forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3571 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
79eb0f915e
commit
3f887c7aff
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "string.h"
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#include "compute_angle_local.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "update.h"
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#include "domain.h"
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#include "force.h"
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#include "angle.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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enum{THETA,ENERGY};
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#define DELTA 10000
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/* ---------------------------------------------------------------------- */
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ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg < 4) error->all("Illegal compute angle/local command");
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if (atom->avec->angles_allow == 0)
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error->all("Compute angle/local used when angles are not allowed");
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local_flag = 1;
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nvalues = narg - 3;
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if (nvalues == 1) size_local_cols = 0;
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else size_local_cols = nvalues;
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which = new int[nvalues];
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pack_choice = new FnPtrPack[nvalues];
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dflag = eflag = 0;
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int i;
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for (int iarg = 3; iarg < narg; iarg++) {
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i = iarg-3;
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if (strcmp(arg[iarg],"theta") == 0) {
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dflag = 1;
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which[i] = THETA;
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pack_choice[i] = &ComputeAngleLocal::pack_theta;
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} else if (strcmp(arg[iarg],"energy") == 0) {
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eflag = 1;
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which[i] = ENERGY;
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pack_choice[i] = &ComputeAngleLocal::pack_energy;
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} else error->all("Invalid keyword in compute angle/local command");
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}
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nmax = 0;
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theta = energy = NULL;
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array = NULL;
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}
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/* ---------------------------------------------------------------------- */
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ComputeAngleLocal::~ComputeAngleLocal()
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{
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delete [] which;
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delete [] pack_choice;
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memory->sfree(theta);
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memory->sfree(energy);
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memory->destroy_2d_double_array(array);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeAngleLocal::init()
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{
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if (force->angle == NULL)
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error->all("No angle style is defined for compute angle/local");
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// do initial memory allocation so that memory_usage() is correct
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ncount = compute_angles(0);
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if (ncount > nmax) reallocate(ncount);
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size_local_rows = ncount;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeAngleLocal::compute_local()
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{
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invoked_local = update->ntimestep;
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// count local entries and compute angle info
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ncount = compute_angles(0);
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if (ncount > nmax) reallocate(ncount);
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size_local_rows = ncount;
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ncount = compute_angles(1);
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// fill array with theta/energy values
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if (nvalues > 1) {
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if (array) buf = array[0];
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for (int n = 0; n < nvalues; n++)
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(this->*pack_choice[n])(n);
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}
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}
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/* ----------------------------------------------------------------------
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count angles and compute angle info on this proc
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only count angle once if newton_angle is off
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all atoms in interaction must be in group
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all atoms in interaction must be known to proc
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if angle is deleted (type = 0), do not count
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if angle is turned off (type < 0), still count
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if flag is set, compute requested info about angle
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------------------------------------------------------------------------- */
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int ComputeAngleLocal::compute_angles(int flag)
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{
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int i,atom1,atom2,atom3;
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double delx1,dely1,delz1,delx2,dely2,delz2;
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double rsq1,rsq2,r1,r2,c;
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double **x = atom->x;
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int *num_angle = atom->num_angle;
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int **angle_atom1 = atom->angle_atom1;
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int **angle_atom2 = atom->angle_atom2;
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int **angle_atom3 = atom->angle_atom3;
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int **angle_type = atom->angle_type;
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int *tag = atom->tag;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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Angle *angle = force->angle;
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int m = 0;
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for (atom2 = 0; atom2 < nlocal; atom2++) {
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if (!(mask[atom2] & groupbit)) continue;
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for (i = 0; i < num_angle[atom2]; i++) {
