diff --git a/src/Makefile b/src/Makefile
index 6d21661b6ce228b1e369a5f4f5289bcb1d403547..b844cfad6bf25e9e38fc7c69e849d965673583e1 100755
--- a/src/Makefile
+++ b/src/Makefile
@@ -15,7 +15,12 @@ OBJ = $(SRC:.cpp=.o)
PACKAGE = asphere class2 colloid dipole dpd granular \
kspace manybody meam molecule opt poems xtc
+
+PACKUSER = user-ackland user-ewaldn
+
PACKUC = $(shell perl -e 'printf("%s", uc("$(PACKAGE)"));')
+PACKUSERUC = $(shell perl -e 'printf("%s", uc("$(PACKUSER)"));')
+
YESDIR = $(shell perl -e 'printf("%s", uc("$(@:yes-%=%)"));')
NODIR = $(shell perl -e 'printf("%s", uc("$(@:no-%=%)"));')
@@ -31,10 +36,15 @@ help:
@echo ''
@echo 'make package list available packages'
@echo 'make package-status status of all packages'
- @echo 'make yes-package install a package in src dir'
- @echo 'make no-package remove package files from src dir'
+ @echo 'make yes-package install a single package in src dir'
+ @echo 'make no-package remove a single package from src dir'
@echo 'make yes-all install all packages in src dir'
- @echo 'make no-all remove all package files from src dir'
+ @echo 'make no-all remove all packages from src dir'
+ @echo 'make yes-standard install all standard packages'
+ @echo 'make no-standard remove all standard packages'
+ @echo 'make yes-user install all user packages'
+ @echo 'make no-user remove all user packages'
+ @echo ''
@echo 'make package-update replace src files with package files'
@echo 'make package-overwrite replace package files with src files'
@echo ''
@@ -86,27 +96,45 @@ makelist:
@csh Make.csh Makefile.list
# Package management
-# status = list differences between src and package files
-# update = replace src files with newer package files
-# overwrite = overwrite package files with newer src files
package:
- @echo 'Available packages:'
- @echo $(PACKAGE)
+ @echo 'Standard packages:' $(PACKAGE)
@echo ''
+ @echo 'User-contributed packages:' $(PACKUSER)
+ @echo ''
+ @echo 'make package list available packages'
@echo 'make package-status status of all packages'
- @echo 'make yes-package install a package in src dir'
- @echo 'make no-package remove package files from src dir'
+ @echo 'make yes-package install a single package in src dir'
+ @echo 'make no-package remove a single package from src dir'
@echo 'make yes-all install all packages in src dir'
- @echo 'make no-all remove all package files from src dir'
+ @echo 'make no-all remove all packages from src dir'
+ @echo 'make yes-standard install all standard packages'
+ @echo 'make no-standard remove all standard packages'
+ @echo 'make yes-user install all user packages'
+ @echo 'make no-user remove all user packages'
+ @echo ''
@echo 'make package-update replace src files with package files'
@echo 'make package-overwrite replace package files with src files'
yes-all:
@for p in $(PACKAGE); do $(MAKE) yes-$$p; done
+ @for p in $(PACKUSER); do $(MAKE) yes-$$p; done
no-all:
@for p in $(PACKAGE); do $(MAKE) no-$$p; done
+ @for p in $(PACKUSER); do $(MAKE) no-$$p; done
+
+yes-standard:
+ @for p in $(PACKAGE); do $(MAKE) yes-$$p; done
+
+no-standard:
+ @for p in $(PACKAGE); do $(MAKE) no-$$p; done
+
+yes-user:
+ @for p in $(PACKUSER); do $(MAKE) yes-$$p; done
+
+no-user:
+ @for p in $(PACKUSER); do $(MAKE) no-$$p; done
yes-%:
@if [ ! -e $(YESDIR) ]; then \
@@ -124,11 +152,21 @@ no-%:
cd $(NODIR); csh -f Install.csh 0; cd ..; $(MAKE) clean-all; \
fi;
+# status = list differences between src and package files
+# update = replace src files with newer package files
+# overwrite = overwrite package files with newer src files
+
package-status:
@for p in $(PACKUC); do csh -f Package.csh $$p status; done
+ @echo ''
+ @for p in $(PACKUSERUC); do csh -f Package.csh $$p status; done
package-update:
@for p in $(PACKUC); do csh -f Package.csh $$p update; done
+ @echo ''
+ @for p in $(PACKUSERUC); do csh -f Package.csh $$p update; done
package-overwrite:
@for p in $(PACKUC); do csh -f Package.csh $$p overwrite; done
+ @echo ''
+ @for p in $(PACKUSERUC); do csh -f Package.csh $$p overwrite; done
diff --git a/src/Package.csh b/src/Package.csh
index 538572d413c364ab98fd434d4644f4c5a849ac07..0ab65a7752296a6fbd0ef52d2d655427baf39378 100644
--- a/src/Package.csh
+++ b/src/Package.csh
@@ -27,7 +27,7 @@
# just longer than the other (has new stuff added)
set glob
-set style = `echo $1 | sed 'y/ABCDEFGHIJKLMNOPQRSTUVWXYZ/abcdefghijklmnopqrstuvwxyz/'`
+set style = `echo $1 | sed 'y/-ABCDEFGHIJKLMNOPQRSTUVWXYZ/_abcdefghijklmnopqrstuvwxyz/'`
cd $1
if ($2 == "status") then
diff --git a/src/atom.cpp b/src/atom.cpp
index 97cf66558e9ebb3c8d5a95c07489c53b705ce7fb..943205b50a4557a22885e5124eb6305b6b28ef55 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -212,7 +212,7 @@ Atom::~Atom()
called from input script, restart file, replicate
------------------------------------------------------------------------- */
-void Atom::create_avec(char *style, int narg, char **arg)
+void Atom::create_avec(const char *style, int narg, char **arg)
{
delete [] atom_style;
if (avec) delete avec;
@@ -232,7 +232,7 @@ void Atom::create_avec(char *style, int narg, char **arg)
generate an AtomVec class
------------------------------------------------------------------------- */
-AtomVec *Atom::new_avec(char *style, int narg, char **arg)
+AtomVec *Atom::new_avec(const char *style, int narg, char **arg)
{
if (0) return NULL;
@@ -274,7 +274,7 @@ void Atom::init()
else return 0
------------------------------------------------------------------------- */
-int Atom::style_match(char *style)
+int Atom::style_match(const char *style)
{
if (strcmp(atom_style,style) == 0) return 1;
else if (strcmp(atom_style,"hybrid") == 0) {
@@ -602,7 +602,7 @@ int Atom::tag_consecutive()
trim anything from '#' onward
------------------------------------------------------------------------- */
-int Atom::count_words(char *line)
+int Atom::count_words(const char *line)
{
int n = strlen(line) + 1;
char *copy = (char *) memory->smalloc(n*sizeof(char),"copy");
@@ -991,7 +991,7 @@ void Atom::allocate_type_arrays()
called from reading of data file
------------------------------------------------------------------------- */
-void Atom::set_mass(char *str)
+void Atom::set_mass(const char *str)
{
if (mass == NULL) error->all("Cannot set mass for this atom style");
@@ -1067,7 +1067,7 @@ void Atom::check_mass()
called from reading of data file
------------------------------------------------------------------------- */
-void Atom::set_shape(char *str)
+void Atom::set_shape(const char *str)
{
if (shape == NULL) error->all("Cannot set shape for this atom style");
@@ -1140,7 +1140,7 @@ void Atom::check_shape()
called from reading of data file
------------------------------------------------------------------------- */
-void Atom::set_dipole(char *str)
+void Atom::set_dipole(const char *str)
{
if (dipole == NULL) error->all("Cannot set dipole for this atom style");
@@ -1244,7 +1244,7 @@ void Atom::add_callback(int flag)
flag = 0 for grow, 1 for restart
------------------------------------------------------------------------- */
-void Atom::delete_callback(char *id, int flag)
+void Atom::delete_callback(const char *id, int flag)
{
int ifix;
for (ifix = 0; ifix < modify->nfix; ifix++)
diff --git a/src/atom.h b/src/atom.h
index 3f18c33c14a0c4a51c5e90897c9796695f149a04..c2e1e0462b88bd8d0a4427af51484cb705895de6 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -97,17 +97,17 @@ class Atom : protected Pointers {
Atom(class LAMMPS *);
~Atom();
- void create_avec(char *, int, char **);
- class AtomVec *new_avec(char *, int, char **);
+ void create_avec(const char *, int, char **);
+ class AtomVec *new_avec(const char *, int, char **);
void init();
- int style_match(char *);
+ int style_match(const char *);
void modify_params(int, char **);
void tag_extend();
int tag_consecutive();
- int parse_data(char *);
- int count_words(char *);
+ int parse_data(const char *);
+ int count_words(const char *);
void data_atoms(int, char *);
void data_vels(int, char *);
@@ -117,22 +117,22 @@ class Atom : protected Pointers {
void data_impropers(int, char *);
void allocate_type_arrays();
- void set_mass(char *);
+ void set_mass(const char *);
void set_mass(int, double);
void set_mass(int, char **);
void set_mass(double *);
void check_mass();
- void set_shape(char *);
+ void set_shape(const char *);
void set_shape(int, char **);
void set_shape(double **);
void check_shape();
- void set_dipole(char *);
+ void set_dipole(const char *);
void set_dipole(int, char **);
void set_dipole(double *);
void check_dipole();
void add_callback(int);
- void delete_callback(char *, int);
+ void delete_callback(const char *, int);
void update_callback(int);
int memory_usage();
diff --git a/src/compute.cpp b/src/compute.cpp
index 0a6312068ec031ac2fdfd17592769a83bb175a81..1e0eee51f6c353c3ed76fff761b36f29c2176975 100644
--- a/src/compute.cpp
+++ b/src/compute.cpp
@@ -49,9 +49,9 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
scalar_flag = vector_flag = peratom_flag = 0;
tempflag = pressflag = 0;
+ npre = 0;
id_pre = NULL;
comm_forward = comm_reverse = 0;
- neigh_half_once = neigh_full_once = 0;
// set modify defaults
@@ -65,6 +65,9 @@ Compute::~Compute()
{
delete [] id;
delete [] style;
+
+ for (int i = 0; i < npre; i++) delete [] id_pre[i];
+ delete [] id_pre;
}
/* ---------------------------------------------------------------------- */
diff --git a/src/compute.h b/src/compute.h
index bae6bc1ab6e80cd0f07f1d17ec7231084096a848..a8f1b0f98f36dbc702179103dd8c25123c9fb3a5 100644
--- a/src/compute.h
+++ b/src/compute.h
@@ -39,18 +39,19 @@ class Compute : protected Pointers {
// must have both compute_scalar, compute_vector
int pressflag; // 1 if Compute can be used as pressure (uses virial)
// must have both compute_scalar, compute_vector
- char *id_pre; // ID of Compute that needs to be computed before this
double dof; // degrees-of-freedom for temperature
+ int npre; // # of computes to compute before this one
+ char **id_pre; // IDs of Computes to compute before this one
+
int comm_forward; // size of forward communication (0 if none)
int comm_reverse; // size of reverse communication (0 if none)
- int neigh_half_once; // 1 if requires half neighbor lists
- int neigh_full_once; // 1 if requires full neighbor lists
Compute(class LAMMPS *, int, char **);
virtual ~Compute();
void modify_params(int, char **);
virtual void init() = 0;
+ virtual void init_list(int, class NeighList *) {}
virtual double compute_scalar() {return 0.0;}
virtual void compute_vector() {}
virtual void compute_peratom() {}
diff --git a/src/compute_centro_atom.cpp b/src/compute_centro_atom.cpp
index 04b9383f3282ea6e8e8c0761e936e173a228897b..3506cc8dced2c984a4e9f755777d92d012ba5744 100644
--- a/src/compute_centro_atom.cpp
+++ b/src/compute_centro_atom.cpp
@@ -17,6 +17,8 @@
#include "modify.h"
#include "update.h"
#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
@@ -34,7 +36,6 @@ ComputeCentroAtom::ComputeCentroAtom(LAMMPS *lmp, int narg, char **arg) :
peratom_flag = 1;
size_peratom = 0;
- neigh_full_once = 1;
nmax = 0;
centro = NULL;
@@ -61,15 +62,31 @@ void ComputeCentroAtom::init()
if (strcmp(modify->compute[i]->style,"centro/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning("More than one compute centro/atom");
+
+ // need an occasional full neighbor list
+
+ int irequest = neighbor->request((void *) this);
+ neighbor->requests[irequest]->pair = 0;
+ neighbor->requests[irequest]->compute = 1;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->full = 1;
+ neighbor->requests[irequest]->occasional = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeCentroAtom::init_list(int id, NeighList *ptr)
+{
+ list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeCentroAtom::compute_peratom()
{
- int j,k,jj,kk,n,numneigh;
+ int i,j,k,ii,jj,kk,n,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq,value;
- int *neighs;
+ int *ilist,*jlist,*numneigh,**firstneigh;
double pairs[66];
// grow centro array if necessary
@@ -82,9 +99,14 @@ void ComputeCentroAtom::compute_peratom()
scalar_atom = centro;
}
- // if needed, build a full neighbor list
+ // invoke full neighbor list (will copy or build if necessary)
+
+ neighbor->build_one(list->index);
- if (!neighbor->full_every) neighbor->build_full();
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
// compute centro-symmetry parameter for each atom in group
// use full neighbor list
@@ -95,20 +117,21 @@ void ComputeCentroAtom::compute_peratom()
int nall = atom->nlocal + atom->nghost;
double cutsq = force->pair->cutforce * force->pair->cutforce;
- for (int i = 0; i < nlocal; i++)
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
if (mask[i] & groupbit) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
- neighs = neighbor->firstneigh_full[i];
- numneigh = neighbor->numneigh_full[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
// insure distsq and nearest arrays are long enough
- if (numneigh > maxneigh) {
+ if (jnum > maxneigh) {
memory->sfree(distsq);
memory->sfree(nearest);
- maxneigh = numneigh;
+ maxneigh = jnum;
distsq = (double *) memory->smalloc(maxneigh*sizeof(double),
"compute/centro/atom:distsq");
nearest = (int *) memory->smalloc(maxneigh*sizeof(int),
@@ -120,8 +143,8 @@ void ComputeCentroAtom::compute_peratom()
// nearest[] = atom indices of neighbors
n = 0;
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
if (j >= nall) j %= nall;
delx = xtmp - x[j][0];
@@ -169,7 +192,8 @@ void ComputeCentroAtom::compute_peratom()
value = 0.0;
for (j = 0; j < 6; j++) value += pairs[j];
centro[i] = value;
- }
+ } else centro[i] = 0.0;
+ }
}
/* ----------------------------------------------------------------------
diff --git a/src/compute_centro_atom.h b/src/compute_centro_atom.h
