git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3508 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -138,11 +138,15 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
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error->all("Compute ID for fix ave/atom does not exist");
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if (modify->compute[icompute]->peratom_flag == 0)
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error->all("Fix ave/atom compute does not calculate per-atom values");
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if (argindex[i] == 0 && modify->compute[icompute]->size_peratom != 0)
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error->all("Fix ave/atom compute does not calculate a per-atom scalar");
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if (argindex[i] && modify->compute[icompute]->size_peratom == 0)
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error->all("Fix ave/atom compute does not calculate a per-atom vector");
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if (argindex[i] && argindex[i] > modify->compute[icompute]->size_peratom)
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if (argindex[i] == 0 &&
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modify->compute[icompute]->size_peratom_cols != 0)
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error->all("Fix ave/atom compute does not "
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"calculate a per-atom vector");
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if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0)
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error->all("Fix ave/atom compute does not "
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"calculate a per-atom array");
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if (argindex[i] &&
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argindex[i] > modify->compute[icompute]->size_peratom_cols)
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error->all("Fix ave/atom compute vector is accessed out-of-range");
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} else if (which[i] == FIX) {
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int ifix = modify->find_fix(ids[i]);
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@ -150,11 +154,11 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
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error->all("Fix ID for fix ave/atom does not exist");
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if (modify->fix[ifix]->peratom_flag == 0)
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error->all("Fix ave/atom fix does not calculate per-atom values");
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if (argindex[i] && modify->fix[ifix]->size_peratom != 0)
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error->all("Fix ave/atom fix does not calculate a per-atom scalar");
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if (argindex[i] && modify->fix[ifix]->size_peratom == 0)
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if (argindex[i] && modify->fix[ifix]->size_peratom_cols != 0)
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error->all("Fix ave/atom fix does not calculate a per-atom vector");
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if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom)
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if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0)
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error->all("Fix ave/atom fix does not calculate a per-atom array");
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if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols)
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error->all("Fix ave/atom fix vector is accessed out-of-range");
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} else if (which[i] == VARIABLE) {
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int ivariable = input->variable->find(ids[i]);
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@ -165,16 +169,16 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
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}
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}
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// this fix produces either a per-atom scalar or vector
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// this fix produces either a per-atom vector or array
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peratom_flag = 1;
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if (nvalues == 1) size_peratom = 0;
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else size_peratom = nvalues;
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if (nvalues == 1) size_peratom_cols = 0;
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else size_peratom_cols = nvalues;
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// perform initial allocation of atom-based array
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// register with Atom class
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vector = NULL;
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array = NULL;
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grow_arrays(atom->nmax);
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atom->add_callback(0);
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@ -184,7 +188,7 @@ FixAveAtom::FixAveAtom(LAMMPS *lmp, int narg, char **arg) :
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++)
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for (int m = 0; m < nvalues; m++)
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vector[i][m] = 0.0;
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array[i][m] = 0.0;
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// nvalid = next step on which end_of_step does something
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// can be this timestep if multiple of peratom_freq and nrepeat = 1
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@ -219,7 +223,7 @@ FixAveAtom::~FixAveAtom()
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delete [] ids;
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delete [] value2index;
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memory->destroy_2d_double_array(vector);
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memory->destroy_2d_double_array(array);
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}
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/* ---------------------------------------------------------------------- */
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@ -291,7 +295,7 @@ void FixAveAtom::end_of_step()
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if (irepeat == 0)
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for (i = 0; i < nlocal; i++)
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for (m = 0; m < nvalues; m++)
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vector[i][m] = 0.0;
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array[i][m] = 0.0;
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// accumulate results of attributes,computes,fixes,variables to local copy
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// compute/fix/variable may invoke computes so wrap with clear/add
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@ -307,7 +311,7 @@ void FixAveAtom::end_of_step()
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if (which[m] == X) {
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double **x = atom->x;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) vector[i][m] += x[i][j];
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if (mask[i] & groupbit) array[i][m] += x[i][j];
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} else if (which[m] == XU) {
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double **x = atom->x;
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@ -316,28 +320,28 @@ void FixAveAtom::end_of_step()
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double xprd = domain->xprd;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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vector[i][m] += x[i][0] + ((image[i] & 1023) - 512) * xprd;
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array[i][m] += x[i][0] + ((image[i] & 1023) - 512) * xprd;
