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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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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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54
src/neighbor.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
@ -18,18 +18,22 @@
#include "limits.h"
#include "neighbor.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "pair.h"
#include "domain.h"
#include "group.h"
#include "modify.h"
#include "fix.h"
#include "compute.h"
#include "update.h"
#include "respa.h"
#include "output.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define PGDELTA 1
#define LB_FACTOR 1.5
#define SMALL 1.0e-6
@ -40,7 +44,7 @@
/* ---------------------------------------------------------------------- */
Neighbor::Neighbor()
Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
@ -104,7 +108,7 @@ Neighbor::Neighbor()
// shear history neighbor list info
history = -1;
fix_history = NULL;
firsttouch = NULL;
firstshear = NULL;
pages_touch = NULL;
@ -174,7 +178,7 @@ Neighbor::~Neighbor()
for (int i = 0; i < maxpage_full; i++) memory->sfree(pages_full[i]);
memory->sfree(pages_full);
if (history >= 0) {
if (fix_history) {
memory->sfree(firsttouch);
memory->sfree(firstshear);
for (int i = 0; i < maxpage; i++) memory->sfree(pages_touch[i]);
@ -264,7 +268,7 @@ void Neighbor::init()
// flag = 0 if both LJ/Coulomb special values are 0.0
// flag = 1 if both LJ/Coulomb special values are 1.0
// flag = 2 otherwise or if KSpace solver is enabled
// (pairwise portion of KSpace solver uses all 1-2,1-3,1-4 neighbors)
// pairwise portion of KSpace solver uses all 1-2,1-3,1-4 neighbors
if (force->special_lj[1] == 0.0 && force->special_coul[1] == 0.0)
special_flag[1] = 0;
@ -368,6 +372,7 @@ void Neighbor::init()
// half and full pairwise neighbor lists
// determine whether to build half and full lists
// query pair,fix,compute for their requirements
maxlocal = atom->nmax;
int half_previous = half;
@ -385,6 +390,11 @@ void Neighbor::init()
if (modify->fix[i]->neigh_full_once) full_once = 1;
}
for (i = 0; i < modify->ncompute; i++) {
if (modify->compute[i]->neigh_half_once) half_once = 1;
if (modify->compute[i]->neigh_full_once) full_once = 1;
}
half = full = 0;
if (half_every || half_once || half_command) half = 1;
if (full_every || full_once) full = 1;
@ -437,15 +447,16 @@ void Neighbor::init()
}
// setup/delete memory for shear history neighbor lists
// history = index of granular shear history fix if it exists
// fix_history = granular shear history fix if it exists
int history_previous = history;
history = -1;
FixShearHistory *fix_previous = fix_history;
fix_history = NULL;
if (force->pair_match("gran/history") || force->pair_match("gran/hertzian"))
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"SHEAR_HISTORY") == 0) history = i;
if (strcmp(modify->fix[i]->style,"SHEAR_HISTORY") == 0)
fix_history = (FixShearHistory *) modify->fix[i];
if (history == -1 && history_previous >= 0) {
if (fix_history == NULL && fix_previous) {
memory->sfree(firsttouch);
memory->sfree(firstshear);
for (i = 0; i < maxpage; i++) memory->sfree(pages_touch[i]);
@ -454,12 +465,12 @@ void Neighbor::init()
memory->sfree(pages_shear);
pages_touch = NULL;
pages_shear = NULL;
} else if (history >= 0 && history_previous == -1) {
} else if (fix_history && fix_previous == NULL) {
firsttouch = (int **) memory->smalloc(maxlocal*sizeof(int *),"firsttouch");
firstshear = (double **)
memory->smalloc(maxlocal*sizeof(double *),"firstshear");
add_pages_history(0);
} else if (history >= 0 && history_previous >= 0) {
} else if (fix_history && fix_previous >= 0) {
memory->sfree(firsttouch);
memory->sfree(firstshear);
firsttouch = (int **) memory->smalloc(maxlocal*sizeof(int *),"firsttouch");
@ -537,7 +548,7 @@ void Neighbor::init()
// cannot combine granular and rRESPA
if (half) {
if (strcmp(atom->style,"granular") == 0) {
if (atom->check_style("granular")) {
if (style == 0) {
if (force->newton_pair == 0)
half_build = &Neighbor::granular_nsq_no_newton;
@ -629,7 +640,7 @@ void Neighbor::init()
bond_off = angle_off = 1;
if (force->bond && force->bond_match("quartic")) bond_off = 1;
if (atom->bonds_allow) {
if (atom->avec->bonds_allow) {
for (i = 0; i < atom->nlocal; i++) {
if (bond_off) break;
for (m = 0; m < atom->num_bond[i]; m++)
@ -637,7 +648,7 @@ void Neighbor::init()
}
}
if (atom->angles_allow) {
if (atom->avec->angles_allow) {
for (i = 0; i < atom->nlocal; i++) {
if (angle_off) break;
for (m = 0; m < atom->num_angle[i]; m++)
@ -646,7 +657,7 @@ void Neighbor::init()
}
int dihedral_off = 0;
if (atom->dihedrals_allow) {
if (atom->avec->dihedrals_allow) {
for (i = 0; i < atom->nlocal; i++) {
if (dihedral_off) break;
for (m = 0; m < atom->num_dihedral[i]; m++)
@ -655,7 +666,7 @@ void Neighbor::init()
}
int improper_off = 0;
if (atom->impropers_allow) {
if (atom->avec->impropers_allow) {
for (i = 0; i < atom->nlocal; i++) {
if (improper_off) break;
for (m = 0; m < atom->num_improper[i]; m++)
@ -780,7 +791,7 @@ void Neighbor::build()
memory->smalloc(maxlocal*sizeof(int *),"neigh:firstneigh_full");
}
if (history >= 0) {
if (fix_history) {
memory->sfree(firsttouch);
memory->sfree(firstshear);
firsttouch = (int **)
@ -1136,7 +1147,8 @@ void Neighbor::modify_params(int narg, char **arg)
} else if (strcmp(arg[iarg+1],"molecule") == 0) {
if (iarg+3 > narg) error->all("Illegal neigh_modify command");
if (atom->molecular == 0) {
char *str = "Must use molecular atom style with neigh_modify exclude molecule";
char *str = "Must use molecular atom style with"
" neigh_modify exclude molecule";
error->all(str);
}
if (nex_mol == maxex_mol) {
@ -1189,7 +1201,7 @@ int Neighbor::memory_usage()
bytes += maxpage_full*pgsize * sizeof(int);
}
if (history >= 0) {
if (fix_history) {
bytes += maxlocal * sizeof(int *);
bytes += maxlocal * sizeof(double *);
bytes += maxpage*pgsize * sizeof(int);