index 6a16d7c0593379e9626f8c23a2bec5a71349f583..1aa47a1d521abb4a50710ba9e679040bbaf5d271 100644
--- a/src/compute_centro_atom.h
+++ b/src/compute_centro_atom.h
@@ -23,6 +23,7 @@ class ComputeCentroAtom : public Compute {
ComputeCentroAtom(class LAMMPS *, int, char **);
~ComputeCentroAtom();
void init();
+ void init_list(int, class NeighList *);
void compute_peratom();
int memory_usage();
@@ -31,6 +32,7 @@ class ComputeCentroAtom : public Compute {
double *distsq;
int *nearest;
double *centro;
+ class NeighList *list;
void select(int, int, double *);
void select2(int, int, double *, int *);
diff --git a/src/compute_coord_atom.cpp b/src/compute_coord_atom.cpp
index 285ad1aa71982bc6e3f0d266e20abefde58817b6..f2d70915c6ea5c5d2fc21a1af530c7923edbf260 100644
--- a/src/compute_coord_atom.cpp
+++ b/src/compute_coord_atom.cpp
@@ -17,6 +17,8 @@
#include "atom.h"
#include "modify.h"
#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
@@ -30,13 +32,12 @@ using namespace LAMMPS_NS;
ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
- if (narg != 4) error->all("Illegal compute centro/atom command");
+ if (narg != 4) error->all("Illegal compute coord/atom command");
cutoff = atof(arg[3]);
peratom_flag = 1;
size_peratom = 0;
- neigh_full_once = 1;
nmax = 0;
coordination = NULL;
@@ -56,6 +57,15 @@ void ComputeCoordAtom::init()
if (force->pair == NULL || cutoff > force->pair->cutforce)
error->all("Compute coord/atom cutoff is longer than pairwise cutoff");
+ // need an occasional full neighbor list
+
+ int irequest = neighbor->request((void *) this);
+ neighbor->requests[irequest]->pair = 0;
+ neighbor->requests[irequest]->compute = 1;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->full = 1;
+ neighbor->requests[irequest]->occasional = 1;
+
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"coord/atom") == 0) count++;
@@ -65,11 +75,18 @@ void ComputeCoordAtom::init()
/* ---------------------------------------------------------------------- */
+void ComputeCoordAtom::init_list(int id, NeighList *ptr)
+{
+ list = ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
void ComputeCoordAtom::compute_peratom()
{
- int j,k,n,numneigh;
+ int i,j,ii,jj,inum,jnum,n;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighs;
+ int *ilist,*jlist,*numneigh,**firstneigh;
// grow coordination array if necessary
@@ -81,9 +98,14 @@ void ComputeCoordAtom::compute_peratom()
scalar_atom = coordination;
}
- // if needed, build a full neighbor list
+ // invoke full neighbor list (will copy or build if necessary)
+
+ neighbor->build_one(list->index);
- if (!neighbor->full_every) neighbor->build_full();
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
// compute coordination number for each atom in group
// use full neighbor list to count atoms less than cutoff
@@ -94,17 +116,18 @@ void ComputeCoordAtom::compute_peratom()
int nall = atom->nlocal + atom->nghost;
double cutsq = cutoff*cutoff;
- for (int i = 0; i < nlocal; i++)
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
if (mask[i] & groupbit) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
- neighs = neighbor->firstneigh_full[i];
- numneigh = neighbor->numneigh_full[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
n = 0;
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
if (j >= nall) j %= nall;
delx = xtmp - x[j][0];
@@ -115,8 +138,10 @@ void ComputeCoordAtom::compute_peratom()
}
coordination[i] = n;
- }
+ } else coordination[i] = 0.0;
+ }
}
+
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
diff --git a/src/compute_coord_atom.h b/src/compute_coord_atom.h
index 74ff9410873bbfecdcda6b2487bdc58a2d4b329f..ca121c1914dcd8bc996e108b9d3dac00d3a6dde9 100644
--- a/src/compute_coord_atom.h
+++ b/src/compute_coord_atom.h
@@ -23,6 +23,7 @@ class ComputeCoordAtom : public Compute {
ComputeCoordAtom(class LAMMPS *, int, char **);
~ComputeCoordAtom();
void init();
+ void init_list(int, class NeighList *);
void compute_peratom();
int memory_usage();
@@ -30,6 +31,7 @@ class ComputeCoordAtom : public Compute {
int nmax;
double cutoff;
double *coordination;
+ class NeighList *list;
};
}
diff --git a/src/compute_ebond_atom.cpp b/src/compute_ebond_atom.cpp
index 664a036e0b8626159931afcebd777ba1953c2981..f3f902bc07bd11e81889f223c3e2929a78ffda64 100644
--- a/src/compute_ebond_atom.cpp
+++ b/src/compute_ebond_atom.cpp
@@ -56,7 +56,7 @@ ComputeEbondAtom::~ComputeEbondAtom()
void ComputeEbondAtom::init()
{
if (force->bond == NULL)
- error->all("Bond style does not support computing per-atom energy");
+ error->all("Bond style does not support computing per-atom bond energy");
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
@@ -69,7 +69,7 @@ void ComputeEbondAtom::init()
void ComputeEbondAtom::compute_peratom()
{
- int i,n,i1,i2,type;
+ int i,n,i1,i2,type,iflag,jflag;
double delx,dely,delz,rsq,fforce,eng;
// grow energy array if necessary
@@ -95,6 +95,7 @@ void ComputeEbondAtom::compute_peratom()
// compute bond energy for atoms via bond->single()
// if neither atom is in compute group, skip that bond
+ // only add energy to atoms in group
double **x = atom->x;
int *mask = atom->mask;
@@ -105,7 +106,9 @@ void ComputeEbondAtom::compute_peratom()
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
- if ((mask[i1] & groupbit) == 0 && (mask[i2] & groupbit) == 0) continue;
+ iflag = mask[i1] & groupbit;
+ jflag = mask[i2] & groupbit;
+ if (iflag == 0 && jflag == 0) continue;
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
@@ -114,8 +117,8 @@ void ComputeEbondAtom::compute_peratom()
rsq = delx*delx + dely*dely + delz*delz;
force->bond->single(type,rsq,i1,i2,0,fforce,eng);
- energy[i] += eng;
- if (newton_bond || i2 < nlocal) energy[i2] += eng;
+ if (iflag) energy[i1] += eng;
+ if (jflag && (newton_bond || i2 < nlocal)) energy[i2] += eng;
}
// communicate energy between neigchbor procs
diff --git a/src/compute_epair_atom.cpp b/src/compute_epair_atom.cpp
index 36a16d92be03b9c75bb83974ab2987a74d1bd946..f7b3a4b7eb49024e89b47feb44ae4efd89725a88 100644
--- a/src/compute_epair_atom.cpp
+++ b/src/compute_epair_atom.cpp
@@ -15,6 +15,8 @@
#include "compute_epair_atom.h"
#include "atom.h"
#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
#include "modify.h"
#include "comm.h"
#include "update.h"
@@ -38,7 +40,6 @@ ComputeEpairAtom::ComputeEpairAtom(LAMMPS *lmp, int narg, char **arg) :
peratom_flag = 1;
size_peratom = 0;
comm_reverse = 1;
- neigh_half_once = 1;
nmax = 0;
energy = NULL;
@@ -58,6 +59,13 @@ void ComputeEpairAtom::init()
if (force->pair == NULL || force->pair->single_enable == 0)
error->all("Pair style does not support computing per-atom energy");
+ // need an occasional half neighbor list
+
+ int irequest = neighbor->request((void *) this);
+ neighbor->requests[irequest]->pair = 0;
+ neighbor->requests[irequest]->compute = 1;
+ neighbor->requests[irequest]->occasional = 1;
+
if (force->pair_match("eam")) eamstyle = 1;
else eamstyle = 0;
@@ -70,12 +78,19 @@ void ComputeEpairAtom::init()
/* ---------------------------------------------------------------------- */
+void ComputeEpairAtom::init_list(int id, NeighList *ptr)
+{
+ list = ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
void ComputeEpairAtom::compute_peratom()
{
- int i,j,k,n,itype,jtype,numneigh,iflag;
+ int i,j,ii,jj,n,inum,jnum,itype,jtype,iflag,jflag;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double factor_coul,factor_lj,eng;
- int *neighs;
+ int *ilist,*jlist,*numneigh,**firstneigh;
Pair::One one;
// grow energy array if necessary
@@ -99,12 +114,18 @@ void ComputeEpairAtom::compute_peratom()
for (i = 0; i < n; i++) energy[i] = 0.0;
- // if needed, build a half neighbor list
+ // invoke half neighbor list (will copy or build if necessary)
+
+ neighbor->build_one(list->index);
- if (!neighbor->half_every) neighbor->build_half();
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
// compute pairwise energy for atoms via pair->single()
// if neither atom is in compute group, skip that pair
+ // only add energy to atoms in group
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@@ -115,18 +136,20 @@ void ComputeEpairAtom::compute_peratom()
int *type = atom->type;
int nall = nlocal + atom->nghost;
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
iflag = mask[i] & groupbit;
- neighs = neighbor->firstneigh[i];
- numneigh = neighbor->numneigh[i];
-
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
- if (iflag == 0 && (mask[j] & groupbit) == 0) continue;
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ jflag = mask[j] & groupbit;
+ if (iflag == 0 && jflag == 0) continue;
if (j < nall) factor_coul = factor_lj = 1.0;
else {
@@ -144,8 +167,8 @@ void ComputeEpairAtom::compute_peratom()
if (rsq < cutsq[itype][jtype]) {
force->pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,1,one);
eng = one.eng_coul + one.eng_vdwl;
- energy[i] += eng;
- if (newton_pair || j < nlocal) energy[j] += eng;
+ if (iflag) energy[i] += eng;
+ if (jflag && (newton_pair || j < nlocal)) energy[j] += eng;
}
}
}
@@ -162,7 +185,8 @@ void ComputeEpairAtom::compute_peratom()
// only for atoms in compute group
if (eamstyle) {
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
if (mask[i] & groupbit) {
force->pair->single_embed(i,type[i],eng);
energy[i] += eng;
diff --git a/src/compute_epair_atom.h b/src/compute_epair_atom.h
index 6ead5058f52aa73e68f3eb34a0bd366e2e701aca..6ab6160b5b8f1658157330ff3c11f6578156432d 100644
--- a/src/compute_epair_atom.h
+++ b/src/compute_epair_atom.h
@@ -23,6 +23,7 @@ class ComputeEpairAtom : public Compute {
ComputeEpairAtom(class LAMMPS *, int, char **);
~ComputeEpairAtom();
void init();
+ void init_list(int, class NeighList *);
void compute_peratom();
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
@@ -30,6 +31,7 @@ class ComputeEpairAtom : public Compute {
private:
int nmax,eamstyle;
+ class NeighList *list;
double *energy;
};
diff --git a/src/compute_etotal_atom.cpp b/src/compute_etotal_atom.cpp
deleted file mode 100644
index e287cdd6f928735f80ba6084ce4e3dc3cfceec73..0000000000000000000000000000000000000000
--- a/src/compute_etotal_atom.cpp
+++ /dev/null
@@ -1,127 +0,0 @@
-/* ----------------------------------------------------------------------
- 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.
-------------------------------------------------------------------------- */
-
-#include "string.h"
-#include "compute_etotal_atom.h"
-#include "atom.h"
-#include "modify.h"
-#include "force.h"
-#include "comm.h"
-#include "memory.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-/* ---------------------------------------------------------------------- */
-
-ComputeEtotalAtom::ComputeEtotalAtom(LAMMPS *lmp, int narg, char **arg) :
- Compute(lmp, narg, arg)
-{
- if (narg != 4) error->all("Illegal compute etotal/atom command");
-
- // store epair ID used by energy computation
-
- int n = strlen(arg[3]) + 1;
- id_pre = new char[n];
- strcpy(id_pre,arg[3]);
-
- peratom_flag = 1;
- size_peratom = 0;
-
- nmax = 0;
- etotal = NULL;
-}
-
-/* ---------------------------------------------------------------------- */
-
-ComputeEtotalAtom::~ComputeEtotalAtom()
-{
- delete [] id_pre;
- memory->sfree(etotal);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void ComputeEtotalAtom::init()
-{
- int count = 0;
- for (int i = 0; i < modify->ncompute; i++)
- if (strcmp(modify->compute[i]->style,"etotal/atom") == 0) count++;
- if (count > 1 && comm->me == 0)
- error->warning("More than one compute etotal/atom");
-
- // set epair Compute used by this compute
-
- int icompute = modify->find_compute(id_pre);
- if (icompute < 0)
- error->all("Could not find compute etotal/atom pre-compute ID");
- compute_epair = modify->compute[icompute];
-
- if (groupbit != compute_epair->groupbit && comm->me == 0)
- error->warning("Group for compute etotal and its epair are not the same");
-}
-
-/* ---------------------------------------------------------------------- */
-
-void ComputeEtotalAtom::compute_peratom()
-{
- // grow etotal array if necessary
-
- if (atom->nlocal > nmax) {
- memory->sfree(etotal);
- nmax = atom->nmax;
- etotal = (double *)
- memory->smalloc(nmax*sizeof(double),"compute/etotal/atom:etotal");
- scalar_atom = etotal;
- }
-
- // compute total energy for each atom in group
-
- double *epair = compute_epair->scalar_atom;
- double mvv2e = force->mvv2e;
- double **v = atom->v;
- double *mass = atom->mass;
- double *rmass = atom->rmass;
- int *mask = atom->mask;
- int *type = atom->type;
- int nlocal = atom->nlocal;
-
- double ke;
-
- if (mass)
- for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- ke = 0.5 * mvv2e * mass[type[i]] *
- (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
- etotal[i] = ke + epair[i];
- }
- }
- else
- for (int i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- ke = 0.5 * mvv2e * rmass[i] *
- (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
- etotal[i] = ke + epair[i];
- }
- }
-}
-
-/* ----------------------------------------------------------------------
- memory usage of local atom-based array
-------------------------------------------------------------------------- */
-
-int ComputeEtotalAtom::memory_usage()
-{
- int bytes = nmax * sizeof(double);
- return bytes;
-}
diff --git a/src/compute_ke_atom.cpp b/src/compute_ke_atom.cpp
index 9734594165bed771c7b83e9ad13692d3e81ee901..27d123bd5d230e18b2611a90df2fc37f61d77e60 100644
--- a/src/compute_ke_atom.cpp
+++ b/src/compute_ke_atom.cpp
@@ -82,14 +82,15 @@ void ComputeKEAtom::compute_peratom()
if (mask[i] & groupbit) {
ke[i] = 0.5 * mvv2e * mass[type[i]] *
(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
- }
+ } else ke[i] = 0.0;
}
+
else
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ke[i] = 0.5 * mvv2e * rmass[i] *
