat);
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else if (which[m] == ArgInfo::DENSITY_MASS)
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norm = mv2d / (binvol * nrepeat);
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else if (which[m] == ArgInfo::TEMPERATURE)
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norm = mvv2e /((repeat*cdof + adof*count) * boltz);
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else
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norm = 1.0/count;
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array3d[iz][iy][ix][m] *= norm;
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}
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count3d[iz][iy][ix] *= invrepeat;
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}
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}
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}
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}
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if (normflag == ALL) normalize_atom(nrepeat);
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else if (normflag == SAMPLE)
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normalize_grid(vec2d_epoch,array2d_epoch,vec3d_epoch,array3d_epoch);
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else if (normflag == NONORM) normalize_atom();
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}
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if (modegrid) {
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double invrepeat = 1.0/nrepeat;
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if (modegrid)
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normalize_grid(vec2d_sample,array2d_sample,vec3d_sample,array3d_sample);
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// create Nfreq output
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if (dimension == 2) {
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if (nvalues == 1) {
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for (iy = nylo_in; iy <= nyhi_in; iy++)
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for (ix = nxlo_in; ix <= nxhi_in; ix++)
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vec2d[iy][ix] *= invrepeat;
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} else {
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for (iy = nylo_in; iy <= nyhi_in; iy++)
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for (ix = nxlo_in; ix <= nxhi_in; ix++)
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for (m = 0; m <= nvalues; m++)
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array2d[iy][ix][m] *= invrepeat;
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}
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} else {
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if (nvalues == 1) {
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for (iz = nzlo_in; iz <= nzhi_in; iz++)
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for (iy = nylo_in; iy <= nyhi_in; iy++)
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for (ix = nxlo_in; ix <= nxhi_in; ix++)
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vec3d[iz][iy][ix] *= invrepeat;
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} else {
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for (iz = nzlo_in; iz <= nzhi_in; iz++)
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for (iy = nylo_in; iy <= nyhi_in; iy++)
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for (ix = nxlo_in; ix <= nxhi_in; ix++)
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for (m = 0; m <= nvalues; m++)
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array3d[iz][iy][ix][m] *= invrepeat;
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}
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}
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}
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}
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/* ----------------------------------------------------------------------
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@ -1430,6 +1301,167 @@ void FixAveGrid::sum_sample_to_epoch()
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}
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}
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/* ----------------------------------------------------------------------
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normalize grid values and per-cell counts for ATOM mode for owned cells
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flag = SAMPLE or EPOCH
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set repeat = 1 for SAMPLE, Nrepeat for EPOCH
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sample_value & count are either for one sample or summed over epoch
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result = sample_value / count
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exception is DENSITY_NUMBER:
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result = value / (current binvol * Nrepeat)
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exception is DENSITY_MASS:
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result = (value * mv2d) / (current binvol * Nrepeat)
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exception is TEMPERATURE:
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result = (value * mvv2e) / (Nrepeat*cdof + adof*count) * boltz)
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------------------------------------------------------------------------- */
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void FixAveGrid::normalize_atom(int flag)
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{
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int ix,iy,iz,m;
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double count,norm;
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double repeat,invrepeat;
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double mvv2e = force->mvv2e;
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double mv2d = force->mv2d;
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double boltz = force->boltz;
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if (flag == EPOCH) {
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repeat = nrepeat;
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invrepeat = 1.0/nrepeat;
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} else if (flag == SAMPLE) {
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repeat = invrepeat = 1.0;
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}
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double *prd = domain->prd;
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double dx = prd[0]/nxgrid;
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double dy = prd[1]/nygrid;
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double dz = prd[2]/nzgrid;
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double binvol;
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if (dimension == 2) binvol = dx*dy;
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else binvol = dx*dy*dz;
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if (dimension == 2) {
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if (nvalues == 1) {
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for (iy = nylo_in; iy <= nyhi_in; iy++)
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for (ix = nxlo_in; ix <= nxhi_in; ix++) {
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count = count2d[iy][ix];
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if (count) {
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if (which[0] == ArgInfo::DENSITY_NUMBER)
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norm = 1.0 / (binvol * repeat);
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else if (which[0] == ArgInfo::DENSITY_MASS)
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norm = mv2d / (binvol * nrepeat);
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else if (which[0] == ArgInfo::TEMPERATURE)
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norm = mvv2e /((repeat*cdof + adof*count) * boltz);
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else
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norm = 1.0/count;
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vec2d_sample[iy][ix] *= norm;
