debug of fix ave/grid
This commit is contained in:
Steve Plimpton
@ -407,7 +407,12 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
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nxlo_in, nxhi_in, nylo_in, nyhi_in,
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nxlo_out, nxhi_out, nylo_out, nyhi_out);
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// ngrid_buf12 converted to nvalues + count
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grid2d->setup(ngrid_buf1, ngrid_buf2);
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ngrid_buf1 *= nvalues + 1;
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ngrid_buf2 *= nvalues + 1;
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memory->create(grid_buf1, ngrid_buf1, "ave/grid:grid_buf1");
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memory->create(grid_buf2, ngrid_buf2, "ave/grid:grid_buf2");
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@ -419,7 +424,12 @@ FixAveGrid::FixAveGrid(LAMMPS *lmp, int narg, char **arg) :
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nxlo_out, nxhi_out, nylo_out, nyhi_out,
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nzlo_out, nzhi_out);
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// ngrid_buf12 converted to nvalues + count
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grid3d->setup(ngrid_buf1, ngrid_buf2);
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ngrid_buf1 *= nvalues + 1;
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ngrid_buf2 *= nvalues + 1;
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memory->create(grid_buf1, ngrid_buf1, "ave/grid:grid_buf1");
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memory->create(grid_buf2, ngrid_buf2, "ave/grid:grid_buf2");
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@ -791,7 +801,7 @@ void FixAveGrid::atom2grid()
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}
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skip[i] = 0;
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count2d[iy][ix] += 1.0;
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count2d_sample[iy][ix] += 1.0;
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bin[i][0] = iy;
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bin[i][1] = ix;
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}
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@ -824,7 +834,7 @@ void FixAveGrid::atom2grid()
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}
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skip[i] = 0;
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count3d[iz][iy][ix] += 1.0;
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count3d_sample[iz][iy][ix] += 1.0;
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bin[i][0] = iz;
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bin[i][1] = iy;
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bin[i][2] = ix;
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@ -857,7 +867,7 @@ void FixAveGrid::atom2grid()
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}
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} else
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for (i = 0; i < nlocal; i++) {
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if (skip[i])
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if (!skip[i])
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array2d_sample[bin[i][0]][bin[i][1]][m] += attribute[i][j];
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}
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} else {
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@ -897,7 +907,7 @@ void FixAveGrid::atom2grid()
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}
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} else
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for (i = 0; i < nlocal; i++) {
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if (skip[i]) {
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if (!skip[i]) {
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if (which[m] == ArgInfo::DENSITY_NUMBER) one = 1.0;
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else if (rmass) one = rmass[i];
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else one = mass[type[i]];
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@ -953,7 +963,7 @@ void FixAveGrid::atom2grid()
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}
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} else
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for (i = 0; i < nlocal; i++) {
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if (skip[i]) {
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if (!skip[i]) {
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vsq = v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2];
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if (rmass) one = rmass[i];
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else one = mass[type[i]];
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@ -1292,35 +1302,35 @@ void FixAveGrid::allocate_grid()
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void FixAveGrid::deallocate_grid()
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{
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memory->destroy2d_offset(vec2d,nylo_out,nxlo_out);
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memory->destroy2d_offset(array2d,nylo_out,nxlo_out);
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memory->destroy3d_offset_last(array2d,nylo_out,nxlo_out);
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memory->destroy2d_offset(count2d,nylo_out,nxlo_out);
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memory->destroy2d_offset(vec2d_sample,nylo_out,nxlo_out);
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memory->destroy2d_offset(array2d_sample,nylo_out,nxlo_out);
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memory->destroy3d_offset_last(array2d_sample,nylo_out,nxlo_out);
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memory->destroy2d_offset(count2d_sample,nylo_out,nxlo_out);
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memory->destroy2d_offset(vec2d_epoch,nylo_out,nxlo_out);
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memory->destroy2d_offset(array2d_epoch,nylo_out,nxlo_out);
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memory->destroy3d_offset_last(array2d_epoch,nylo_out,nxlo_out);
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memory->destroy2d_offset(count2d_epoch,nylo_out,nxlo_out);
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memory->destroy2d_offset(vec2d_running,nylo_out,nxlo_out);
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memory->destroy2d_offset(array2d_running,nylo_out,nxlo_out);
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memory->destroy3d_offset_last(array2d_running,nylo_out,nxlo_out);
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memory->destroy2d_offset(count2d_running,nylo_out,nxlo_out);
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memory->destroy3d_offset(vec3d,nzlo_out,nylo_out,nxlo_out);
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memory->destroy3d_offset(array3d,nzlo_out,nylo_out,nxlo_out);
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memory->destroy4d_offset_last(array3d,nzlo_out,nylo_out,nxlo_out);
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memory->destroy3d_offset(count3d,nzlo_out,nylo_out,nxlo_out);
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memory->destroy3d_offset(vec3d_sample,nzlo_out,nylo_out,nxlo_out);
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memory->destroy3d_offset(array3d_sample,nzlo_out,nylo_out,nxlo_out);
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memory->destroy4d_offset_last(array3d_sample,nzlo_out,nylo_out,nxlo_out);
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memory->destroy3d_offset(count3d_sample,nzlo_out,nylo_out,nxlo_out);
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memory->destroy3d_offset(vec3d_epoch,nzlo_out,nylo_out,nxlo_out);
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memory->destroy3d_offset(array3d_epoch,nzlo_out,nylo_out,nxlo_out);
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memory->destroy4d_offset_last(array3d_epoch,nzlo_out,nylo_out,nxlo_out);
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memory->destroy3d_offset(count3d_epoch,nzlo_out,nylo_out,nxlo_out);
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memory->destroy3d_offset(vec3d_running,nzlo_out,nylo_out,nxlo_out);
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memory->destroy3d_offset(array3d_running,nzlo_out,nylo_out,nxlo_out);
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memory->destroy4d_offset_last(array3d_running,nzlo_out,nylo_out,nxlo_out);
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memory->destroy3d_offset(count3d_running,nzlo_out,nylo_out,nxlo_out);
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}
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@ -1448,6 +1458,150 @@ void FixAveGrid::copy_epoch_to_sample()
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}
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}
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/* ----------------------------------------------------------------------
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copy sample grid values to output grid, just for owned grid cells