(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
- }
+ } else ke[i] = 0.0;
}
}
diff --git a/src/compute_pressure.cpp b/src/compute_pressure.cpp
index d32f16230df790961be366d9c924a65bc402ed1e..554fb57837b6e82ffa29db02cd553ede6bacb0c1 100644
--- a/src/compute_pressure.cpp
+++ b/src/compute_pressure.cpp
@@ -42,11 +42,13 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
// store temperature ID used by pressure computation
// insure it is valid for temperature computation
+ npre = 1;
+ id_pre = new char*[1];
int n = strlen(arg[3]) + 1;
- id_pre = new char[n];
- strcpy(id_pre,arg[3]);
+ id_pre[0] = new char[n];
+ strcpy(id_pre[0],arg[3]);
- int icompute = modify->find_compute(id_pre);
+ int icompute = modify->find_compute(id_pre[0]);
if (icompute < 0) error->all("Could not find compute pressure temp ID");
if (modify->compute[icompute]->tempflag == 0)
@@ -66,7 +68,6 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
ComputePressure::~ComputePressure()
{
- delete [] id_pre;
delete [] vector;
delete [] vptr;
}
@@ -81,7 +82,7 @@ void ComputePressure::init()
// set temperature used by pressure
- int icompute = modify->find_compute(id_pre);
+ int icompute = modify->find_compute(id_pre[0]);
if (icompute < 0) error->all("Could not find compute pressure temp ID");
temperature = modify->compute[icompute];
diff --git a/src/compute_stress_atom.cpp b/src/compute_stress_atom.cpp
index 1ff75411244487ba297db8799a4356ef9899b30b..eb113fec274fbe7508e911d3146953240528eb50 100644
--- a/src/compute_stress_atom.cpp
+++ b/src/compute_stress_atom.cpp
@@ -15,6 +15,8 @@
#include "compute_stress_atom.h"
#include "atom.h"
#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
#include "modify.h"
#include "comm.h"
#include "update.h"
@@ -40,7 +42,6 @@ ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
peratom_flag = 1;
size_peratom = 6;
comm_reverse = 6;
- neigh_half_once = 1;
// process args
@@ -85,6 +86,14 @@ void ComputeStressAtom::init()
if (force->pair == NULL || force->pair->single_enable == 0)
error->all("Pair style does not support computing per-atom stress");
pairflag = 1;
+
+ // need an occasional half neighbor list
+
+ int irequest = neighbor->request((void *) this);
+ neighbor->requests[irequest]->pair = 0;
+ neighbor->requests[irequest]->compute = 1;
+ neighbor->requests[irequest]->occasional = 1;
+
} else pairflag = 0;
if (bondrequest && force->bond) bondflag = 1;
@@ -99,12 +108,19 @@ void ComputeStressAtom::init()
/* ---------------------------------------------------------------------- */
+void ComputeStressAtom::init_list(int id, NeighList *ptr)
+{
+ list = ptr;
+}
+
+/* ---------------------------------------------------------------------- */
+
void ComputeStressAtom::compute_peratom()
{
- int i,j,k,n,i1,i2,itype,jtype,numneigh,iflag;
+ int i,j,ii,jj,n,i1,i2,inum,jnum,itype,jtype,iflag,jflag;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq,eng;
double factor_coul,factor_lj,fforce,rmass;
- int *neighs;
+ int *ilist,*jlist,*numneigh,**firstneigh;
Pair::One one;
// grow stress array if necessary
@@ -136,12 +152,18 @@ void ComputeStressAtom::compute_peratom()
// compute pairwise stress for atoms via pair->single()
// if neither atom is in compute group, skip that pair
+ // only add stress to atoms in group
if (pairflag) {
- // if needed, build a half neighbor list
+ // invoke half neighbor list (will copy or build if necessary)
- if (!neighbor->half_every) neighbor->build_half();
+ neighbor->build_one(list->index);
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
@@ -153,18 +175,20 @@ void ComputeStressAtom::compute_peratom()
int *type = atom->type;
int nall = nlocal + atom->nghost;
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
iflag = mask[i] & groupbit;
- neighs = neighbor->firstneigh[i];
- numneigh = neighbor->numneigh[i];
-
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
- if (iflag == 0 && (mask[j] & groupbit) == 0) continue;
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ jflag = mask[j] & groupbit;
+ if (iflag == 0 && jflag == 0) continue;
if (j < nall) factor_coul = factor_lj = 1.0;
else {
@@ -183,13 +207,15 @@ void ComputeStressAtom::compute_peratom()
force->pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,0,one);
fforce = one.fforce;
- stress[i][0] -= delx*delx*fforce;
- stress[i][1] -= dely*dely*fforce;
- stress[i][2] -= delz*delz*fforce;
- stress[i][3] -= delx*dely*fforce;
- stress[i][4] -= delx*delz*fforce;
- stress[i][5] -= dely*delz*fforce;
- if (newton_pair || j < nlocal) {
+ if (iflag) {
+ stress[i][0] -= delx*delx*fforce;
+ stress[i][1] -= dely*dely*fforce;
+ stress[i][2] -= delz*delz*fforce;
+ stress[i][3] -= delx*dely*fforce;
+ stress[i][4] -= delx*delz*fforce;
+ stress[i][5] -= dely*delz*fforce;
+ }
+ if (jflag && (newton_pair || j < nlocal)) {
stress[j][0] -= delx*delx*fforce;
stress[j][1] -= dely*dely*fforce;
stress[j][2] -= delz*delz*fforce;
@@ -205,6 +231,7 @@ void ComputeStressAtom::compute_peratom()
// compute bond stress for atoms via bond->single()
// if neither atom is in compute group, skip that bond
+ // only add stress to atoms in group
if (bondflag) {
double **x = atom->x;
@@ -218,7 +245,9 @@ void ComputeStressAtom::compute_peratom()
i1 = bondlist[n][0];
i2 = bondlist[n][1];
type = bondlist[n][2];
- if ((mask[i1] & groupbit) == 0 && (mask[i2] & groupbit) == 0) continue;
+ iflag = mask[i1] & groupbit;
+ jflag = mask[i2] & groupbit;
+ if (iflag == 0 && jflag == 0) continue;
delx = x[i1][0] - x[i2][0];
dely = x[i1][1] - x[i2][1];
@@ -228,14 +257,16 @@ void ComputeStressAtom::compute_peratom()
rsq = delx*delx + dely*dely + delz*delz;
force->bond->single(type,rsq,i1,i2,0,fforce,eng);
- stress[i1][0] -= delx*delx*fforce;
- stress[i1][1] -= dely*dely*fforce;
- stress[i1][2] -= delz*delz*fforce;
- stress[i1][3] -= delx*dely*fforce;
- stress[i1][4] -= delx*delz*fforce;
- stress[i1][5] -= dely*delz*fforce;
-
- if (newton_bond || i2 < nlocal) {
+ if (iflag) {
+ stress[i1][0] -= delx*delx*fforce;
+ stress[i1][1] -= dely*dely*fforce;
+ stress[i1][2] -= delz*delz*fforce;
+ stress[i1][3] -= delx*dely*fforce;
+ stress[i1][4] -= delx*delz*fforce;
+ stress[i1][5] -= dely*delz*fforce;
+ }
+
+ if (jflag && (newton_bond || i2 < nlocal)) {
stress[i2][0] -= delx*delx*fforce;
stress[i2][1] -= dely*dely*fforce;
stress[i2][2] -= delz*delz*fforce;
diff --git a/src/compute_stress_atom.h b/src/compute_stress_atom.h
index 469fc331e30deeda5ae8ce9cbfa99e15fc7f6275..b936be80415446d9bbaf8fa04da058bb384efe9a 100644
--- a/src/compute_stress_atom.h
+++ b/src/compute_stress_atom.h
@@ -24,6 +24,7 @@ class ComputeStressAtom : public Compute {
ComputeStressAtom(class LAMMPS *, int, char **);
~ComputeStressAtom();
void init();
+ void init_list(int, class NeighList *);
void compute_peratom();
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
@@ -33,7 +34,7 @@ class ComputeStressAtom : public Compute {
int pairrequest,bondrequest,kerequest;
int pairflag,bondflag;
int nmax;
-
+ class NeighList *list;
double **stress;
};
diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp
index 081741541a6d8102e64fb54f651bf68180a2d2ea..4fcc982956f50f3a76a9ec56dc9461ffdeb1348e 100644
--- a/src/delete_atoms.cpp
+++ b/src/delete_atoms.cpp
@@ -22,6 +22,8 @@
#include "group.h"
#include "region.h"
#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
#include "comm.h"
#include "force.h"
#include "error.h"
@@ -53,15 +55,15 @@ void DeleteAtoms::command(int narg, char **arg)
// allocate and initialize deletion list
int nlocal = atom->nlocal;
- int *list = new int[nlocal];
+ int *dlist = new int[nlocal];
- for (int i = 0; i < nlocal; i++) list[i] = 0;
+ for (int i = 0; i < nlocal; i++) dlist[i] = 0;
// delete the atoms
- if (strcmp(arg[0],"group") == 0) delete_group(narg,arg,list);
- else if (strcmp(arg[0],"region") == 0) delete_region(narg,arg,list);
- else if (strcmp(arg[0],"overlap") == 0) delete_overlap(narg,arg,list);
+ if (strcmp(arg[0],"group") == 0) delete_group(narg,arg,dlist);
+ else if (strcmp(arg[0],"region") == 0) delete_region(narg,arg,dlist);
+ else if (strcmp(arg[0],"overlap") == 0) delete_overlap(narg,arg,dlist);
else error->all("Illegal delete_atoms command");
// delete local atoms in list
@@ -71,14 +73,14 @@ void DeleteAtoms::command(int narg, char **arg)
int i = 0;
while (i < nlocal) {
- if (list[i]) {
+ if (dlist[i]) {
avec->copy(nlocal-1,i);
- list[i] = list[nlocal-1];
+ dlist[i] = dlist[nlocal-1];
nlocal--;
} else i++;
}
atom->nlocal = nlocal;
- delete [] list;
+ delete [] dlist;
// if non-molecular system, reset atom tags to be contiguous
// set all atom IDs to 0, call tag_extend()
@@ -120,7 +122,7 @@ void DeleteAtoms::command(int narg, char **arg)
group will still exist
------------------------------------------------------------------------- */
-void DeleteAtoms::delete_group(int narg, char **arg, int *list)
+void DeleteAtoms::delete_group(int narg, char **arg, int *dlist)
{
if (narg != 2) error->all("Illegal delete_atoms command");
@@ -132,14 +134,14 @@ void DeleteAtoms::delete_group(int narg, char **arg, int *list)
int groupbit = group->bitmask[igroup];
for (int i = 0; i < nlocal; i++)
- if (mask[i] & groupbit) list[i] = 1;
+ if (mask[i] & groupbit) dlist[i] = 1;
}
/* ----------------------------------------------------------------------
delete all atoms in region
------------------------------------------------------------------------- */
-void DeleteAtoms::delete_region(int narg, char **arg, int *list)
+void DeleteAtoms::delete_region(int narg, char **arg, int *dlist)
{
if (narg != 2) error->all("Illegal delete_atoms command");
@@ -150,7 +152,7 @@ void DeleteAtoms::delete_region(int narg, char **arg, int *list)
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
- if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) list[i] = 1;
+ if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) dlist[i] = 1;
}
/* ----------------------------------------------------------------------
@@ -160,7 +162,7 @@ void DeleteAtoms::delete_region(int narg, char **arg, int *list)
no guarantee that minimium number of atoms will be deleted
------------------------------------------------------------------------- */
-void DeleteAtoms::delete_overlap(int narg, char **arg, int *list)
+void DeleteAtoms::delete_overlap(int narg, char **arg, int *dlist)
{
if (narg < 2) error->all("Illegal delete_atoms command");
@@ -180,19 +182,29 @@ void DeleteAtoms::delete_overlap(int narg, char **arg, int *list)
type2 = atoi(arg[3]);
} else error->all("Illegal delete_atoms command");
- // init entire system since comm->borders and neighbor->build is done
- // comm::init needs neighbor::init needs pair::init needs kspace::init, etc
- // set half_command since will require half neigh list even if
- // neighbor would otherwise not create one, then unset it
-
if (comm->me == 0 && screen)
fprintf(screen,"System init for delete_atoms ...\n");
- neighbor->half_command = 1;
+
+ // request a half neighbor list for use by this command
+
+ int irequest = neighbor->request((void *) this);
+ neighbor->requests[irequest]->pair = 0;
+ neighbor->requests[irequest]->command = 1;
+ neighbor->requests[irequest]->occasional = 1;
+
+ // init entire system since comm->borders and neighbor->build is done
+ // comm::init needs neighbor::init needs pair::init needs kspace::init, etc
+
lmp->init();
- neighbor->half_command = 0;
+
+ // error check on cutoff
+
+ if (cut > neighbor->cutghost)
+ error->all("Delete_atoms cutoff > ghost cutoff");
// setup domain, communication and neighboring
// acquire ghosts
+ // build neighbor list based on earlier request
if (domain->triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
@@ -203,16 +215,8 @@ void DeleteAtoms::delete_overlap(int narg, char **arg, int *list)
comm->borders();
if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
- // call to build() forces memory allocation for neighbor lists
- // build half list explicitly if build() doesn't do it
-
- neighbor->build();
- if (!neighbor->half_every) neighbor->build_half();
-
- // error check on cutoff
-
- if (cut > neighbor->cutghost)
- error->all("Delete_atoms cutoff > ghost cutoff");
+ NeighList *list = neighbor->lists[irequest];
+ neighbor->build_one(irequest);
// create an atom map if one doesn't exist already
@@ -245,30 +249,37 @@ void DeleteAtoms::delete_overlap(int narg, char **arg, int *list)
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
- int i,j,k,m,itype,jtype,numneigh;
+ int i,j,ii,jj,m,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighs;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
- neighs = neighbor->firstneigh[i];
- numneigh = neighbor->numneigh[i];
-
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+
if (j >= nall) {
if (special_coul[j/nall] == 0.0 && special_lj[j/nall] == 0.0) continue;
j %= nall;
}
if (j < nlocal) {
- if (list[j]) continue;
+ if (dlist[j]) continue;
} else {
m = atom->map(tag[j]);
- if (m < nlocal && list[m]) continue;
+ if (m < nlocal && dlist[m]) continue;
}
delx = xtmp - x[j][0];
@@ -286,7 +297,7 @@ void DeleteAtoms::delete_overlap(int narg, char **arg, int *list)
if (j >= nlocal && newton_pair == 0 && tag[j] < tag[i]) continue;
- list[i] = 1;
+ dlist[i] = 1;
break;
}
}
diff --git a/src/domain.cpp b/src/domain.cpp
index c4a69443eb24e7077de419c0ab517f98aea19de4..cece653486f5cb86e0805e442319618c455bf541 100644
--- a/src/domain.cpp
+++ b/src/domain.cpp
@@ -811,7 +811,7 @@ void Domain::set_boundary(int narg, char **arg)
print box info, orthogonal or triclinic
------------------------------------------------------------------------- */
-void Domain::print_box(char *str)
+void Domain::print_box(const char *str)
{
if (comm->me == 0) {
if (screen) {
@@ -819,7 +819,7 @@ void Domain::print_box(char *str)