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if (tag[atom2] != angle_atom2[atom2][i]) continue;
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atom1 = atom->map(angle_atom1[atom2][i]);
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if (atom1 < 0 || !(mask[atom1] & groupbit)) continue;
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atom3 = atom->map(angle_atom3[atom2][i]);
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if (atom3 < 0 || !(mask[atom3] & groupbit)) continue;
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if (flag) {
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if (dflag) {
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delx1 = x[atom1][0] - x[atom2][0];
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dely1 = x[atom1][1] - x[atom2][1];
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delz1 = x[atom1][2] - x[atom2][2];
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domain->minimum_image(delx1,dely1,delz1);
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rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
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r1 = sqrt(rsq1);
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delx2 = x[atom3][0] - x[atom2][0];
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dely2 = x[atom3][1] - x[atom2][1];
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delz2 = x[atom3][2] - x[atom2][2];
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domain->minimum_image(delx2,dely2,delz2);
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rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
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r2 = sqrt(rsq2);
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// c = cosine of angle
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c = delx1*delx2 + dely1*dely2 + delz1*delz2;
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c /= r1*r2;
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if (c > 1.0) c = 1.0;
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if (c < -1.0) c = -1.0;
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theta[m] = acos(c);
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}
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if (eflag)
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energy[m] = angle->single(angle_type[atom1][i],atom1,atom2,atom3);
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}
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m++;
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}
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeAngleLocal::pack_theta(int n)
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{
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for (int m = 0; m < ncount; m++) {
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buf[n] = theta[m];
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n += nvalues;
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeAngleLocal::pack_energy(int n)
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{
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for (int m = 0; m < ncount; m++) {
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buf[n] = energy[m];
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n += nvalues;
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeAngleLocal::reallocate(int n)
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{
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// grow vector or array and indices array
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while (nmax < n) nmax += DELTA;
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if (dflag) {
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memory->sfree(theta);
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theta = (double *) memory->smalloc(nmax*sizeof(double),
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"bond/local:theta");
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}
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if (eflag) {
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memory->sfree(energy);
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energy = (double *) memory->smalloc(nmax*sizeof(double),
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"bond/local:energy");
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}
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if (nvalues == 1) {
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if (dflag) vector_local = theta;
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if (eflag) vector_local = energy;
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} else {
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memory->destroy_2d_double_array(array);
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array = memory->create_2d_double_array(nmax,nvalues,
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"bond/local:array");
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array_local = array;
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}
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}
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/* ----------------------------------------------------------------------
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memory usage of local data
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------------------------------------------------------------------------- */
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double ComputeAngleLocal::memory_usage()
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{
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double bytes = 0.0;
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if (dflag) bytes += nmax * sizeof(double);
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if (eflag) bytes += nmax * sizeof(double);
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if (nvalues > 1) bytes += nmax*nvalues * sizeof(double);
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return bytes;
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}
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@ -0,0 +1,52 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifndef COMPUTE_ANGLE_LOCAL_H
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#define COMPUTE_ANGLE_LOCAL_H
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#include "compute.h"
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namespace LAMMPS_NS {
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class ComputeAngleLocal : public Compute {
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public:
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ComputeAngleLocal(class LAMMPS *, int, char **);
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~ComputeAngleLocal();
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void init();
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void compute_local();
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double memory_usage();
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private:
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int nvalues,dflag,eflag;
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int *which;
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int ncount;
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int nmax;
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double *theta;
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double *energy;
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double **array;
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double *buf;
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int compute_angles(int);
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void reallocate(int);
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typedef void (ComputeAngleLocal::*FnPtrPack)(int);
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FnPtrPack *pack_choice; // ptrs to pack functions
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void pack_theta(int);