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} else if (j == 1) {
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double yprd = domain->yprd;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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vector[i][m] += x[i][1] + ((image[i] >> 10 & 1023) - 512) * yprd;
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array[i][m] += x[i][1] + ((image[i] >> 10 & 1023) - 512) * yprd;
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} else {
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double zprd = domain->zprd;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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vector[i][m] += x[i][2] + ((image[i] >> 20) - 512) * zprd;
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array[i][m] += x[i][2] + ((image[i] >> 20) - 512) * zprd;
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}
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} else if (which[m] == V) {
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double **v = atom->v;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) vector[i][m] += v[i][j];
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if (mask[i] & groupbit) array[i][m] += v[i][j];
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} else if (which[m] == F) {
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double **f = atom->f;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) vector[i][m] += f[i][j];
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if (mask[i] & groupbit) array[i][m] += f[i][j];
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// invoke compute if not previously invoked
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@ -349,34 +353,34 @@ void FixAveAtom::end_of_step()
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}
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if (j == 0) {
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double *compute_scalar = compute->scalar_atom;
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double *compute_vector = compute->vector_atom;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) vector[i][m] += compute_scalar[i];
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if (mask[i] & groupbit) array[i][m] += compute_vector[i];
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} else {
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int jm1 = j - 1;
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double **compute_vector = compute->vector_atom;
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double **compute_array = compute->array_atom;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) vector[i][m] += compute_vector[i][jm1];
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if (mask[i] & groupbit) array[i][m] += compute_array[i][jm1];
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}
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// access fix fields, guaranteed to be ready
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} else if (which[m] == FIX) {
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if (j == 0) {
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double *fix_scalar = modify->fix[n]->scalar_atom;
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double *fix_vector = modify->fix[n]->vector_atom;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) vector[i][m] += fix_scalar[i];
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if (mask[i] & groupbit) array[i][m] += fix_vector[i];
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} else {
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int jm1 = j - 1;
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double **fix_vector = modify->fix[n]->vector_atom;
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double **fix_array = modify->fix[n]->array_atom;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) vector[i][m] += fix_vector[i][jm1];
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if (mask[i] & groupbit) array[i][m] += fix_array[i][jm1];
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}
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// evaluate atom-style variable
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} else if (which[m] == VARIABLE)
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input->variable->compute_atom(n,igroup,&vector[0][m],nvalues,1);
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input->variable->compute_atom(n,igroup,&array[0][m],nvalues,1);
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}
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// done if irepeat < nrepeat
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@ -398,7 +402,7 @@ void FixAveAtom::end_of_step()
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double repeat = nrepeat;
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for (i = 0; i < nlocal; i++)
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for (m = 0; m < nvalues; m++)
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vector[i][m] /= repeat;
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array[i][m] /= repeat;
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}
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/* ----------------------------------------------------------------------
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@ -418,10 +422,10 @@ double FixAveAtom::memory_usage()
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void FixAveAtom::grow_arrays(int nmax)
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{
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vector = memory->grow_2d_double_array(vector,nmax,nvalues,
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"fix_ave/atom:vector");
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vector_atom = vector;
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scalar_atom = vector[0];
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array = memory->grow_2d_double_array(array,nmax,nvalues,
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"fix_ave/atom:array");
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array_atom = array;
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vector_atom = array[0];
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}
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/* ----------------------------------------------------------------------
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@ -431,7 +435,7 @@ void FixAveAtom::grow_arrays(int nmax)
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void FixAveAtom::copy_arrays(int i, int j)
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{
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for (int m = 0; m < nvalues; m++)
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vector[j][m] = vector[i][m];
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array[j][m] = array[i][m];
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}
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/* ----------------------------------------------------------------------
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@ -440,7 +444,7 @@ void FixAveAtom::copy_arrays(int i, int j)
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int FixAveAtom::pack_exchange(int i, double *buf)
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{
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for (int m = 0; m < nvalues; m++) buf[m] = vector[i][m];
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for (int m = 0; m < nvalues; m++) buf[m] = array[i][m];
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return nvalues;
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}
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@ -450,6 +454,6 @@ int FixAveAtom::pack_exchange(int i, double *buf)
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int FixAveAtom::unpack_exchange(int nlocal, double *buf)
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{
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for (int m = 0; m < nvalues; m++) vector[nlocal][m] = buf[m];
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for (int m = 0; m < nvalues; m++) array[nlocal][m] = buf[m];
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return nvalues;
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}
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