fprintf(screen,"%sorthogonal box = (%g %g %g) to (%g %g %g)\n",
str,boxlo[0],boxlo[1],boxlo[2],boxhi[0],boxhi[1],boxhi[2]);
else {
- char *format =
+ char *format = (char *)
"%striclinic box = (%g %g %g) to (%g %g %g) with tilt (%g %g %g)\n";
fprintf(screen,format,
str,boxlo[0],boxlo[1],boxlo[2],boxhi[0],boxhi[1],boxhi[2],
@@ -831,7 +831,7 @@ void Domain::print_box(char *str)
fprintf(logfile,"%sorthogonal box = (%g %g %g) to (%g %g %g)\n",
str,boxlo[0],boxlo[1],boxlo[2],boxhi[0],boxhi[1],boxhi[2]);
else {
- char *format =
+ char *format = (char *)
"%striclinic box = (%g %g %g) to (%g %g %g) with tilt (%g %g %g)\n";
fprintf(logfile,format,
str,boxlo[0],boxlo[1],boxlo[2],boxhi[0],boxhi[1],boxhi[2],
diff --git a/src/domain.h b/src/domain.h
index 07b4d13594270136e15a1cc0ca636d9179c43639..a0bd61eec5984c0581f4adb9d5d6a98df7c1a96b 100644
--- a/src/domain.h
+++ b/src/domain.h
@@ -97,7 +97,7 @@ class Domain : protected Pointers {
void add_region(int, char **);
int find_region(char *);
void set_boundary(int, char **);
- void print_box(char *);
+ void print_box(const char *);
void lamda2x(int);
void x2lamda(int);
diff --git a/src/dump_atom.cpp b/src/dump_atom.cpp
index 02bcd0836c47ee7c15161a011d348e778277a7b9..50aea9be29042a82c8e4f2a2fc402b83deb8889d 100644
--- a/src/dump_atom.cpp
+++ b/src/dump_atom.cpp
@@ -59,8 +59,8 @@ void DumpAtom::init()
strcat(format,"\n");
} else {
char *str;
- if (image_flag == 0) str = "%d %d %g %g %g";
- else str = "%d %d %g %g %g %d %d %d";
+ if (image_flag == 0) str = (char *) "%d %d %g %g %g";
+ else str = (char *) "%d %d %g %g %g %d %d %d";
int n = strlen(str) + 2;
format = new char[n];
strcpy(format,str);
diff --git a/src/dump_custom.cpp b/src/dump_custom.cpp
index 3561aea034a2983d8a3ba743c330b5b76b88a2ee..a167a5e3ce841c5646f017a258d3c9143e9cf524 100644
--- a/src/dump_custom.cpp
+++ b/src/dump_custom.cpp
@@ -22,6 +22,7 @@
#include "update.h"
#include "modify.h"
#include "compute.h"
+#include "fix.h"
#include "memory.h"
#include "error.h"
@@ -33,8 +34,7 @@ enum{TAG,MOL,TYPE,X,Y,Z,XS,YS,ZS,XU,YU,ZU,IX,IY,IZ,
VX,VY,VZ,FX,FY,FZ,
Q,MUX,MUY,MUZ,
QUATW,QUATI,QUATJ,QUATK,TQX,TQY,TQZ,
- EPAIR,EBOND,KE,ETOTAL,CENTRO,SXX,SYY,SZZ,SXY,SXZ,SYZ,
- COMPUTE};
+ COMPUTE,FIX};
enum{LT,LE,GT,GE,EQ,NEQ};
enum{INT,DOUBLE};
@@ -45,6 +45,8 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
{
if (narg == 5) error->all("No dump custom arguments specified");
+ nevery = atoi(arg[3]);
+
size_one = nfield = narg-5;
pack_choice = new FnPtrPack[nfield];
vtype = new int[nfield];
@@ -55,17 +57,7 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
thresh_op = NULL;
thresh_value = NULL;
- // flags, IDs, and memory for compute objects dump may create
-
- index_epair = index_ebond = index_ke =
- index_etotal = index_centro = index_stress = -1;
-
- style_epair = "epair/atom";
- style_ebond = "ebond/atom";
- style_ke = "ke/atom";
- style_etotal = "etotal/atom";
- style_centro = "centro/atom";
- style_stress = "stress/atom";
+ // compute and fix objects dump may create
ncompute = 0;
id_compute = NULL;
@@ -74,19 +66,16 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
"dump:field2compute");
arg_compute = (int *) memory->smalloc(nfield*sizeof(int),"dump:arg_compute");
+ nfix = 0;
+ id_fix = NULL;
+ fix = NULL;
+ field2fix = (int *) memory->smalloc(nfield*sizeof(int),"dump:field2fix");
+ arg_fix = (int *) memory->smalloc(nfield*sizeof(int),"dump:arg_fix");
+
// process keywords
parse_fields(narg,arg);
- // create the requested Computes
-
- if (index_epair >= 0) create_compute(style_epair,NULL);
- if (index_ebond >= 0) create_compute(style_ebond,NULL);
- if (index_ke >= 0) create_compute(style_ke,NULL);
- if (index_etotal >= 0) create_compute(style_etotal,style_epair);
- if (index_centro >= 0) create_compute(style_centro,NULL);
- if (index_stress >= 0) create_compute(style_stress,NULL);
-
// atom selection arrays
maxlocal = 0;
@@ -122,21 +111,18 @@ DumpCustom::~DumpCustom()
memory->sfree(thresh_op);
memory->sfree(thresh_value);
- // delete Compute classes if dump custom created them
-
- if (index_epair >= 0) modify->delete_compute(id_compute[index_epair]);
- if (index_ebond >= 0) modify->delete_compute(id_compute[index_ebond]);
- if (index_ke >= 0) modify->delete_compute(id_compute[index_ke]);
- if (index_etotal >= 0) modify->delete_compute(id_compute[index_etotal]);
- if (index_centro >= 0) modify->delete_compute(id_compute[index_centro]);
- if (index_stress >= 0) modify->delete_compute(id_compute[index_stress]);
-
for (int i = 0; i < ncompute; i++) delete [] id_compute[i];
memory->sfree(id_compute);
memory->sfree(compute);
memory->sfree(field2compute);
memory->sfree(arg_compute);
+ for (int i = 0; i < nfix; i++) delete [] id_fix[i];
+ memory->sfree(id_fix);
+ memory->sfree(fix);
+ memory->sfree(field2fix);
+ memory->sfree(arg_fix);
+
delete [] choose;
delete [] dchoose;
@@ -177,7 +163,8 @@ void DumpCustom::init()
if (binary) write_choice = &DumpCustom::write_binary;
else write_choice = &DumpCustom::write_text;
- // find current ptr for each Compute ID
+ // find current ptr for each compute and fix ID
+ // check that fix frequency is acceptable
int icompute;
for (int i = 0; i < ncompute; i++) {
@@ -185,6 +172,15 @@ void DumpCustom::init()
if (icompute < 0) error->all("Could not find dump custom compute ID");
compute[i] = modify->compute[icompute];
}
+
+ int ifix;
+ for (int i = 0; i < nfix; i++) {
+ ifix = modify->find_fix(id_fix[i]);
+ if (ifix < 0) error->all("Could not find dump custom fix ID");
+ fix[i] = modify->fix[ifix];
+ if (nevery % modify->fix[ifix]->peratom_freq)
+ error->all("Dump custom and fix not computed at compatible times");
+ }
}
/* ---------------------------------------------------------------------- */
@@ -431,39 +427,7 @@ int DumpCustom::count()
} else if (thresh_array[ithresh] == TQZ) {
ptr = &atom->torque[0][2];
nstride = 3;
- } else if (thresh_array[ithresh] == EPAIR) {
- ptr = compute[index_epair]->scalar_atom;
- nstride = 1;
- } else if (thresh_array[ithresh] == EBOND) {
- ptr = compute[index_ebond]->scalar_atom;
- nstride = 1;
- } else if (thresh_array[ithresh] == KE) {
- ptr = compute[index_ke]->scalar_atom;
- nstride = 1;
- } else if (thresh_array[ithresh] == ETOTAL) {
- ptr = compute[index_etotal]->scalar_atom;
- nstride = 1;
- } else if (thresh_array[ithresh] == CENTRO) {
- ptr = compute[index_centro]->scalar_atom;
- nstride = 1;
- } else if (thresh_array[ithresh] == SXX) {
- ptr = &compute[index_stress]->vector_atom[0][0];
- nstride = 6;
- } else if (thresh_array[ithresh] == SYY) {
- ptr = &compute[index_stress]->vector_atom[0][1];
- nstride = 6;
- } else if (thresh_array[ithresh] == SZZ) {
- ptr = &compute[index_stress]->vector_atom[0][2];
- nstride = 6;
- } else if (thresh_array[ithresh] == SXY) {
- ptr = &compute[index_stress]->vector_atom[0][3];
- nstride = 6;
- } else if (thresh_array[ithresh] == SXZ) {
- ptr = &compute[index_stress]->vector_atom[0][4];
- nstride = 6;
- } else if (thresh_array[ithresh] == SYZ) {
- ptr = &compute[index_stress]->vector_atom[0][5];
- nstride = 6;
+
} else if (thresh_array[ithresh] == COMPUTE) {
i = nfield + ithresh;
if (arg_compute[i] == 0) {
@@ -473,6 +437,16 @@ int DumpCustom::count()
ptr = &compute[field2compute[i]]->vector_atom[0][arg_compute[i]-1];
nstride = compute[field2compute[i]]->size_peratom;
}
+
+ } else if (thresh_array[ithresh] == FIX) {
+ i = nfield + ithresh;
+ if (arg_fix[i] == 0) {
+ ptr = fix[field2fix[i]]->scalar_atom;
+ nstride = 1;
+ } else {
+ ptr = &fix[field2fix[i]]->vector_atom[0][arg_fix[i]-1];
+ nstride = fix[field2fix[i]]->size_peratom;
+ }
}
// unselect atoms that don't meet threshhold criterion
@@ -704,56 +678,9 @@ void DumpCustom::parse_fields(int narg, char **arg)
pack_choice[i] = &DumpCustom::pack_tqz;
vtype[i] = DOUBLE;
- } else if (strcmp(arg[iarg],"epair") == 0) {
- pack_choice[i] = &DumpCustom::pack_epair;
- vtype[i] = DOUBLE;
- index_epair = add_compute(style_epair,1);
- } else if (strcmp(arg[iarg],"ebond") == 0) {
- pack_choice[i] = &DumpCustom::pack_ebond;
- vtype[i] = DOUBLE;
- index_ebond = add_compute(style_ebond,1);
- } else if (strcmp(arg[iarg],"ke") == 0) {
- pack_choice[i] = &DumpCustom::pack_ke;
- vtype[i] = DOUBLE;
- index_ke = add_compute(style_ke,1);
- } else if (strcmp(arg[iarg],"etotal") == 0) {
- pack_choice[i] = &DumpCustom::pack_etotal;
- vtype[i] = DOUBLE;
- index_epair = add_compute(style_epair,1);
- index_etotal = add_compute(style_etotal,1);
- } else if (strcmp(arg[iarg],"centro") == 0) {
- pack_choice[i] = &DumpCustom::pack_centro;
- vtype[i] = DOUBLE;
- index_centro = add_compute(style_centro,1);
-
- } else if (strcmp(arg[iarg],"sxx") == 0) {
- pack_choice[i] = &DumpCustom::pack_sxx;
- vtype[i] = DOUBLE;
- index_stress = add_compute(style_stress,1);
- } else if (strcmp(arg[iarg],"syy") == 0) {
- pack_choice[i] = &DumpCustom::pack_syy;
- vtype[i] = DOUBLE;
- index_stress = add_compute(style_stress,1);
- } else if (strcmp(arg[iarg],"szz") == 0) {
- pack_choice[i] = &DumpCustom::pack_szz;
- vtype[i] = DOUBLE;
- index_stress = add_compute(style_stress,1);
- } else if (strcmp(arg[iarg],"sxy") == 0) {
- pack_choice[i] = &DumpCustom::pack_sxy;
- vtype[i] = DOUBLE;
- index_stress = add_compute(style_stress,1);
- } else if (strcmp(arg[iarg],"sxz") == 0) {
- pack_choice[i] = &DumpCustom::pack_sxz;
- vtype[i] = DOUBLE;
- index_stress = add_compute(style_stress,1);
- } else if (strcmp(arg[iarg],"syz") == 0) {
- pack_choice[i] = &DumpCustom::pack_syz;
- vtype[i] = DOUBLE;
- index_stress = add_compute(style_stress,1);
-
// compute value = c_ID
// if no trailing [], then arg is set to 0, else arg is between []
- // if Compute has pre-compute, first add it to list
+ // if Compute has pre-computes, first add them to list
} else if (strncmp(arg[iarg],"c_",2) == 0) {
pack_choice[i] = &DumpCustom::pack_compute;
@@ -782,9 +709,43 @@ void DumpCustom::parse_fields(int narg, char **arg)
if (arg_compute[i] > 0 &&
arg_compute[i] > modify->compute[n]->size_peratom)
error->all("Dump custom compute ID vector is not large enough");
- if (modify->compute[n]->id_pre)
- int tmp = add_compute(modify->compute[n]->id_pre,0);
- field2compute[i] = add_compute(suffix,0);
+ if (modify->compute[n]->npre)
+ for (int ic = 0; ic < modify->compute[n]->npre; ic++)
+ int tmp = add_compute(modify->compute[n]->id_pre[ic]);
+ field2compute[i] = add_compute(suffix);
+ delete [] suffix;
+
+ // fix value = f_ID
+ // if no trailing [], then arg is set to 0, else arg is between []
+
+ } else if (strncmp(arg[iarg],"f_",2) == 0) {
+ pack_choice[i] = &DumpCustom::pack_fix;
+ vtype[i] = DOUBLE;
+
+ int n = strlen(arg[iarg]);
+ char *suffix = new char[n];
+ strcpy(suffix,&arg[iarg][2]);
+
+ char *ptr = strchr(suffix,'[');
+ if (ptr) {
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all("Invalid keyword in dump custom command");
+ arg_fix[i] = atoi(ptr+1);
+ *ptr = '\0';
+ } else arg_fix[i] = 0;
+
+ n = modify->find_fix(suffix);
+ if (n < 0) error->all("Could not find dump custom fix ID");
+ if (modify->fix[n]->peratom_flag == 0)
+ error->all("Dump custom fix ID does not compute peratom info");
+ if (arg_fix[i] == 0 && modify->fix[n]->size_peratom > 0)
+ error->all("Dump custom fix ID does not compute scalar per atom");
+ if (arg_fix[i] > 0 && modify->fix[n]->size_peratom == 0)
+ error->all("Dump custom fix ID does not compute vector per atom");
+ if (arg_fix[i] > 0 &&
+ arg_fix[i] > modify->fix[n]->size_peratom)
+ error->all("Dump custom fix ID vector is not large enough");
+ field2fix[i] = add_fix(suffix);
delete [] suffix;
} else error->all("Invalid keyword in dump custom command");
@@ -792,76 +753,53 @@ void DumpCustom::parse_fields(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- add Compute to list of Compute objects to call
- return index of where this Compute is in call list
- compute ID = dump-ID + "_" + keyword if appendflag is set, else just keyword
- if already in call list, do not add, just return index, else add to list
+ add Compute to list of Compute objects used by dump
+ return index of where this Compute is in list
+ if already in list, do not add, just return index, else add to list
------------------------------------------------------------------------- */
-int DumpCustom::add_compute(char *keyword, int appendflag)
+int DumpCustom::add_compute(char *id)
{
- int n = strlen(id) + strlen(keyword) + 2;
- char *name = new char[n];
- if (appendflag) {
- strcpy(name,id);
- strcat(name,"_");
- strcat(name,keyword);
- } else strcpy(name,keyword);
-
int icompute;
for (icompute = 0; icompute < ncompute; icompute++)
- if (strcmp(name,id_compute[icompute]) == 0) break;
- if (icompute < ncompute) {
- delete [] name;
- return icompute;
- }
+ if (strcmp(id,id_compute[icompute]) == 0) break;
+ if (icompute < ncompute) return icompute;
id_compute = (char **)
memory->srealloc(id_compute,(ncompute+1)*sizeof(char *),"dump:id_compute");
compute = (Compute **)
memory->srealloc(compute,(ncompute+1)*sizeof(Compute *),"dump:compute");
- n = strlen(name) + 1;
+ int n = strlen(id) + 1;
id_compute[ncompute] = new char[n];
- strcpy(id_compute[ncompute],name);
- delete [] name;
+ strcpy(id_compute[ncompute],id);
ncompute++;
return ncompute-1;
}
/* ----------------------------------------------------------------------
- create a compute
- compute ID = dump-ID + "_" + keyword, compute style = keyword
- pass additional extra arg to Modify::add_compute() if defined
+ add Fix to list of Fix objects used by dump
+ return index of where this Fix is in list
+ if already in list, do not add, just return index, else add to list
------------------------------------------------------------------------- */
-void DumpCustom::create_compute(char *keyword, char *extra)
+int DumpCustom::add_fix(char *id)
{
- int n = strlen(id) + strlen(keyword) + 2;