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void pack_energy(int);
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};
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}
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#endif
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@ -0,0 +1,233 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "string.h"
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#include "compute_bond_local.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "update.h"
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#include "domain.h"
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#include "force.h"
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#include "bond.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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enum{DISTANCE,ENERGY};
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#define DELTA 10000
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/* ---------------------------------------------------------------------- */
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ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg < 4) error->all("Illegal compute bond/local command");
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if (atom->avec->bonds_allow == 0)
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error->all("Compute bond/local used when bonds are not allowed");
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local_flag = 1;
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nvalues = narg - 3;
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if (nvalues == 1) size_local_cols = 0;
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else size_local_cols = nvalues;
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which = new int[nvalues];
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pack_choice = new FnPtrPack[nvalues];
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dflag = eflag = 0;
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int i;
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for (int iarg = 3; iarg < narg; iarg++) {
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i = iarg-3;
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if (strcmp(arg[iarg],"distance") == 0) {
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dflag = 1;
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which[i] = DISTANCE;
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pack_choice[i] = &ComputeBondLocal::pack_distance;
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} else if (strcmp(arg[iarg],"energy") == 0) {
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eflag = 1;
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which[i] = ENERGY;
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pack_choice[i] = &ComputeBondLocal::pack_energy;
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} else error->all("Invalid keyword in compute bond/local command");
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}
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nmax = 0;
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distance = energy = NULL;
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array = NULL;
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}
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/* ---------------------------------------------------------------------- */
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ComputeBondLocal::~ComputeBondLocal()
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{
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delete [] which;
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delete [] pack_choice;
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memory->sfree(distance);
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memory->sfree(energy);
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memory->destroy_2d_double_array(array);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeBondLocal::init()
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{
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if (force->bond == NULL)
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error->all("No bond style is defined for compute bond/local");
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// do initial memory allocation so that memory_usage() is correct
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ncount = compute_bonds(0);
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if (ncount > nmax) reallocate(ncount);
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size_local_rows = ncount;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeBondLocal::compute_local()
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{
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invoked_local = update->ntimestep;
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// count local entries and compute bond info
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ncount = compute_bonds(0);
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if (ncount > nmax) reallocate(ncount);
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size_local_rows = ncount;
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ncount = compute_bonds(1);
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// fill array with distance/energy values
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if (nvalues > 1) {
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if (array) buf = array[0];
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for (int n = 0; n < nvalues; n++)
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(this->*pack_choice[n])(n);
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}
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}
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/* ----------------------------------------------------------------------
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count bonds and compute bond info on this proc
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only count bond once if newton_bond is off
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all atoms in interaction must be in group
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all atoms in interaction must be known to proc
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if bond is deleted (type = 0), do not count
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if bond is turned off (type < 0), still count
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if flag is set, compute requested info about bond
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------------------------------------------------------------------------- */
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int ComputeBondLocal::compute_bonds(int flag)
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{
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int i,atom1,atom2;
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double delx,dely,delz,rsq;
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double **x = atom->x;
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int *num_bond = atom->num_bond;
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int **bond_atom = atom->bond_atom;
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int **bond_type = atom->bond_type;
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int *tag = atom->tag;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int newton_bond = force->newton_bond;
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Bond *bond = force->bond;
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int m = 0;
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for (atom1 = 0; atom1 < nlocal; atom1++) {
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if (!(mask[atom1] & groupbit)) continue;
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for (i = 0; i < num_bond[atom1]; i++) {
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atom2 = atom->map(bond_atom[atom1][i]);
