git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@254 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -1,7 +1,7 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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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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@ -18,10 +18,13 @@
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#include "stdlib.h"
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#include "group.h"
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#include "domain.h"
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#include "atom.h"
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#include "atom_vec_hybrid.h"
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#include "region.h"
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#include "memory.h"
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#include "error.h"
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#include "atom.h"
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using namespace LAMMPS_NS;
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#define MAX_GROUP 32
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@ -44,7 +47,7 @@
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initialize group memory
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------------------------------------------------------------------------- */
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Group::Group()
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Group::Group(LAMMPS *lmp) : Pointers(lmp)
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{
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MPI_Comm_rank(world,&me);
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@ -124,7 +127,29 @@ void Group::assign(int narg, char **arg)
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if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
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mask[i] |= bit;
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// style = logical condition
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// style = hybrid
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} else if (strcmp(arg[1],"hybrid") == 0) {
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if (narg != 3) error->all("Illegal group command");
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if (strcmp(atom->atom_style,"hybrid") != 0)
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error->all("Group hybrid command requires atom style hybrid");
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AtomVecHybrid *avec_hybrid = (AtomVecHybrid *) atom->avec;
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int ihybrid;
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for (ihybrid = 0; ihybrid < avec_hybrid->nstyles; ihybrid++)
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if (strcmp(avec_hybrid->keywords[ihybrid],arg[2]) == 0) break;
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if (ihybrid == avec_hybrid->nstyles)
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error->all("Group hybrid sub-style does not exist");
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// add to group if atom matches hybrid sub-style
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int *hybrid = atom->hybrid;
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for (i = 0; i < nlocal; i++)
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if (hybrid[i] == ihybrid) mask[i] |= bit;
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// style = logical condition
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} else if (strcmp(arg[2],"<") == 0 || strcmp(arg[2],">") == 0 ||
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strcmp(arg[2],"<=") == 0 || strcmp(arg[2],">=") == 0 ||
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@ -173,7 +198,7 @@ void Group::assign(int narg, char **arg)
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if (attribute[i] >= bound1 && attribute[i] <= bound2) mask[i] |= bit;
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}
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// style = list of values
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// style = list of values
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} else if (strcmp(arg[1],"type") == 0 || strcmp(arg[1],"molecule") == 0 ||
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strcmp(arg[1],"id") == 0) {
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@ -205,7 +230,7 @@ void Group::assign(int narg, char **arg)
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delete [] list;
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// style = subtract
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// style = subtract
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} else if (strcmp(arg[1],"subtract") == 0) {
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@ -241,7 +266,7 @@ void Group::assign(int narg, char **arg)
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delete [] list;
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// style = union
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// style = union
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} else if (strcmp(arg[1],"union") == 0) {
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@ -269,7 +294,7 @@ void Group::assign(int narg, char **arg)
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delete [] list;
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// style = intersect
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// style = intersect
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} else if (strcmp(arg[1],"intersect") == 0) {
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@ -300,7 +325,7 @@ void Group::assign(int narg, char **arg)
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delete [] list;
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// not a valid group style
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// not a valid group style
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} else error->all("Illegal group command");
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@ -443,7 +468,7 @@ double Group::mass(int igroup)
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double m = 0.0;
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if (atom->mass_require) {
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if (mass) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) m += mass[type[i]];
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} else {
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@ -547,7 +572,7 @@ void Group::xcm(int igroup, double masstotal, double *cm)
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int xbox,ybox,zbox;
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double massone;
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if (atom->mass_require) {
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if (mass) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & 1023) - 512;
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@ -596,7 +621,7 @@ void Group::vcm(int igroup, double masstotal, double *cm)
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double p[3],massone;
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p[0] = p[1] = p[2] = 0.0;
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if (atom->mass_require) {
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if (mass) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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massone = mass[type[i]];
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@ -636,7 +661,6 @@ double Group::gyration(int igroup, double masstotal, double *cm)
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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int mass_require = atom->mass_require;
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int xbox,ybox,zbox;
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double dx,dy,dz,massone;
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@ -653,7 +677,7 @@ double Group::gyration(int igroup, double masstotal, double *cm)
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dx = (x[i][0] + xbox*xprd) - cm[0];
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dy = (x[i][1] + ybox*yprd) - cm[1];
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dz = (x[i][2] + zbox*zprd) - cm[2];
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if (mass_require) massone = mass[type[i]];
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if (mass) massone = mass[type[i]];
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else massone = rmass[i];
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rg += (dx*dx + dy*dy + dz*dz) * massone;
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}
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@ -680,7 +704,6 @@ void Group::angmom(int igroup, double *cm, double *lmom)
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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int mass_require = atom->mass_require;
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int xbox,ybox,zbox;
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double dx,dy,dz,massone;
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@ -698,7 +721,7 @@ void Group::angmom(int igroup, double *cm, double *lmom)
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dx = (x[i][0] + xbox*xprd) - cm[0];
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dy = (x[i][1] + ybox*yprd) - cm[1];
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dz = (x[i][2] + zbox*zprd) - cm[2];
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if (mass_require) massone = mass[type[i]];
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if (mass) massone = mass[type[i]];
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else massone = rmass[i];
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p[0] += massone * (dy*v[i][2] - dz*v[i][1]);
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p[1] += massone * (dz*v[i][0] - dx*v[i][2]);
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@ -726,7 +749,6 @@ void Group::inertia(int igroup, double *cm, double itensor[3][3])
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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int mass_require = atom->mass_require;
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int xbox,ybox,zbox;
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double dx,dy,dz,massone;
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@ -746,7 +768,7 @@ void Group::inertia(int igroup, double *cm, double itensor[3][3])
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dx = (x[i][0] + xbox*xprd) - cm[0];
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dy = (x[i][1] + ybox*yprd) - cm[1];
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dz = (x[i][2] + zbox*zprd) - cm[2];
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if (mass_require) massone = mass[type[i]];
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if (mass) massone = mass[type[i]];
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else massone = rmass[i];
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ione[0][0] += massone * (dy*dy + dz*dz);
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ione[1][1] += massone * (dx*dx + dz*dz);
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@ -764,14 +786,11 @@ void Group::inertia(int igroup, double *cm, double itensor[3][3])
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/* ----------------------------------------------------------------------
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compute angular velocity omega from L = Iw, inverting I to solve for w
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really not a group operation, but L and I were computed for a group
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------------------------------------------------------------------------- */
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void Group::omega(int igroup, double *angmom, double inertia[3][3], double *w)
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void Group::omega(double *angmom, double inertia[3][3], double *w)
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{
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int i,j;
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int groupbit = bitmask[igroup];
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double inverse[3][3];
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inverse[0][0] = inertia[1][1]*inertia[2][2] - inertia[1][2]*inertia[2][1];
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@ -793,6 +812,7 @@ void Group::omega(int igroup, double *angmom, double inertia[3][3], double *w)
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inertia[0][1]*inertia[1][0]*inertia[2][2] -
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inertia[2][0]*inertia[1][1]*inertia[0][2];
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int i,j;
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for (i = 0; i < 3; i++)
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for (j = 0; j < 3; j++)
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inverse[i][j] /= determinant;
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