- char *name = new char[n];
- strcpy(name,id);
- strcat(name,"_");
- strcat(name,keyword);
-
- char **newarg = new char*[4];
- newarg[0] = name;
- newarg[1] = group->names[igroup];
- newarg[2] = keyword;
-
- if (extra) {
- n = strlen(id) + strlen(extra) + 2;
- newarg[3] = new char[n];
- strcpy(newarg[3],id);
- strcat(newarg[3],"_");
- strcat(newarg[3],extra);
- } else newarg[3] = NULL;
-
- if (extra) modify->add_compute(4,newarg);
- else modify->add_compute(3,newarg);
-
- delete [] name;
- delete [] newarg[3];
- delete [] newarg;
+ int ifix;
+ for (ifix = 0; ifix < nfix; ifix++)
+ if (strcmp(id,id_fix[ifix]) == 0) break;
+ if (ifix < nfix) return ifix;
+
+ id_fix = (char **)
+ memory->srealloc(id_fix,(nfix+1)*sizeof(char *),"dump:id_fix");
+ fix = (Fix **)
+ memory->srealloc(fix,(nfix+1)*sizeof(Fix *),"dump:fix");
+
+ int n = strlen(id) + 1;
+ id_fix[nfix] = new char[n];
+ strcpy(id_fix[nfix],id);
+ nfix++;
+ return nfix-1;
}
/* ---------------------------------------------------------------------- */
@@ -948,84 +886,14 @@ int DumpCustom::modify_param(int narg, char **arg)
else if (strcmp(arg[1],"tqx") == 0) thresh_array[nthresh] = TQX;
else if (strcmp(arg[1],"tqy") == 0) thresh_array[nthresh] = TQY;
else if (strcmp(arg[1],"tqz") == 0) thresh_array[nthresh] = TQZ;
- else if (strcmp(arg[1],"epair") == 0) {
- thresh_array[nthresh] = EPAIR;
- if (index_epair < 0) {
- index_epair = add_compute(style_epair,1);
- create_compute(style_epair,NULL);
- }
- } else if (strcmp(arg[1],"ebond") == 0) {
- thresh_array[nthresh] = EBOND;
- if (index_ebond < 0) {
- index_ebond = add_compute(style_ebond,1);
- create_compute(style_ebond,NULL);
- }
- } else if (strcmp(arg[1],"ke") == 0) {
- thresh_array[nthresh] = KE;
- if (index_ke < 0) {
- index_ke = add_compute(style_ke,1);
- create_compute(style_ke,NULL);
- }
- } else if (strcmp(arg[1],"etotal") == 0) {
- thresh_array[nthresh] = ETOTAL;
- if (index_etotal < 0) {
- if (index_epair < 0) {
- index_epair = add_compute(style_epair,1);
- create_compute(style_epair,NULL);
- }
- index_etotal = add_compute(style_etotal,1);
- create_compute(style_etotal,style_epair);
- }
- } else if (strcmp(arg[1],"centro") == 0) {
- thresh_array[nthresh] = CENTRO;
- if (index_centro < 0) {
- index_centro = add_compute(style_centro,1);
- create_compute(style_centro,NULL);
- }
- } else if (strcmp(arg[1],"sxx") == 0) {
- thresh_array[nthresh] = SXX;
- if (index_stress < 0) {
- index_stress = add_compute(style_stress,1);
- create_compute(style_stress,NULL);
- }
- } else if (strcmp(arg[1],"syy") == 0) {
- thresh_array[nthresh] = SYY;
- if (index_stress < 0) {
- index_stress = add_compute(style_stress,1);
- create_compute(style_stress,NULL);
- }
- } else if (strcmp(arg[1],"szz") == 0) {
- thresh_array[nthresh] = SZZ;
- if (index_stress < 0) {
- index_stress = add_compute(style_stress,1);
- create_compute(style_stress,NULL);
- }
- } else if (strcmp(arg[1],"sxy") == 0) {
- thresh_array[nthresh] = SXY;
- if (index_stress < 0) {
- index_stress = add_compute(style_stress,1);
- create_compute(style_stress,NULL);
- }
- } else if (strcmp(arg[1],"sxz") == 0) {
- thresh_array[nthresh] = SXZ;
- if (index_stress < 0) {
- index_stress = add_compute(style_stress,1);
- create_compute(style_stress,NULL);
- }
- } else if (strcmp(arg[1],"syz") == 0) {
- thresh_array[nthresh] = SYZ;
- if (index_stress < 0) {
- index_stress = add_compute(style_stress,1);
- create_compute(style_stress,NULL);
- }
// compute value = c_ID
// if no trailing [], then arg is set to 0, else arg is between []
// must grow field2compute and arg_compute arrays,
// since access is beyond nfield
- // if Compute has pre-compute, first add it to list
+ // if Compute has pre-computes, first add them to list
- } else if (strncmp(arg[1],"c_",2) == 0) {
+ else if (strncmp(arg[1],"c_",2) == 0) {
thresh_array[nthresh] = COMPUTE;
field2compute = (int *) memory->srealloc(field2compute,
(nfield+nthresh+1)*sizeof(int),
@@ -1059,9 +927,52 @@ int DumpCustom::modify_param(int narg, char **arg)
if (arg_compute[nfield+nthresh] > 0 &&
arg_compute[nfield+nthresh] > modify->compute[n]->size_peratom)
error->all("Dump custom compute ID vector is not large enough");
- if (modify->compute[n]->id_pre)
- int tmp = add_compute(modify->compute[n]->id_pre,0);
- field2compute[nfield+nthresh] = add_compute(suffix,0);
+ if (modify->compute[n]->npre)
+ for (int ic = 0; ic < modify->compute[n]->npre; ic++)
+ int tmp = add_compute(modify->compute[n]->id_pre[ic]);
+ field2compute[nfield+nthresh] = add_compute(suffix);
+ delete [] suffix;
+
+ // fix value = f_ID
+ // if no trailing [], then arg is set to 0, else arg is between []
+ // must grow field2compute and arg_compute arrays,
+ // since access is beyond nfield
+
+ } else if (strncmp(arg[1],"f_",2) == 0) {
+ thresh_array[nthresh] = FIX;
+ field2fix = (int *) memory->srealloc(field2fix,
+ (nfield+nthresh+1)*sizeof(int),
+ "dump:field2fix");
+ arg_fix = (int *) memory->srealloc(arg_fix,
+ (nfield+nthresh+1)*sizeof(int),
+ "dump:arg_fix");
+ int n = strlen(arg[1]);
+ char *suffix = new char[n];
+ strcpy(suffix,&arg[1][2]);
+
+ char *ptr = strchr(suffix,'[');
+ if (ptr) {
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all("Invalid keyword in dump custom command");
+ arg_fix[nfield+nthresh] = atoi(ptr+1);
+ *ptr = '\0';
+ } else arg_fix[nfield+nthresh] = 0;
+
+ n = modify->find_fix(suffix);
+ if (n < 0) error->all("Could not find dump custom fix ID");
+
+ if (modify->fix[n]->peratom_flag == 0)
+ error->all("Dump custom fix ID does not compute peratom info");
+ if (arg_fix[nfield+nthresh] == 0 &&
+ modify->fix[n]->size_peratom > 0)
+ error->all("Dump custom fix ID does not compute scalar per atom");
+ if (arg_fix[nfield+nthresh] > 0 &&
+ modify->fix[n]->size_peratom == 0)
+ error->all("Dump custom fix ID does not compute vector per atom");
+ if (arg_fix[nfield+nthresh] > 0 &&
+ arg_fix[nfield+nthresh] > modify->fix[n]->size_peratom)
+ error->all("Dump custom fix ID vector is not large enough");
+ field2fix[nfield+nthresh] = add_fix(suffix);
delete [] suffix;
} else error->all("Invalid dump_modify threshhold operator");
@@ -1083,6 +994,7 @@ int DumpCustom::modify_param(int narg, char **arg)
nthresh++;
return 4;
}
+
return 0;
}
@@ -1106,31 +1018,6 @@ int DumpCustom::memory_usage()
/* ---------------------------------------------------------------------- */
-void DumpCustom::pack_compute(int n)
-{
- double *vector = compute[field2compute[n]]->scalar_atom;
- double **array = compute[field2compute[n]]->vector_atom;
- int index = arg_compute[n];
- int nlocal = atom->nlocal;
-
- if (index == 0) {
- for (int i = 0; i < nlocal; i++)
- if (choose[i]) {
- buf[n] = vector[i];
- n += size_one;
- }
- } else {
- index--;
- for (int i = 0; i < nlocal; i++)
- if (choose[i]) {
- buf[n] = array[i][index];
- n += size_one;
- }
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
void DumpCustom::pack_tag(int n)
{
int *tag = atom->tag;
@@ -1594,154 +1481,50 @@ void DumpCustom::pack_tqz(int n)
/* ---------------------------------------------------------------------- */
-void DumpCustom::pack_epair(int n)
-{
- double *epair = compute[index_epair]->scalar_atom;
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++)
- if (choose[i]) {
- buf[n] = epair[i];
- n += size_one;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void DumpCustom::pack_ebond(int n)
-{
- double *ebond = compute[index_ebond]->scalar_atom;
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++)
- if (choose[i]) {
- buf[n] = ebond[i];
- n += size_one;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void DumpCustom::pack_ke(int n)
-{
- double *ke = compute[index_ke]->scalar_atom;
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++)
- if (choose[i]) {
- buf[n] = ke[i];
- n += size_one;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void DumpCustom::pack_etotal(int n)
-{
- double *etotal = compute[index_etotal]->scalar_atom;
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++)
- if (choose[i]) {
- buf[n] = etotal[i];
- n += size_one;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void DumpCustom::pack_centro(int n)
-{
- double *centro = compute[index_centro]->scalar_atom;
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++)
- if (choose[i]) {
- buf[n] = centro[i];
- n += size_one;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void DumpCustom::pack_sxx(int n)
-{
- double **stress = compute[index_stress]->vector_atom;
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++)
- if (choose[i]) {
- buf[n] = stress[i][0];
- n += size_one;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void DumpCustom::pack_syy(int n)
-{
- double **stress = compute[index_stress]->vector_atom;
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++)
- if (choose[i]) {
- buf[n] = stress[i][1];
- n += size_one;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void DumpCustom::pack_szz(int n)
-{
- double **stress = compute[index_stress]->vector_atom;
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++)
- if (choose[i]) {
- buf[n] = stress[i][2];
- n += size_one;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void DumpCustom::pack_sxy(int n)
-{
- double **stress = compute[index_stress]->vector_atom;
- int nlocal = atom->nlocal;
-
- for (int i = 0; i < nlocal; i++)
- if (choose[i]) {
- buf[n] = stress[i][3];
- n += size_one;
- }
-}
-
-/* ---------------------------------------------------------------------- */
-
-void DumpCustom::pack_sxz(int n)
+void DumpCustom::pack_compute(int n)
{
- double **stress = compute[index_stress]->vector_atom;
+ double *vector = compute[field2compute[n]]->scalar_atom;
+ double **array = compute[field2compute[n]]->vector_atom;
+ int index = arg_compute[n];
int nlocal = atom->nlocal;
- for (int i = 0; i < nlocal; i++)
- if (choose[i]) {
- buf[n] = stress[i][4];
- n += size_one;
- }
+ if (index == 0) {
+ for (int i = 0; i < nlocal; i++)
+ if (choose[i]) {
+ buf[n] = vector[i];
+ n += size_one;
+ }
+ } else {
+ index--;
+ for (int i = 0; i < nlocal; i++)
+ if (choose[i]) {
+ buf[n] = array[i][index];
+ n += size_one;
+ }
+ }
}
/* ---------------------------------------------------------------------- */
-void DumpCustom::pack_syz(int n)
+void DumpCustom::pack_fix(int n)
{
- double **stress = compute[index_stress]->vector_atom;
+ double *vector = fix[field2fix[n]]->scalar_atom;
+ double **array = fix[field2fix[n]]->vector_atom;
+ int index = arg_fix[n];
int nlocal = atom->nlocal;
- for (int i = 0; i < nlocal; i++)
- if (choose[i]) {
- buf[n] = stress[i][5];
- n += size_one;
- }
+ if (index == 0) {
+ for (int i = 0; i < nlocal; i++)
+ if (choose[i]) {
+ buf[n] = vector[i];
+ n += size_one;
+ }
+ } else {
+ index--;
+ for (int i = 0; i < nlocal; i++)
+ if (choose[i]) {
+ buf[n] = array[i][index];
+ n += size_one;
+ }
+ }
}
diff --git a/src/dump_custom.h b/src/dump_custom.h
index 501a9fa03ee98d8e00bda487b444042f54e176c7..878f7c6a45d4bcb8c376adb2e16d7ad00421fc71 100644
--- a/src/dump_custom.h
+++ b/src/dump_custom.h
@@ -26,6 +26,7 @@ class DumpCustom : public Dump {
int memory_usage();
private:
+ int nevery; // dump frequency to check Fix against
int iregion; // -1 if no region, else which region
int nthresh; // # of defined threshholds
int *thresh_array; // array to threshhhold on for each nthresh
@@ -41,18 +42,20 @@ class DumpCustom : public Dump {
double *dchoose; // value for each atom to threshhold against
int nfield; // # of keywords listed by user
- int ncompute; // # of Compute objects called by dump
+
+ int ncompute; // # of Compute objects used by dump
char **id_compute; // their IDs
class Compute **compute; // list of ptrs to the Compute objects
- int *field2compute; // which Compute computes this field
+ int *field2compute; // which Compute calculates this field
int *arg_compute; // index into Compute scalar_atom,vector_atom
// 0 for scalar_atom, 1-N for vector_atom values
- // index = where keyword's Compute is in list
- // style = style of Compute object
- int index_epair,index_ebond,index_ke,index_etotal,index_centro,index_stress;
- char *style_epair,*style_ebond,*style_ke,*style_etotal;
- char *style_centro,*style_stress;
+ int nfix; // # of Fix objects used by dump
+ char **id_fix; // their IDs
+ class Fix **fix; // list of ptrs to the Fix objects
+ int *field2fix; // which Fix calculates this field
+ int *arg_fix; // index into Fix scalar_atom,vector_atom
+ // 0 for scalar_atom, 1-N for vector_atom values
// private methods
@@ -62,8 +65,8 @@ class DumpCustom : public Dump {
void write_data(int, double *);
void parse_fields(int, char **);
- int add_compute(char *, int);
- void create_compute(char *, char *);
+ int add_compute(char *);
+ int add_fix(char *);
int modify_param(int, char **);
typedef void (DumpCustom::*FnPtrHeader)(int);
@@ -81,8 +84,6 @@ class DumpCustom : public Dump {
typedef void (DumpCustom::*FnPtrPack)(int);
FnPtrPack *pack_choice; // ptrs to pack functions
- void pack_compute(int);
-
void pack_tag(int);
void pack_molecule(int);
void pack_type(int);
@@ -115,17 +116,9 @@ class DumpCustom : public Dump {
void pack_tqx(int);
void pack_tqy(int);
void pack_tqz(int);
- void pack_etotal(int);
- void pack_ke(int);
- void pack_epair(int);
- void pack_ebond(int);
- void pack_centro(int);
- void pack_sxx(int);
- void pack_syy(int);
- void pack_szz(int);
- void pack_sxy(int);
- void pack_sxz(int);
- void pack_syz(int);
+
+ void pack_compute(int);
+ void pack_fix(int);
};
}
diff --git a/src/dump_dcd.cpp b/src/dump_dcd.cpp
index 92c5a3382c86ce6030299e124feb6b7b47a9a88c..701cb050b02abe446620bcce1417f73cc544c359 100644
--- a/src/dump_dcd.cpp
+++ b/src/dump_dcd.cpp
@@ -245,7 +245,7 @@ void DumpDCD::write_frame()
/* ---------------------------------------------------------------------- */