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if (atom2 < 0 || !(mask[atom2] & groupbit)) continue;
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if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue;
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if (bond_type[atom1][i] == 0) continue;
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if (flag) {
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delx = x[atom1][0] - x[atom2][0];
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dely = x[atom1][1] - x[atom2][1];
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delz = x[atom1][2] - x[atom2][2];
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domain->minimum_image(delx,dely,delz);
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rsq = delx*delx + dely*dely + delz*delz;
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if (dflag) distance[m] = sqrt(rsq);
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if (eflag)
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energy[m] = bond->single(bond_type[atom1][i],rsq,atom1,atom2);
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}
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m++;
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}
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeBondLocal::pack_distance(int n)
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{
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for (int m = 0; m < ncount; m++) {
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buf[n] = distance[m];
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n += nvalues;
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeBondLocal::pack_energy(int n)
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{
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for (int m = 0; m < ncount; m++) {
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buf[n] = energy[m];
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n += nvalues;
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}
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}
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/* ---------------------------------------------------------------------- */
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void ComputeBondLocal::reallocate(int n)
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{
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// grow vector or array and indices array
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||||
while (nmax < n) nmax += DELTA;
|
||||
|
||||
if (dflag) {
|
||||
memory->sfree(distance);
|
||||
distance = (double *) memory->smalloc(nmax*sizeof(double),
|
||||
"bond/local:distance");
|
||||
}
|
||||
if (eflag) {
|
||||
memory->sfree(energy);
|
||||
energy = (double *) memory->smalloc(nmax*sizeof(double),
|
||||
"bond/local:energy");
|
||||
}
|
||||
|
||||
if (nvalues == 1) {
|
||||
if (dflag) vector_local = distance;
|
||||
if (eflag) vector_local = energy;
|
||||
} else {
|
||||
memory->destroy_2d_double_array(array);
|
||||
array = memory->create_2d_double_array(nmax,nvalues,
|
||||
"bond/local:array");
|
||||
array_local = array;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local data
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double ComputeBondLocal::memory_usage()
|
||||
{
|
||||
double bytes = 0.0;
|
||||
if (dflag) bytes += nmax * sizeof(double);
|
||||
if (eflag) bytes += nmax * sizeof(double);
|
||||
if (nvalues > 1) bytes += nmax*nvalues * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,52 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef COMPUTE_BOND_LOCAL_H
|
||||
#define COMPUTE_BOND_LOCAL_H
|
||||
|
||||
#include "compute.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ComputeBondLocal : public Compute {
|
||||
public:
|
||||
ComputeBondLocal(class LAMMPS *, int, char **);
|
||||
~ComputeBondLocal();
|
||||
void init();
|
||||
void compute_local();
|
||||
double memory_usage();
|
||||
|
||||
private:
|
||||
int nvalues,dflag,eflag;
|
||||
int *which;
|
||||
int ncount;
|
||||
|
||||
int nmax;
|
||||
double *distance;
|
||||
double *energy;
|
||||
double **array;
|
||||
double *buf;
|
||||
|
||||
int compute_bonds(int);
|
||||
void reallocate(int);
|
||||
|
||||
typedef void (ComputeBondLocal::*FnPtrPack)(int);
|
||||
FnPtrPack *pack_choice; // ptrs to pack functions
|
||||
|
||||
void pack_distance(int);
|
||||
void pack_energy(int);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
|
|
@ -40,7 +40,7 @@ enum{NONE,BOND,ANGLE,DIHEDRAL,IMPROPER};
|
|||
ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) :
|
||||
Compute(lmp, narg, arg)
|
||||
{
|
||||
if (narg < 4) error->all("Illegal compute property/atom command");
|
||||
if (narg < 4) error->all("Illegal compute property/local command");
|
||||
|
||||
local_flag = 1;
|
||||
nvalues = narg - 3;
|
||||
|
|
@ -233,6 +233,8 @@ void ComputePropertyLocal::compute_local()
|
|||
|
||||
int ComputePropertyLocal::count_bonds(int flag)
|
||||
{
|
||||
int i,atom1,atom2;
|
||||
|
||||
int *num_bond = atom->num_bond;
|
||||
int **bond_atom = atom->bond_atom;
|
||||
int **bond_type = atom->bond_type;
|
||||
|
|
@ -241,8 +243,6 @@ int ComputePropertyLocal::count_bonds(int flag)
|
|||
int nlocal = atom->nlocal;
|
||||
int newton_bond = force->newton_bond;
|
||||
|
||||
int i,atom1,atom2;
|
||||
|
||||
int m = 0;
|
||||
for (atom1 = 0; atom1 < nlocal; atom1++) {
|
||||
if (!(mask[atom1] & groupbit)) continue;
|
||||
|
|
@ -272,6 +272,8 @@ int ComputePropertyLocal::count_bonds(int flag)
|
|||
|
||||
int ComputePropertyLocal::count_angles(int flag)
|
||||
{
|
||||
int i,atom1,atom2,atom3;
|
||||
|
||||
int *num_angle = atom->num_angle;
|
||||
int **angle_atom1 = atom->angle_atom1;
|
||||
int **angle_atom2 = atom->angle_atom2;
|
||||
|
|
@ -281,8 +283,6 @@ int ComputePropertyLocal::count_angles(int flag)
|
|||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int i,atom1,atom2,atom3;
|
||||
|
||||
int m = 0;
|
||||
for (atom2 = 0; atom2 < nlocal; atom2++) {
|
||||
if (!(mask[atom2] & groupbit)) continue;
|
||||
|
|
@ -313,6 +313,8 @@ int ComputePropertyLocal::count_angles(int flag)
|
|||
|
||||
int ComputePropertyLocal::count_dihedrals(int flag)
|
||||
{
|
||||
int i,atom1,atom2,atom3,atom4;
|
||||
|
||||
int *num_dihedral = atom->num_dihedral;
|
||||
int **dihedral_atom1 = atom->dihedral_atom1;
|
||||
int **dihedral_atom2 = atom->dihedral_atom2;
|
||||
|
|
@ -323,8 +325,6 @@ int ComputePropertyLocal::count_dihedrals(int flag)
|
|||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int i,atom1,atom2,atom3,atom4;
|
||||
|
||||
int m = 0;
|
||||
for (atom2 = 0; atom2 < nlocal; atom2++) {
|
||||
if (!(mask[atom2] & groupbit)) continue;
|
||||
|
|
@ -357,6 +357,8 @@ int ComputePropertyLocal::count_dihedrals(int flag)
|
|||
|
||||
int ComputePropertyLocal::count_impropers(int flag)
|
||||
{
|
||||
int i,atom1,atom2,atom3,atom4;
|
||||
|
||||
int *num_improper = atom->num_improper;
|
||||
int **improper_atom1 = atom->improper_atom1;
|
||||
int **improper_atom2 = atom->improper_atom2;
|
||||
|
|
@ -367,8 +369,6 @@ int ComputePropertyLocal::count_impropers(int flag)
|
|||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int i,atom1,atom2,atom3,atom4;
|
||||
|
||||
int m = 0;
|
||||
for (atom2 = 0; atom2 < nlocal; atom2++) {
|
||||
if (!(mask[atom2] & groupbit)) continue;
|
||||
|
|
|
|||
|
|
@ -76,6 +76,8 @@ CommandStyle(write_restart,WriteRestart)
|
|||
#endif
|
||||
|
||||
#ifdef ComputeInclude
|
||||
#include "compute_angle_local.h"
|
||||
#include "compute_bond_local.h"
|
||||
#include "compute_centro_atom.h"
|
||||
#include "compute_cna_atom.h"
|
||||
#include "compute_com.h"
|
||||
|
|
@ -108,6 +110,8 @@ CommandStyle(write_restart,WriteRestart)
|
|||
#endif
|
||||
|
||||
#ifdef ComputeClass
|
||||
ComputeStyle(angle/local,ComputeAngleLocal)
|
||||
ComputeStyle(bond/local,ComputeBondLocal)
|
||||
ComputeStyle(centro/atom,ComputeCentroAtom)
|
||||
ComputeStyle(cna/atom,ComputeCNAAtom)
|
||||
ComputeStyle(com,ComputeCOM)
|
||||
|
|
|
|||
Loading…
Reference in New Issue