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count2d_sample[iy][ix] *= invrepeat;
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}
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}
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} else {
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for (iy = nylo_in; iy <= nyhi_in; iy++)
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for (ix = nxlo_in; ix <= nxhi_in; ix++) {
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count = count2d[iy][ix];
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if (count) {
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for (m = 0; m <= nvalues; m++) {
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if (which[m] == ArgInfo::DENSITY_NUMBER)
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norm = 1.0 / (binvol * repeat);
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else if (which[m] == ArgInfo::DENSITY_MASS)
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norm = mv2d / (binvol * nrepeat);
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else if (which[m] == ArgInfo::TEMPERATURE)
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norm = mvv2e /((repeat*cdof + adof*count) * boltz);
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else
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norm = 1.0/count;
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array2d_sample[iy][ix][m] *= norm;
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}
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count2d_sample[iy][ix] *= invrepeat;
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}
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}
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}
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} else {
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if (nvalues == 1) {
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for (iz = nzlo_in; iz <= nzhi_in; iz++)
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for (iy = nylo_in; iy <= nyhi_in; iy++)
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for (ix = nxlo_in; ix <= nxhi_in; ix++) {
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count = count3d[iz][iy][ix];
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if (count) {
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if (which[0] == ArgInfo::DENSITY_NUMBER)
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norm = 1.0 / (binvol * repeat);
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else if (which[0] == ArgInfo::DENSITY_MASS)
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norm = mv2d / (binvol * nrepeat);
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else if (which[0] == ArgInfo::TEMPERATURE)
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norm = mvv2e /((repeat*cdof + adof*count) * boltz);
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else
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norm = 1.0/count;
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vec3d_sample[iz][iy][ix] *= norm;
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count3d_value[iz][iy][ix] *= invrepeat;
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}
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}
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} else {
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for (iz = nzlo_in; iz <= nzhi_in; iz++)
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for (iy = nylo_in; iy <= nyhi_in; iy++)
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for (ix = nxlo_in; ix <= nxhi_in; ix++) {
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count = count3d[iz][iy][ix];
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if (count) {
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for (m = 0; m <= nvalues; m++) {
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if (which[m] == ArgInfo::DENSITY_NUMBER)
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norm = 1.0 / (binvol * repeat);
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else if (which[m] == ArgInfo::DENSITY_MASS)
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norm = mv2d / (binvol * nrepeat);
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else if (which[m] == ArgInfo::TEMPERATURE)
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norm = mvv2e /((repeat*cdof + adof*count) * boltz);
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else
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norm = 1.0/count;
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array3d_sample[iz][iy][ix][m] *= norm;
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}
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count3d_sample[iz][iy][ix] *= invrepeat;
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}
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}
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}
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}
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}
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/* ----------------------------------------------------------------------
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normalize grid values by Nrepeat
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used for GRID mode
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used for ATOM MODE with norm = SAMPLE
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------------------------------------------------------------------------- */
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void FixAveGrid::normalize_grid(double **v2d, double ***a2d,
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double ***v3d, double ****a3d)
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{
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int ix,iy,iz,m;
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double invrepeat = 1.0/nrepeat;
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if (dimension == 2) {
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if (nvalues == 1) {
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for (iy = nylo_in; iy <= nyhi_in; iy++)
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for (ix = nxlo_in; ix <= nxhi_in; ix++)
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v2d[iy][ix] *= invrepeat;
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} else {
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for (iy = nylo_in; iy <= nyhi_in; iy++)
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for (ix = nxlo_in; ix <= nxhi_in; ix++)
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for (m = 0; m <= nvalues; m++)
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a2d[iy][ix][m] *= invrepeat;
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}
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} else {
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if (nvalues == 1) {
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for (iz = nzlo_in; iz <= nzhi_in; iz++)
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for (iy = nylo_in; iy <= nyhi_in; iy++)
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for (ix = nxlo_in; ix <= nxhi_in; ix++)
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v3d[iz][iy][ix] *= invrepeat;
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} else {
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for (iz = nzlo_in; iz <= nzhi_in; iz++)
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for (iy = nylo_in; iy <= nyhi_in; iy++)
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for (ix = nxlo_in; ix <= nxhi_in; ix++)
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for (m = 0; m <= nvalues; m++)
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a3d[iz][iy][ix][m] *= invrepeat;
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}
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}
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}
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/* ----------------------------------------------------------------------
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pack ghost values into buf to send to another proc
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nvalues per grid point + count
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