-void DumpDCD::write_dcd_header(char *remarks)
+void DumpDCD::write_dcd_header(const char *remarks)
{
uint32_t out_integer;
float out_float;
diff --git a/src/dump_dcd.h b/src/dump_dcd.h
index f190eb1432b70f7136ea8ddbbb681217803e9b74..defd52fc46f959c745ca57b24f2dbc673208f627 100644
--- a/src/dump_dcd.h
+++ b/src/dump_dcd.h
@@ -38,7 +38,7 @@ class DumpDCD : public Dump {
void write_data(int, double *);
void write_frame();
- void write_dcd_header(char *);
+ void write_dcd_header(const char *);
void fwrite_int32(FILE *, uint32_t);
};
diff --git a/src/dump_xyz.cpp b/src/dump_xyz.cpp
index 5a5ba59974b3df3222ed373d2e5fdf21af7bcc66..4c8b9ab9acaacd6e88da33818c33dd3db5afd9c6 100644
--- a/src/dump_xyz.cpp
+++ b/src/dump_xyz.cpp
@@ -29,7 +29,7 @@ DumpXYZ::DumpXYZ(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg)
size_one = 5;
- char *str = "%d %g %g %g";
+ char *str = (char *) "%d %g %g %g";
int n = strlen(str) + 1;
format_default = new char[n];
strcpy(format_default,str);
diff --git a/src/error.cpp b/src/error.cpp
index 8307760aefc3b3bc0870c7cbb8d83297fe4ed9e2..b63b8a895ec58c9ebcb6251102fa4ea72dd50e3f 100644
--- a/src/error.cpp
+++ b/src/error.cpp
@@ -29,7 +29,7 @@ Error::Error(LAMMPS *lmp) : Pointers(lmp) {}
close all output, screen, and log files in world and universe
------------------------------------------------------------------------- */
-void Error::universe_all(char *str)
+void Error::universe_all(const char *str)
{
MPI_Barrier(universe->uworld);
@@ -53,7 +53,7 @@ void Error::universe_all(char *str)
called by one proc in universe
------------------------------------------------------------------------- */
-void Error::universe_one(char *str)
+void Error::universe_one(const char *str)
{
if (universe->uscreen)
fprintf(universe->uscreen,"ERROR on proc %d: %s\n",universe->me,str);
@@ -65,7 +65,7 @@ void Error::universe_one(char *str)
close all output, screen, and log files in world
------------------------------------------------------------------------- */
-void Error::all(char *str)
+void Error::all(const char *str)
{
MPI_Barrier(world);
@@ -91,7 +91,7 @@ void Error::all(char *str)
always write to universe screen
------------------------------------------------------------------------- */
-void Error::one(char *str)
+void Error::one(const char *str)
{
int me;
MPI_Comm_rank(world,&me);
@@ -106,7 +106,7 @@ void Error::one(char *str)
only write to screen if non-NULL on this proc since could be file
------------------------------------------------------------------------- */
-void Error::warning(char *str)
+void Error::warning(const char *str)
{
if (screen) fprintf(screen,"WARNING: %s\n",str);
}
diff --git a/src/error.h b/src/error.h
index 248ecdd6049de04196c8978316496de88f5ad7cc..b6c1d53f80739e04df96b1344f4d02be8b5f1ff7 100644
--- a/src/error.h
+++ b/src/error.h
@@ -22,12 +22,12 @@ class Error : protected Pointers {
public:
Error(class LAMMPS *);
- void universe_all(char *);
- void universe_one(char *);
+ void universe_all(const char *);
+ void universe_one(const char *);
- void all(char *);
- void one(char *);
- void warning(char *);
+ void all(const char *);
+ void one(const char *);
+ void warning(const char *);
};
}
diff --git a/src/finish.cpp b/src/finish.cpp
index 8af0f57743fcd2b503476f8dad268d74a175c415..09441d4ff4a988fbacbfacb8c4229893a32963d6 100644
--- a/src/finish.cpp
+++ b/src/finish.cpp
@@ -23,6 +23,8 @@
#include "update.h"
#include "min.h"
#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
#include "output.h"
#include "memory.h"
@@ -36,7 +38,7 @@ Finish::Finish(LAMMPS *lmp) : Pointers(lmp) {}
void Finish::end(int flag)
{
- int i;
+ int i,m;
int histo[10];
double time,tmp,ave,max,min;
@@ -291,11 +293,17 @@ void Finish::end(int flag)
}
}
+ // find a half non-skip neighbor list
+
+ for (m = 0; m < neighbor->old_nrequest; m++)
+ if ((neighbor->old_requests[m]->half ||
+ neighbor->old_requests[m]->half_from_full) &&
+ neighbor->old_requests[m]->skip == 0) break;
+
int nneigh = 0;
- if (neighbor->half_every)
- for (i = 0; i < atom->nlocal; i++) nneigh += neighbor->numneigh[i];
- else if (neighbor->full_every)
- for (i = 0; i < atom->nlocal; i++) nneigh += neighbor->numneigh_full[i];
+ if (m < neighbor->old_nrequest)
+ for (i = 0; i < atom->nlocal; i++)
+ nneigh += neighbor->lists[m]->numneigh[i];
tmp = nneigh;
stats(1,&tmp,&ave,&max,&min,10,histo);
@@ -314,10 +322,17 @@ void Finish::end(int flag)
}
}
- if (neighbor->half_every && neighbor->full_every) {
+ // find a full non-skip neighbor list
+
+ for (m = 0; m < neighbor->old_nrequest; m++)
+ if (neighbor->old_requests[m]->full &&
+ neighbor->old_requests[m]->skip == 0) break;
+
+ if (m < neighbor->old_nrequest) {
nneigh = 0;
- for (i = 0; i < atom->nlocal; i++) nneigh += neighbor->numneigh_full[i];
+ for (i = 0; i < atom->nlocal; i++)
+ nneigh += neighbor->lists[m]->numneigh[i];
tmp = nneigh;
stats(1,&tmp,&ave,&max,&min,10,histo);
diff --git a/src/fix.cpp b/src/fix.cpp
index 1a50c866433814908a038740b22a9c0a176ab69d..ae48cf47646db052568c0ef20bdd71519021641a 100644
--- a/src/fix.cpp
+++ b/src/fix.cpp
@@ -42,10 +42,9 @@ Fix::Fix(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
rigid_flag = 0;
virial_flag = 0;
no_change_box = 0;
+ peratom_flag = 0;
comm_forward = comm_reverse = 0;
- neigh_half_once = neigh_half_every = 0;
- neigh_full_once = neigh_full_every = 0;
// mask settings - same as in modify.cpp
diff --git a/src/fix.h b/src/fix.h
index 9d1fc93cfd3306ab6391bf20a44c3f9b9c041186..e43ce3c72c57563404de70acf4ac268435656bf1 100644
--- a/src/fix.h
+++ b/src/fix.h
@@ -35,12 +35,14 @@ class Fix : protected Pointers {
int virial_flag; // 1 if Fix contributes to virial, 0 if not
int no_change_box; // 1 if cannot swap ortho <-> triclinic
+ int peratom_flag; // 0/1 if per-atom data is stored
+ int size_peratom; // 0 = scalar_atom, N = size of vector_atom
+ double *scalar_atom; // computed per-atom scalar
+ double **vector_atom; // computed per-atom vector
+ int peratom_freq; // frequency per-atom data is available at
+
int comm_forward; // size of forward communication (0 if none)
int comm_reverse; // size of reverse communication (0 if none)
- int neigh_half_once; // 0/1 if needs half neigh list occasionally
- int neigh_half_every; // 0/1 if needs half neigh list every step
- int neigh_full_once; // 0/1 if needs full neigh list occasionally
- int neigh_full_every; // 0/1 if needs full neigh list every step
double virial[6]; // fix contribution to pressure virial
@@ -56,6 +58,7 @@ class Fix : protected Pointers {
virtual int setmask() = 0;
virtual void init() {}
+ virtual void init_list(int, class NeighList *) {}
virtual void setup() {}
virtual void min_setup() {}
virtual void initial_integrate() {}
diff --git a/src/fix_ave_spatial.cpp b/src/fix_ave_spatial.cpp
index a7ef8d40e5ca1b47384af41adca4bc6f2a51b960..f9697c053bb2505069888e999618d5f4b670712c 100644
--- a/src/fix_ave_spatial.cpp
+++ b/src/fix_ave_spatial.cpp
@@ -31,7 +31,7 @@
using namespace LAMMPS_NS;
enum{LOWER,CENTER,UPPER,COORD};
-enum{DENSITY_MASS,DENSITY_NUM,VX,VY,VZ,FX,FY,FZ,COMPUTE};
+enum{DENSITY_MASS,DENSITY_NUM,COMPUTE,FIX};
enum{SAMPLE,ALL};
enum{BOX,LATTICE,REDUCED};
@@ -40,56 +40,51 @@ enum{BOX,LATTICE,REDUCED};
FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
- if (narg < 11) error->all("Illegal fix ave/spatial command");
+ if (narg < 12) error->all("Illegal fix ave/spatial command");
no_change_box = 1;
nevery = atoi(arg[3]);
- nfreq = atoi(arg[4]);
+ nrepeat = atoi(arg[4]);
+ nfreq = atoi(arg[5]);
- if (strcmp(arg[5],"x") == 0) dim = 0;
- else if (strcmp(arg[5],"y") == 0) dim = 1;
- else if (strcmp(arg[5],"z") == 0) dim = 2;
+ if (strcmp(arg[6],"x") == 0) dim = 0;
+ else if (strcmp(arg[6],"y") == 0) dim = 1;
+ else if (strcmp(arg[6],"z") == 0) dim = 2;
else error->all("Illegal fix ave/spatial command");
- if (strcmp(arg[6],"lower") == 0) originflag = LOWER;
- if (strcmp(arg[6],"center") == 0) originflag = CENTER;
- if (strcmp(arg[6],"upper") == 0) originflag = UPPER;
+ if (strcmp(arg[7],"lower") == 0) originflag = LOWER;
+ if (strcmp(arg[7],"center") == 0) originflag = CENTER;
+ if (strcmp(arg[7],"upper") == 0) originflag = UPPER;
else originflag = COORD;
if (originflag == COORD) origin = atof(arg[6]);
- delta = atof(arg[7]);
+ delta = atof(arg[8]);
MPI_Comm_rank(world,&me);
if (me == 0) {
- fp = fopen(arg[8],"w");
+ fp = fopen(arg[9],"w");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix ave/spatial file %s",arg[8]);
+ sprintf(str,"Cannot open fix ave/spatial file %s",arg[9]);
error->one(str);
}
}
- if (strcmp(arg[9],"density") == 0) {
- if (strcmp(arg[10],"mass") == 0) which = DENSITY_MASS;
- else if (strcmp(arg[10],"number") == 0) which = DENSITY_NUM;
+ if (strcmp(arg[10],"density") == 0) {
+ if (strcmp(arg[11],"mass") == 0) which = DENSITY_MASS;
+ else if (strcmp(arg[11],"number") == 0) which = DENSITY_NUM;
else error->all("Illegal fix ave/spatial command");
-
- } else if (strcmp(arg[9],"atom") == 0) {
- if (strcmp(arg[10],"vx") == 0) which = VX;
- else if (strcmp(arg[10],"vy") == 0) which = VY;
- else if (strcmp(arg[10],"vz") == 0) which = VZ;
- else if (strcmp(arg[10],"fx") == 0) which = FX;
- else if (strcmp(arg[10],"fy") == 0) which = FY;
- else if (strcmp(arg[10],"fz") == 0) which = FZ;
- else error->all("Illegal fix ave/spatial command");
-
- } else if (strcmp(arg[9],"compute") == 0) {
+ } else if (strcmp(arg[10],"compute") == 0) {
which = COMPUTE;
- int n = strlen(arg[10]) + 1;
+ int n = strlen(arg[11]) + 1;
id_compute = new char[n];
- strcpy(id_compute,arg[10]);
-
+ strcpy(id_compute,arg[11]);
+ } else if (strcmp(arg[10],"fix") == 0) {
+ which = FIX;
+ int n = strlen(arg[11]) + 1;
+ id_fix = new char[n];
+ strcpy(id_fix,arg[11]);
} else error->all("Illegal fix ave/spatial command");
// parse optional args
@@ -97,7 +92,7 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
normflag = ALL;
scaleflag = BOX;
- int iarg = 11;
+ int iarg = 12;
while (iarg < narg) {
if (strcmp(arg[iarg],"norm") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
@@ -149,34 +144,61 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
// setup and error check
if (nevery <= 0) error->all("Illegal fix ave/spatial command");
- if (nfreq < nevery || nfreq % nevery)
+ if (nfreq < nevery || nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
error->all("Illegal fix ave/spatial command");
if (delta <= 0.0) error->all("Illegal fix ave/spatial command");
invdelta = 1.0/delta;
+ // nvalues = # of quantites per line of output file
+ // for COMPUTE, setup list of computes to call, including pre-computes
+
nvalues = 1;
+ compute = NULL;
+
if (which == COMPUTE) {
int icompute = modify->find_compute(id_compute);
if (icompute < 0)
error->all("Compute ID for fix ave/spatial does not exist");
if (modify->compute[icompute]->peratom_flag == 0)
error->all("Fix ave/spatial compute does not calculate per-atom info");
- nvalues = compute_size_peratom = modify->compute[icompute]->size_peratom;
+ nvalues = size_peratom = modify->compute[icompute]->size_peratom;
if (nvalues == 0) nvalues = 1;
+ ncompute = 1 + modify->compute[icompute]->npre;
+ compute = new Compute*[ncompute];
}
+ if (which == FIX) {
+ int ifix = modify->find_fix(id_fix);
+ if (ifix < 0)
+ error->all("Fix ID for fix ave/spatial does not exist");
+ if (modify->fix[ifix]->peratom_flag == 0)
+ error->all("Fix ave/spatial fix does not calculate per-atom info");
+ nvalues = size_peratom = modify->fix[ifix]->size_peratom;
+ if (nvalues == 0) nvalues = 1;
+ }
+
+ // print header into file
+
if (me == 0) {
fprintf(fp,"Spatial-averaged data for fix %s, group %s, and %s %s\n",
- id,group->names[igroup],arg[9],arg[10]);
+ id,group->names[igroup],arg[10],arg[11]);
fprintf(fp,"TimeStep Number-of-layers (one per snapshot)\n");
fprintf(fp,"Layer Coord Atoms Value(s) (one per layer)\n");
}
- nsum = nlayers = maxlayer = 0;
+ nlayers = maxlayer = 0;
coord = NULL;
count_one = count_many = count_total = NULL;
values_one = values_many = values_total = NULL;
+
+ // nvalid = next step on which end_of_step does something
+
+ irepeat = 0;
+ nvalid = (update->ntimestep/nfreq)*nfreq + nfreq;
+ nvalid -= (nrepeat-1)*nevery;
+ if (nvalid <= update->ntimestep)
+ error->all("Fix ave/spatial cannot be started on this timestep");
}
/* ---------------------------------------------------------------------- */
@@ -184,8 +206,11 @@ FixAveSpatial::FixAveSpatial(LAMMPS *lmp, int narg, char **arg) :
FixAveSpatial::~FixAveSpatial()
{
if (which == COMPUTE) delete [] id_compute;
+ if (which == FIX) delete [] id_fix;
if (me == 0) fclose(fp);
+ delete [] compute;
+
memory->sfree(coord);
memory->sfree(count_one);
memory->sfree(count_many);
@@ -208,21 +233,37 @@ int FixAveSpatial::setmask()
void FixAveSpatial::init()
{
- // set ptrs to current compute and precompute
+ // set ptrs to one or more computes called each end-of-step
if (which == COMPUTE) {
int icompute = modify->find_compute(id_compute);
- if (icompute < 0)
+ if (icompute < 0)
error->all("Compute ID for fix ave/spatial does not exist");
- compute = modify->compute[icompute];
- if (compute->id_pre) {
- icompute = modify->find_compute(compute->id_pre);
- if (icompute < 0)
- error->all("Precompute ID for fix ave/spatial does not exist");
- precompute = modify->compute[icompute];
- } else precompute = NULL;
+ ncompute = 0;
+ if (modify->compute[icompute]->npre)
+ for (int i = 0; i < modify->compute[icompute]->npre; i++) {
+ int ic = modify->find_compute(modify->compute[icompute]->id_pre[i]);
+ if (ic < 0)
+ error->all("Precompute ID for fix ave/spatial does not exist");
+ compute[ncompute++] = modify->compute[ic];
+ }
+
+ compute[ncompute++] = modify->compute[icompute];
+ }
+
+ // set ptr to fix ID
+ // check that fix frequency is acceptable
