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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@254 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2007-01-30 00:22:05 +00:00
parent 9cdbeaf9f2
commit 209f169cbc
414 changed files with 6935 additions and 10462 deletions
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64
src/delete_bonds.cpp
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@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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
@ -15,8 +15,8 @@
#include "stdlib.h"
#include "string.h"
#include "delete_bonds.h"
#include "system.h"
#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "neighbor.h"
#include "comm.h"
@ -26,6 +26,8 @@
#include "special.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MULTI 1
#define ATOM 2
#define BOND 3
@ -36,6 +38,10 @@
/* ---------------------------------------------------------------------- */
DeleteBonds::DeleteBonds(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void DeleteBonds::command(int narg, char **arg)
{
if (domain->box_exist == 0)
@ -51,7 +57,7 @@ void DeleteBonds::command(int narg, char **arg)
if (comm->me == 0 && screen)
fprintf(screen,"System init for delete_bonds ...\n");
sys->init();
lmp->init();
if (comm->me == 0 && screen) fprintf(screen,"Deleting bonds ...\n");
@ -122,7 +128,7 @@ void DeleteBonds::command(int narg, char **arg)
int i,m,n,flag;
int atom1,atom2,atom3,atom4;
if (atom->bonds_allow) {
if (atom->avec->bonds_allow) {
int *num_bond = atom->num_bond;
int **bond_type = atom->bond_type;
@ -147,7 +153,7 @@ void DeleteBonds::command(int narg, char **arg)
}
}
if (atom->angles_allow) {
if (atom->avec->angles_allow) {
int *num_angle = atom->num_angle;
int **angle_type = atom->angle_type;
@ -177,7 +183,7 @@ void DeleteBonds::command(int narg, char **arg)
}
}
if (atom->dihedrals_allow) {
if (atom->avec->dihedrals_allow) {
int *num_dihedral = atom->num_dihedral;
int **dihedral_type = atom->dihedral_type;
@ -208,7 +214,7 @@ void DeleteBonds::command(int narg, char **arg)
}
}
if (atom->impropers_allow) {
if (atom->avec->impropers_allow) {
int *num_improper = atom->num_improper;
int **improper_type = atom->improper_type;
@ -244,7 +250,7 @@ void DeleteBonds::command(int narg, char **arg)
if (remove_flag) {
if (atom->bonds_allow) {
if (atom->avec->bonds_allow) {
for (i = 0; i < nlocal; i++) {
m = 0;
while (m < atom->num_bond[i]) {
@ -261,7 +267,7 @@ void DeleteBonds::command(int narg, char **arg)
}
}
if (atom->angles_allow) {
if (atom->avec->angles_allow) {
for (i = 0; i < nlocal; i++) {
m = 0;
while (m < atom->num_angle[i]) {
@ -283,7 +289,7 @@ void DeleteBonds::command(int narg, char **arg)
}
}
if (atom->dihedrals_allow) {
if (atom->avec->dihedrals_allow) {
for (i = 0; i < nlocal; i++) {
m = 0;
while (m < atom->num_dihedral[i]) {
@ -307,7 +313,7 @@ void DeleteBonds::command(int narg, char **arg)
}
}
if (atom->impropers_allow) {
if (atom->avec->impropers_allow) {
for (i = 0; i < nlocal; i++) {
m = 0;
while (m < atom->num_improper[i]) {
@ -337,28 +343,28 @@ void DeleteBonds::command(int narg, char **arg)
if (remove_flag) {
if (atom->bonds_allow) {
if (atom->avec->bonds_allow) {
int nbonds = 0;
for (i = 0; i < nlocal; i++) nbonds += atom->num_bond[i];
MPI_Allreduce(&nbonds,&atom->nbonds,1,MPI_INT,MPI_SUM,world);
if (force->newton_bond == 0) atom->nbonds /= 2;