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if ATOM mode, also copy per-cell counts
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------------------------------------------------------------------------- */
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void FixAveGrid::copy_sample_to_output()
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{
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int ix,iy,iz,m;
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if (!ngridout) return;
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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] = vec2d_sample[iy][ix];
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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] = array2d_sample[iy][ix][m];
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}
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if (modeatom)
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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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count2d[iy][ix] = count2d_sample[iy][ix];
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} else {
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if (nvalues == 1) {
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for (iz = nylo_in; iz <= nyhi_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] = vec3d_sample[iz][iy][ix];
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} else {
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for (iz = nylo_in; iz <= nyhi_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] = array3d_sample[iz][iy][ix][m];
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}
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if (modeatom)
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for (iz = nylo_in; iz <= nyhi_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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count3d[iz][iy][ix] = count3d_sample[iz][iy][ix];
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}
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}
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/* ----------------------------------------------------------------------
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copy running grid values to output grid, just for owned grid cells
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if ATOM mode, also copy per-cell counts
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------------------------------------------------------------------------- */
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void FixAveGrid::copy_running_to_output()
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{
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int ix,iy,iz,m;
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if (!ngridout) return;
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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] = vec2d_running[iy][ix];
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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] = array2d_running[iy][ix][m];
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}
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if (modeatom)
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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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count2d[iy][ix] = count2d_running[iy][ix];
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} else {
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if (nvalues == 1) {
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for (iz = nylo_in; iz <= nyhi_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] = vec3d_running[iz][iy][ix];
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} else {
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for (iz = nylo_in; iz <= nyhi_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] = array3d_running[iz][iy][ix][m];
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}
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if (modeatom)
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for (iz = nylo_in; iz <= nyhi_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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count3d[iz][iy][ix] = count3d_running[iz][iy][ix];
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}
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}
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/* ----------------------------------------------------------------------
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sum sample grid values to running grid, just for owned grid cells
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if ATOM mode, also copy per-cell counts
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------------------------------------------------------------------------- */
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void FixAveGrid::sum_sample_to_running()
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{
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int ix,iy,iz,m;
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if (!ngridout) return;
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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_running[iy][ix] += vec2d_sample[iy][ix];
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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_running[iy][ix][m] += array2d_sample[iy][ix][m];
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}
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if (modeatom)
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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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count2d_running[iy][ix] += count2d_sample[iy][ix];
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} else {
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if (nvalues == 1) {
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for (iz = nylo_in; iz <= nyhi_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_running[iz][iy][ix] += vec3d_sample[iz][iy][ix];
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} else {
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for (iz = nylo_in; iz <= nyhi_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_running[iz][iy][ix][m] += array3d_sample[iz][iy][ix][m];
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}
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if (modeatom)
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for (iz = nylo_in; iz <= nyhi_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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count3d_running[iz][iy][ix] += count3d_sample[iz][iy][ix];
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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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numsamples = normalization factor
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@ -1496,7 +1650,7 @@ void FixAveGrid::normalize_atom(int numsamples)
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norm = mvv2e /((repeat*cdof + adof*count) * boltz);
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else if (normflag == NONORM)
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norm = 1.0/invrepeat;
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else if (normflag == NONORM)
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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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@ -1507,7 +1661,7 @@ void FixAveGrid::normalize_atom(int numsamples)
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for (ix = nxlo_in; ix <= nxhi_in; ix++) {
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count = count2d_sample[iy][ix];
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if (count) {
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for (m = 0; m <= nvalues; m++) {
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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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@ -1551,7 +1705,7 @@ void FixAveGrid::normalize_atom(int numsamples)
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for (ix = nxlo_in; ix <= nxhi_in; ix++) {
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count = count3d_sample[iz][iy][ix];
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if (count) {
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for (m = 0; m <= nvalues; m++) {
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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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@ -1641,8 +1795,6 @@ void FixAveGrid::pack_reverse_grid(int /*flag*/, void *vbuf, int nlist, int *lis
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}
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} else {
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for (i = 0; i < nlist; i++) {
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printf("PACK i %d nlist %d, listI %d nvalues %d count %d\n",
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i,nlist,list[i],nvalues,count[list[i]]);
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buf[m++] = count[list[i]];
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values = &data[nvalues*list[i]];
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for (j = 0; j < nvalues; j++)
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