+
+ if (which == FIX) {
+ int ifix = modify->find_fix(id_fix);
+ if (ifix < 0)
+ error->all("Fix ID for fix ave/spatial does not exist");
+ fix = modify->fix[ifix];
+ if (nevery % modify->fix[ifix]->peratom_freq)
+ error->all("Fix ave/spatial and fix not computed at compatible times");
}
+
}
/* ---------------------------------------------------------------------- */
@@ -232,13 +273,17 @@ void FixAveSpatial::end_of_step()
int i,j,m,ilayer;
double lo,hi;
+ // skip if not step which requires doing something
+
+ if (update->ntimestep != nvalid) return;
+
// if computing the first sample, setup layers
// compute current origin = boundary for some layer
// lo = layer boundary immediately below boxlo
// hi = layer boundary immediately above boxhi
// allocate and initialize arrays based on new layer count
- if (nsum == 0) {
+ if (irepeat == 0) {
double *boxlo,*boxhi,*prd;
if (scaleflag == REDUCED) {
boxlo = domain->boxlo_lamda;
@@ -306,7 +351,6 @@ void FixAveSpatial::end_of_step()
// zero out arrays for one sample
- nsum++;
for (m = 0; m < nlayers; m++) {
count_one[m] = 0.0;
for (i = 0; i < nvalues; i++) values_one[m][i] = 0.0;
@@ -361,17 +405,12 @@ void FixAveSpatial::end_of_step()
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
- // ATOM (VX,FX,etc) adds atom attribute to values
+ // COMPUTE adds its scalar or vector quantity to values
- } else if (which != COMPUTE) {
- double *vector;
- int nstride = 3;
- if (which == VX) vector = &atom->v[0][0];
- else if (which == VY) vector = &atom->v[0][1];
- else if (which == VZ) vector = &atom->v[0][2];
- else if (which == FX) vector = &atom->f[0][0];
- else if (which == FY) vector = &atom->f[0][1];
- else if (which == FZ) vector = &atom->f[0][2];
+ } else if (which == COMPUTE) {
+ for (i = 0; i < ncompute; i++) compute[i]->compute_peratom();
+ double *scalar = compute[ncompute-1]->scalar_atom;
+ double **vector = compute[ncompute-1]->vector_atom;
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
@@ -382,20 +421,20 @@ void FixAveSpatial::end_of_step()
if (ilayer < 0) ilayer = 0;
if (ilayer >= nlayers) ilayer = nlayers-1;
count_one[ilayer] += 1.0;
- values_one[ilayer][0] += vector[m];
+ if (size_peratom == 0) values_one[ilayer][0] += scalar[i];
+ else
+ for (j = 0; j < nvalues; j++)
+ values_one[ilayer][j] += vector[i][j];
}
- m += nstride;
}
if (scaleflag == REDUCED) domain->lamda2x(nlocal);
- // COMPUTE adds its compute scalar or vector quantity to values
+ // FIX adds its scalar or vector quantity to values
- } else {
- if (precompute) precompute->compute_peratom();
- compute->compute_peratom();
- double *scalar = compute->scalar_atom;
- double **vector = compute->vector_atom;
+ } else if (which == FIX) {
+ double *scalar = fix->scalar_atom;
+ double **vector = fix->vector_atom;
if (scaleflag == REDUCED) domain->x2lamda(nlocal);
@@ -406,7 +445,7 @@ void FixAveSpatial::end_of_step()
if (ilayer < 0) ilayer = 0;
if (ilayer >= nlayers) ilayer = nlayers-1;
count_one[ilayer] += 1.0;
- if (compute_size_peratom == 0) values_one[ilayer][0] += scalar[i];
+ if (size_peratom == 0) values_one[ilayer][0] += scalar[i];
else
for (j = 0; j < nvalues; j++)
values_one[ilayer][j] += vector[i][j];
@@ -434,11 +473,19 @@ void FixAveSpatial::end_of_step()
}
}
+ // update counters
+
+ irepeat++;
+ nvalid += nevery;
+
// output the results
// time average across samples
// if density, also normalize by volume
+ // reset irepeat and nvalid
+
+ if (irepeat == nrepeat) {
+ double repeat = nrepeat;
- if (update->ntimestep % nfreq == 0) {
if (normflag == ALL) {
MPI_Allreduce(count_many,count_total,nlayers,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&values_many[0][0],&values_total[0][0],nlayers*nvalues,
@@ -447,15 +494,15 @@ void FixAveSpatial::end_of_step()
if (count_total[m] > 0.0)
for (j = 0; j < nvalues; j++)
values_total[m][j] /= count_total[m];
- count_total[m] /= nsum;
+ count_total[m] /= repeat;
}
} else {
MPI_Allreduce(&values_many[0][0],&values_total[0][0],nlayers*nvalues,
MPI_DOUBLE,MPI_SUM,world);
for (m = 0; m < nlayers; m++) {
for (j = 0; j < nvalues; j++)
- values_total[m][j] /= nsum;
- count_total[m] /= nsum;
+ values_total[m][j] /= repeat;
+ count_total[m] /= repeat;
}
}
@@ -474,6 +521,7 @@ void FixAveSpatial::end_of_step()
fflush(fp);
}
- nsum = 0;
+ irepeat = 0;
+ nvalid = update->ntimestep+nfreq - (nrepeat-1)*nevery;
}
}
diff --git a/src/fix_ave_spatial.h b/src/fix_ave_spatial.h
index 2e23ac782133d7db612195a336683b6aca4ff516..9c9cff604c429054ab714b39d4da80ed8747b793 100644
--- a/src/fix_ave_spatial.h
+++ b/src/fix_ave_spatial.h
@@ -29,22 +29,22 @@ class FixAveSpatial : public Fix {
private:
int me;
- int nfreq;
+ int nrepeat,nfreq,irepeat,nvalid;
int dim,originflag,which,normflag;
double origin,delta;
- char *id_compute;
+ char *id_compute,*id_fix;
FILE *fp;
- int nlayers,nvalues,nsum,maxlayer,scaleflag;
- int compute_size_peratom;
+ int nlayers,nvalues,maxlayer,scaleflag,size_peratom;
double xscale,yscale,zscale;
double layer_volume;
double *coord;
double *count_one,*count_many,*count_total;
double **values_one,**values_many,**values_total;
double offset,invdelta;
- class Compute *compute;
- class Compute *precompute;
+ int ncompute;
+ class Compute **compute;
+ class Fix *fix;
};
}
diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp
index c0f1f1569019ffbd0bd48908012d1416a9e7e960..ac8f7b1adf53700362095137d1d36dbd0ec2f91e 100644
--- a/src/fix_ave_time.cpp
+++ b/src/fix_ave_time.cpp
@@ -31,23 +31,24 @@ using namespace LAMMPS_NS;
FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
- if (narg != 8) error->all("Illegal fix ave/time command");
+ if (narg != 9) error->all("Illegal fix ave/time command");
nevery = atoi(arg[3]);
- nfreq = atoi(arg[4]);
+ nrepeat = atoi(arg[4]);
+ nfreq = atoi(arg[5]);
- int n = strlen(arg[5]) + 1;
+ int n = strlen(arg[6]) + 1;
id_compute = new char[n];
- strcpy(id_compute,arg[5]);
+ strcpy(id_compute,arg[6]);
- int flag = atoi(arg[6]);
+ int flag = atoi(arg[7]);
MPI_Comm_rank(world,&me);
if (me == 0) {
- fp = fopen(arg[7],"w");
+ fp = fopen(arg[8],"w");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open fix ave/time file %s",arg[7]);
+ sprintf(str,"Cannot open fix ave/time file %s",arg[8]);
error->one(str);
}
}
@@ -55,7 +56,7 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
// setup and error check
if (nevery <= 0) error->all("Illegal fix ave/time command");
- if (nfreq < nevery || nfreq % nevery)
+ if (nfreq < nevery || nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
error->all("Illegal fix ave/time command");
int icompute = modify->find_compute(id_compute);
@@ -73,6 +74,13 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
if (modify->compute[icompute]->pressflag) pressure_every = nevery;
+ // setup list of computes to call, including pre-computes
+
+ ncompute = 1 + modify->compute[icompute]->npre;
+ compute = new Compute*[ncompute];
+
+ // print header into file
+
if (me == 0) {
fprintf(fp,"Time-averaged data for fix %s, group %s, and compute %s\n",
id,group->names[modify->compute[icompute]->igroup],id_compute);
@@ -84,14 +92,19 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
fprintf(fp,"TimeStep Scalar-value Vector-values\n");
}
- nsum = 0;
- scalar = 0.0;
vector = NULL;
if (vflag) {
size_vector = modify->compute[icompute]->size_vector;
vector = new double[size_vector];
- for (int i = 0; i < size_vector; i++) vector[i] = 0.0;
}
+
+ // nvalid = next step on which end_of_step does something
+
+ irepeat = 0;
+ nvalid = (update->ntimestep/nfreq)*nfreq + nfreq;
+ nvalid -= (nrepeat-1)*nevery;
+ if (nvalid <= update->ntimestep)
+ error->all("Fix ave/time cannot be started on this timestep");
}
/* ---------------------------------------------------------------------- */
@@ -100,6 +113,7 @@ FixAveTime::~FixAveTime()
{
delete [] id_compute;
if (me == 0) fclose(fp);
+ delete [] compute;
delete [] vector;
}
@@ -116,18 +130,22 @@ int FixAveTime::setmask()
void FixAveTime::init()
{
- // set ptrs to current compute and precompute
+ // set ptrs to one or more computes called each end-of-step
int icompute = modify->find_compute(id_compute);
- if (icompute < 0) error->all("Compute ID for fix ave/time does not exist");
- compute = modify->compute[icompute];
-
- if (compute->id_pre) {
- icompute = modify->find_compute(compute->id_pre);
- if (icompute < 0)
- error->all("Precompute ID for fix ave/time does not exist");
- precompute = modify->compute[icompute];
- } else precompute = NULL;
+ if (icompute < 0)
+ error->all("Compute ID for fix ave/time does not exist");
+
+ ncompute = 0;
+ if (modify->compute[icompute]->npre)
+ for (int i = 0; i < modify->compute[icompute]->npre; i++) {
+ int ic = modify->find_compute(modify->compute[icompute]->id_pre[i]);
+ if (ic < 0)
+ error->all("Precompute ID for fix ave/time does not exist");
+ compute[ncompute++] = modify->compute[ic];
+ }
+
+ compute[ncompute++] = modify->compute[icompute];
}
/* ---------------------------------------------------------------------- */
@@ -136,32 +154,50 @@ void FixAveTime::end_of_step()
{
int i;
- if (precompute) {
- if (sflag) double tmp = precompute->compute_scalar();
- if (vflag) precompute->compute_vector();
+ // skip if not step which requires doing something
+
+ if (update->ntimestep != nvalid) return;
+
+ // zero if first step
+
+ if (irepeat == 0) {
+ scalar = 0.0;
+ if (vflag)
+ for (i = 0; i < size_vector; i++) vector[i] = 0.0;
}
- nsum++;
- if (sflag) scalar += compute->compute_scalar();
+ // accumulate results of compute to local copy
+
+ if (sflag) {
+ double value;
+ for (i = 0; i < ncompute; i++) value = compute[i]->compute_scalar();
+ scalar += value;
+ }
if (vflag) {
- compute->compute_vector();
- double *cvector = compute->vector;
+ for (i = 0; i < ncompute; i++) compute[i]->compute_vector();
+ double *cvector = compute[ncompute-1]->vector;
for (i = 0; i < size_vector; i++) vector[i] += cvector[i];
}
- if (update->ntimestep % nfreq == 0) {
+ irepeat++;
+ nvalid += nevery;
+
+ // output the results
+ // reset irepeat and nvalid
+
+ if (irepeat == nrepeat) {
+ double repeat = nrepeat;
+
if (me == 0) {
fprintf(fp,"%d",update->ntimestep);
- if (sflag) fprintf(fp," %g",scalar/nsum);
+ if (sflag) fprintf(fp," %g",scalar/repeat);
if (vflag)
- for (i = 0; i < size_vector; i++) fprintf(fp," %g",vector[i]/nsum);
+ for (i = 0; i < size_vector; i++) fprintf(fp," %g",vector[i]/repeat);
fprintf(fp,"\n");
fflush(fp);
}
- nsum = 0;
- scalar = 0.0;
- if (vflag)
- for (i = 0; i < size_vector; i++) vector[i] = 0.0;
- }
+ irepeat = 0;
+ nvalid = update->ntimestep+nfreq - (nrepeat-1)*nevery;
+ }
}
diff --git a/src/fix_ave_time.h b/src/fix_ave_time.h
index 8c732064d956c88e137e8f72f8fcf3f3fa0cf014..01fb897c483582b521818f0effc049dab55f5825 100644
--- a/src/fix_ave_time.h
+++ b/src/fix_ave_time.h
@@ -29,16 +29,15 @@ class FixAveTime : public Fix {
private:
int me;
-
- int nfreq;
+ int nrepeat,nfreq,nvalid,irepeat;
char *id_compute;
FILE *fp;
int sflag,vflag;
int size_vector,nsum;
double scalar,*vector;
- class Compute *compute;
- class Compute *precompute;
+ int ncompute;
+ class Compute **compute;
};
}
diff --git a/src/fix_nph.cpp b/src/fix_nph.cpp
index f9fc6e70873cd1d52fd6613e2d4fbbee51c03ca5..d8b2076d8851c72c7524553627526212618a6d18 100644
--- a/src/fix_nph.cpp
+++ b/src/fix_nph.cpp
@@ -162,8 +162,8 @@ FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) :
char **newarg = new char*[3];
newarg[0] = id_temp;
- newarg[1] = "all";
- newarg[2] = "temp";
+ newarg[1] = (char *) "all";
+ newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
delete [] newarg;
tflag = 1;
@@ -179,8 +179,8 @@ FixNPH::FixNPH(LAMMPS *lmp, int narg, char **arg) :
newarg = new char*[4];
newarg[0] = id_press;
- newarg[1] = "all";
- newarg[2] = "pressure";
+ newarg[1] = (char *) "all";
+ newarg[2] = (char *) "pressure";
newarg[3] = id_temp;
modify->add_compute(4,newarg);
delete [] newarg;
@@ -231,7 +231,7 @@ void FixNPH::init()
error->all("Cannot use fix nph without per-type mass defined");
// set temperature and pressure ptrs
- // set ptemperature only if pressure's id_pre is not id_temp
+ // set ptemperature only if pressure's id_pre[0] is not id_temp
int icompute = modify->find_compute(id_temp);
if (icompute < 0) error->all("Temp ID for fix nph does not exist");
@@ -241,9 +241,9 @@ void FixNPH::init()
if (icompute < 0) error->all("Press ID for fix nph does not exist");
pressure = modify->compute[icompute];
- if (strcmp(id_temp,pressure->id_pre) == 0) ptemperature = NULL;
+ if (strcmp(id_temp,pressure->id_pre[0]) == 0) ptemperature = NULL;
else {
- icompute = modify->find_compute(pressure->id_pre);
+ icompute = modify->find_compute(pressure->id_pre[0]);
if (icompute < 0)
error->all("Temp ID of press ID for fix nph does not exist");
ptemperature = modify->compute[icompute];
@@ -733,13 +733,13 @@ int FixNPH::modify_param(int narg, char **arg)
if (temperature->igroup != 0 && comm->me == 0)
error->warning("Temperature for NPH is not for group all");
- // reset id_pre of pressure to new temp ID
+ // reset id_pre[0] of pressure to new temp ID
icompute = modify->find_compute(id_press);
if (icompute < 0) error->all("Press ID for fix npt does not exist");
- delete [] modify->compute[icompute]->id_pre;
- modify->compute[icompute]->id_pre = new char[n];
- strcpy(modify->compute[icompute]->id_pre,id_temp);
+ delete [] modify->compute[icompute]->id_pre[0];
+ modify->compute[icompute]->id_pre[0] = new char[n];
+ strcpy(modify->compute[icompute]->id_pre[0],id_temp);
return 2;
diff --git a/src/fix_npt.cpp b/src/fix_npt.cpp
index 6b2c6f2b99bd6d193db19f851b87a5e68e5bd1b1..f57df6fc25743dae32a7cc71626ad1580a84c3d7 100644
--- a/src/fix_npt.cpp
+++ b/src/fix_npt.cpp
@@ -169,9 +169,10 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) :