}
if (atom->angles_allow) {
if (atom->avec->angles_allow) {
int nangles = 0;
for (i = 0; i < nlocal; i++) nangles += atom->num_angle[i];
MPI_Allreduce(&nangles,&atom->nangles,1,MPI_INT,MPI_SUM,world);
if (force->newton_bond == 0) atom->nangles /= 3;
}
if (atom->dihedrals_allow) {
if (atom->avec->dihedrals_allow) {
int ndihedrals = 0;
for (i = 0; i < nlocal; i++) ndihedrals += atom->num_dihedral[i];
MPI_Allreduce(&ndihedrals,&atom->ndihedrals,1,MPI_INT,MPI_SUM,world);
if (force->newton_bond == 0) atom->ndihedrals /= 4;
}
if (atom->impropers_allow) {
if (atom->avec->impropers_allow) {
int nimpropers = 0;
for (i = 0; i < nlocal; i++) nimpropers += atom->num_improper[i];
MPI_Allreduce(&nimpropers,&atom->nimpropers,1,MPI_INT,MPI_SUM,world);
@ -375,7 +381,7 @@ void DeleteBonds::command(int narg, char **arg)
int dihedral_on,dihedral_off;
int improper_on,improper_off;
if (atom->bonds_allow) {
if (atom->avec->bonds_allow) {
bond_on = bond_off = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_bond[i]; m++)
@ -391,7 +397,7 @@ void DeleteBonds::command(int narg, char **arg)
}
}
if (atom->angles_allow) {
if (atom->avec->angles_allow) {
angle_on = angle_off = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_angle[i]; m++)
@ -407,7 +413,7 @@ void DeleteBonds::command(int narg, char **arg)
}
}
if (atom->dihedrals_allow) {
if (atom->avec->dihedrals_allow) {
dihedral_on = dihedral_off = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_dihedral[i]; m++)
@ -423,7 +429,7 @@ void DeleteBonds::command(int narg, char **arg)
}
}
if (atom->impropers_allow) {
if (atom->avec->impropers_allow) {
improper_on = improper_off = 0;
for (i = 0; i < nlocal; i++)
for (m = 0; m < atom->num_improper[i]; m++)
@ -441,30 +447,30 @@ void DeleteBonds::command(int narg, char **arg)
if (comm->me == 0) {
if (screen) {
if (atom->bonds_allow)
if (atom->avec->bonds_allow)
fprintf(screen," %d total bonds, %d turned on, %d turned off\n",
atom->nbonds,bond_on,bond_off);
if (atom->angles_allow)
if (atom->avec->angles_allow)
fprintf(screen," %d total angles, %d turned on, %d turned off\n",
atom->nangles,angle_on,angle_off);
if (atom->dihedrals_allow)
if (atom->avec->dihedrals_allow)
fprintf(screen," %d total dihedrals, %d turned on, %d turned off\n",
atom->ndihedrals,dihedral_on,dihedral_off);
if (atom->impropers_allow)
if (atom->avec->impropers_allow)
fprintf(screen," %d total impropers, %d turned on, %d turned off\n",
atom->nimpropers,improper_on,improper_off);
}
if (logfile) {
if (atom->bonds_allow)
if (atom->avec->bonds_allow)
fprintf(logfile," %d total bonds, %d turned on, %d turned off\n",
atom->nbonds,bond_on,bond_off);
if (atom->angles_allow)
if (atom->avec->angles_allow)
fprintf(logfile," %d total angles, %d turned on, %d turned off\n",
atom->nangles,angle_on,angle_off);
if (atom->dihedrals_allow)
if (atom->avec->dihedrals_allow)
fprintf(logfile," %d total dihedrals, %d turned on, %d turned off\n",
atom->ndihedrals,dihedral_on,dihedral_off);
if (atom->impropers_allow)
if (atom->avec->impropers_allow)
fprintf(logfile," %d total impropers, %d turned on, %d turned off\n",
atom->nimpropers,improper_on,improper_off);
}
@ -473,7 +479,7 @@ void DeleteBonds::command(int narg, char **arg)
// re-compute special list if requested
if (special_flag) {
Special special;
Special special(lmp);
special.build();
}
}