char **newarg = new char*[3];
newarg[0] = id_temp;
- newarg[1] = "all";
- if (strcmp(style,"npt") == 0) newarg[2] = "temp";
- else if (strcmp(style,"npt/asphere") == 0) newarg[2] = "temp/asphere";
+ newarg[1] = (char *) "all";
+ if (strcmp(style,"npt") == 0) newarg[2] = (char *) "temp";
+ else if (strcmp(style,"npt/asphere") == 0)
+ newarg[2] = (char *) "temp/asphere";
modify->add_compute(3,newarg);
delete [] newarg;
tflag = 1;
@@ -187,8 +188,8 @@ FixNPT::FixNPT(LAMMPS *lmp, int narg, char **arg) :
newarg = new char*[4];
newarg[0] = id_press;
- newarg[1] = "all";
- newarg[2] = "pressure";
+ newarg[1] = (char *) "all";
+ newarg[2] = (char *) "pressure";
newarg[3] = id_temp;
modify->add_compute(4,newarg);
delete [] newarg;
@@ -240,7 +241,7 @@ void FixNPT::init()
error->all("Cannot use fix npt without per-type mass defined");
// set temperature and pressure ptrs
- // set ptemperature only if pressure's id_pre is not id_temp
+ // set ptemperature only if pressure's id_pre[0] is not id_temp
int icompute = modify->find_compute(id_temp);
if (icompute < 0) error->all("Temp ID for fix npt does not exist");
@@ -250,9 +251,9 @@ void FixNPT::init()
if (icompute < 0) error->all("Press ID for fix npt does not exist");
pressure = modify->compute[icompute];
- if (strcmp(id_temp,pressure->id_pre) == 0) ptemperature = NULL;
+ if (strcmp(id_temp,pressure->id_pre[0]) == 0) ptemperature = NULL;
else {
- icompute = modify->find_compute(pressure->id_pre);
+ icompute = modify->find_compute(pressure->id_pre[0]);
if (icompute < 0)
error->all("Temp ID of press ID for fix npt does not exist");
ptemperature = modify->compute[icompute];
@@ -761,13 +762,13 @@ int FixNPT::modify_param(int narg, char **arg)
if (temperature->igroup != 0 && comm->me == 0)
error->warning("Temperature for NPT is not for group all");
- // reset id_pre of pressure to new temp ID
+ // reset id_pre[0] of pressure to new temp ID
icompute = modify->find_compute(id_press);
if (icompute < 0) error->all("Press ID for fix npt does not exist");
- delete [] modify->compute[icompute]->id_pre;
- modify->compute[icompute]->id_pre = new char[n];
- strcpy(modify->compute[icompute]->id_pre,id_temp);
+ delete [] modify->compute[icompute]->id_pre[0];
+ modify->compute[icompute]->id_pre[0] = new char[n];
+ strcpy(modify->compute[icompute]->id_pre[0],id_temp);
return 2;
diff --git a/src/fix_nvt.cpp b/src/fix_nvt.cpp
index 1d0cb9a8eab01bf75c0c843a2aefb24f3b8283ae..7a56cbd23b88728c98a44e87aa6b9b84c00afe92 100644
--- a/src/fix_nvt.cpp
+++ b/src/fix_nvt.cpp
@@ -69,9 +69,9 @@ FixNVT::FixNVT(LAMMPS *lmp, int narg, char **arg) :
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = group->names[igroup];
- if (strcmp(style,"nvt") == 0) newarg[2] = "temp";
- else if (strcmp(style,"nvt/asphere") == 0) newarg[2] = "temp/asphere";
- else if (strcmp(style,"nvt/sllod") == 0) newarg[2] = "temp/deform";
+ if (strcmp(style,"nvt") == 0) newarg[2] = (char *) "temp";
+ else if (strcmp(style,"nvt/asphere") == 0) newarg[2] = (char *) "temp/asphere";
+ else if (strcmp(style,"nvt/sllod") == 0) newarg[2] = (char *) "temp/deform";
modify->add_compute(3,newarg);
delete [] newarg;
tflag = 1;
diff --git a/src/fix_orient_fcc.cpp b/src/fix_orient_fcc.cpp
index 73b9f3b8958bec574ec5a20c374c5c1ca02015db..c4b9246179ddd69c7986f2f06d67031ec17dc5c3 100644
--- a/src/fix_orient_fcc.cpp
+++ b/src/fix_orient_fcc.cpp
@@ -24,6 +24,8 @@
#include "update.h"
#include "respa.h"
#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
#include "comm.h"
#include "output.h"
#include "error.h"
@@ -44,8 +46,6 @@ FixOrientFCC::FixOrientFCC(LAMMPS *lmp, int narg, char **arg) :
if (narg != 11) error->all("Illegal fix orient/fcc command");
- neigh_full_every = 1;
-
nstats = atoi(arg[3]);
direction_of_motion = atoi(arg[4]);
a = atof(arg[5]);
@@ -173,6 +173,21 @@ void FixOrientFCC::init()
{
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
+
+ // need a full neighbor list, built when ever re-neighboring occurs
+
+ int irequest = neighbor->request((void *) this);
+ neighbor->requests[irequest]->pair = 0;
+ neighbor->requests[irequest]->fix = 1;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->full = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixOrientFCC::init_list(int id, NeighList *ptr)
+{
+ list = ptr;
}
/* ---------------------------------------------------------------------- */
@@ -194,8 +209,8 @@ void FixOrientFCC::setup()
void FixOrientFCC::post_force(int vflag)
{
- int i,j,k,m,n,nn,nsort,id_self;
- int *neighs;
+ int i,j,k,ii,jj,inum,jnum,m,n,nn,nsort,id_self;
+ int *ilist,*jlist,*numneigh,**firstneigh;
double edelta,added_energy,omega;
double dx,dy,dz,rsq,xismooth,xi_sq,duxi,duxi_other;
double dxi[3];
@@ -215,6 +230,11 @@ void FixOrientFCC::post_force(int vflag)
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
// insure nbr data structure is adequate size
if (nall > nmax) {
@@ -231,15 +251,16 @@ void FixOrientFCC::post_force(int vflag)
int mincount = BIG;
int maxcount = 0;
- for (i = 0; i < nlocal; i++) {
- neighs = neighbor->firstneigh_full[i];
- n = neighbor->numneigh_full[i];
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
- if (n < mincount) mincount = n;
- if (n > maxcount) {
+ if (jnum < mincount) mincount = jnum;
+ if (jnum > maxcount) {
if (maxcount) delete [] sort;
- sort = new Sort[n];
- maxcount = n;
+ sort = new Sort[jnum];
+ maxcount = jnum;
}
// loop over all neighbors of atom i
@@ -247,8 +268,8 @@ void FixOrientFCC::post_force(int vflag)
// store local id, rsq, delta vector, xismooth (if included)
nsort = 0;
- for (k = 0; k < n; k++) {
- j = neighs[k];
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
count++;
dx = x[i][0] - x[j][0];
@@ -319,7 +340,8 @@ void FixOrientFCC::post_force(int vflag)
// compute grain boundary force on each owned atom
// skip atoms not in group
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
if (!(mask[i] & groupbit)) continue;
n = nbr[i].n;
duxi = nbr[i].duxi;
diff --git a/src/fix_orient_fcc.h b/src/fix_orient_fcc.h
index 9b34e41535fb9d703ba71853f6c1b49cc9a69dc0..a28f6181874323ecb3dbd2a09df9d5e0b13e3757 100644
--- a/src/fix_orient_fcc.h
+++ b/src/fix_orient_fcc.h
@@ -41,6 +41,7 @@ class FixOrientFCC : public Fix {
~FixOrientFCC();
int setmask();
void init();
+ void init_list(int, class NeighList *);
void setup();
void post_force(int);
void post_force_respa(int, int, int);
@@ -70,6 +71,7 @@ class FixOrientFCC : public Fix {
Nbr *nbr;
Sort *sort;
+ class NeighList *list;
void find_best_ref(double *, int, double &, double *);
static int compare(const void *, const void *);
diff --git a/src/fix_rdf.cpp b/src/fix_rdf.cpp
index f671687baef9dbb50c031f4d514575fadd96decc..f39081ce470cc9513eda0cf052fd4c9a27cbac3f 100644
--- a/src/fix_rdf.cpp
+++ b/src/fix_rdf.cpp
@@ -27,6 +27,8 @@
#include "group.h"
#include "modify.h"
#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
#include "pair.h"
#include "force.h"
#include "memory.h"
@@ -41,8 +43,6 @@ FixRDF::FixRDF(LAMMPS *lmp, int narg, char **arg) :
{
if (narg < 8 || (narg-6) % 2) error->all("Illegal fix rdf command");
- neigh_half_once = 1;
-
nevery = atoi(arg[3]);
if (nevery <= 0) error->all("Illegal fix rdf command");
first = 1;
@@ -129,6 +129,13 @@ void FixRDF::init()
if (force->pair) delr = force->pair->cutforce / maxbin;
else error->all("Fix rdf requires a pair style be defined");
+ // need an occasional half neighbor list
+
+ int irequest = neighbor->request((void *) this);
+ neighbor->requests[irequest]->pair = 0;
+ neighbor->requests[irequest]->fix = 1;
+ neighbor->requests[irequest]->occasional = 1;
+
delrinv = 1.0/delr;
nframes = 0;
@@ -143,6 +150,14 @@ void FixRDF::init()
for (bin = 0; bin < maxbin; bin++)
gr_ave[irdf][bin] = ncoord_ave[irdf][bin] = 0.0;
}
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixRDF::init_list(int id, NeighList *ptr)
+{
+ list = ptr;
}
/* ---------------------------------------------------------------------- */
@@ -166,13 +181,18 @@ void FixRDF::end_of_step()
int nall = atom->nlocal + atom->nghost;
int newton_pair = force->newton_pair;
- int i,j,k,numneigh,itype,jtype,ipair,jpair,bin;
+ int i,j,ii,jj,inum,jnum,itype,jtype,ipair,jpair,bin;
double xtmp,ytmp,ztmp,delx,dely,delz,r;
- int *neighs;
+ int *ilist,*jlist,*numneigh,**firstneigh;
- // if needed, build a half neighbor list
+ // invoke half neighbor list (will copy or build if necessary)
- if (!neighbor->half_every) neighbor->build_half();
+ neighbor->build_one(list->index);
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
// zero the histogram counts
@@ -188,17 +208,19 @@ void FixRDF::end_of_step()
// count the interaction once even if neighbor pair is stored on 2 procs
// if itype = jtype, count the interaction twice
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
if (mask[i] & groupbit) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
- neighs = neighbor->firstneigh[i];
- numneigh = neighbor->numneigh[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
if (j >= nall) {
if (special_coul[j/nall] == 0.0 && special_lj[j/nall] == 0.0)
continue;
diff --git a/src/fix_rdf.h b/src/fix_rdf.h
index 47a3f97fc4ac4e46c8a1df0476faf2fbdff91e0b..4b2148402bd1771b97b785d58bd2127237990b56 100644
--- a/src/fix_rdf.h
+++ b/src/fix_rdf.h
@@ -25,6 +25,7 @@ class FixRDF : public Fix {
~FixRDF();
int setmask();
void init();
+ void init_list(int, class NeighList *);
void setup();
void end_of_step();
@@ -39,6 +40,7 @@ class FixRDF : public Fix {
int **hist,**hist_all; // histogram bins
int *nrdfatoms; // # of atoms of each type in the group
double **gr_ave,**ncoord_ave; // accumulators for average rdf statistics
+ class NeighList *list; // half neighbor list
};
}
diff --git a/src/fix_shear_history.cpp b/src/fix_shear_history.cpp
index cde7edcdadc9bb7532d0e1301ccb86f77ac1af9b..54956003efa3e3b2dbf5e00e8eb4c6fc4f362bc3 100644
--- a/src/fix_shear_history.cpp
+++ b/src/fix_shear_history.cpp
@@ -16,7 +16,9 @@
#include "fix_shear_history.h"
#include "atom.h"
#include "neighbor.h"
+#include "neigh_list.h"
#include "force.h"
+#include "pair.h"
#include "update.h"
#include "modify.h"
#include "memory.h"
@@ -89,7 +91,10 @@ void FixShearHistory::init()
void FixShearHistory::pre_exchange()
{
- int i,j,k,m;
+ int i,j,ii,jj,m,inum,jnum;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+ int *touch,**firsttouch;
+ double *shear,*allshear,**firstshear;
// zero npartners for all current atoms
@@ -97,24 +102,28 @@ void FixShearHistory::pre_exchange()
for (i = 0; i < nlocal; i++) npartner[i] = 0;
// copy shear info from neighbor list atoms to atom arrays
- // nlocal = nlocal_neighbor = nlocal when neighbor list last built,
- // which might be pre-insert on this step
- int numneigh;
- int *neighs,*touch;
- double *firstshear,*shear;
int *tag = atom->tag;
- nlocal = neighbor->nlocal_neighbor;
-
- for (i = 0; i < nlocal; i++) {
- neighs = neighbor->firstneigh[i];
- touch = neighbor->firsttouch[i];
- firstshear = neighbor->firstshear[i];
- numneigh = neighbor->numneigh[i];
- for (k = 0; k < numneigh; k++) {
- if (touch[k]) {
- shear = &firstshear[3*k];
- j = neighs[k];
+
+ NeighList *list = pair->list;
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+ firsttouch = list->listgranhistory->firstneigh;
+ firstshear = list->listgranhistory->firstdouble;
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ jlist = firstneigh[i];
+ allshear = firstshear[i];
+ jnum = numneigh[i];
+ touch = firsttouch[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ if (touch[jj]) {
+ shear = &allshear[3*jj];
+ j = jlist[jj];
if (npartner[i] < MAXTOUCH) {
m = npartner[i];
partner[i][m] = tag[j];
diff --git a/src/fix_shear_history.h b/src/fix_shear_history.h
index 7b2d7346b5cd962f9b9491ff16ae4dd5f9cd8b2c..054834f269bb67104b38f11ddb1e9192295a0ba0 100644
--- a/src/fix_shear_history.h
+++ b/src/fix_shear_history.h
@@ -20,6 +20,7 @@ namespace LAMMPS_NS {
class FixShearHistory : public Fix {
friend class Neighbor;
+ friend class PairGranHistory;
friend class FixPour;
public:
@@ -43,6 +44,8 @@ class FixShearHistory : public Fix {
int *npartner; // # of touching partners of each atom
int **partner; // tags for the partners
double ***shearpartner; // 3 shear values with the partner
+
+ class Pair *pair;
};
}
diff --git a/src/fix_temp_rescale.cpp b/src/fix_temp_rescale.cpp
index 05ecfe836da4778a0fa7f8415209452978d78531..7d5f20003062bdb2990e6eeb80c0342c18d8a015 100644
--- a/src/fix_temp_rescale.cpp
+++ b/src/fix_temp_rescale.cpp
@@ -86,20 +86,20 @@ FixTempRescale::FixTempRescale(LAMMPS *lmp, int narg, char **arg) :
newarg[0] = id_temp;
newarg[1] = group->names[igroup];
if (type == STANDARD) {
- newarg[2] = "temp";
+ newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
} else if (type == REGION) {
- newarg[2] = "temp/region";
+ newarg[2] = (char *) "temp/region";
newarg[3] = domain->regions[iregion]->id;
modify->add_compute(4,newarg);
} else if (type == PARTIAL) {
- newarg[2] = "temp/partial";
- if (xflag) newarg[3] = "1";
- else newarg[3] = "0";
- if (yflag) newarg[4] = "1";
- else newarg[4] = "0";
- if (zflag) newarg[5] = "1";
- else newarg[5] = "0";
+ newarg[2] = (char *) "temp/partial";
+ if (xflag) newarg[3] = (char *) "1";
+ else newarg[3] = (char *) "0";
+ if (yflag) newarg[4] = (char *) "1";
+ else newarg[4] = (char *) "0";
+ if (zflag) newarg[5] = (char *) "1";
+ else newarg[5] = (char *) "0";
modify->add_compute(6,newarg);
}
delete [] newarg;
diff --git a/src/force.cpp b/src/force.cpp
index 802c1061d214184f7492405d7c1138bef4b872c3..e7cf40ea41e94992014676510435212064db721e 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -65,7 +65,7 @@ Force::Force(LAMMPS *lmp) : Pointers(lmp)
improper = NULL;
kspace = NULL;
- char *str = "none";
+ char *str = (char *) "none";
int n = strlen(str) + 1;
pair_style = new char[n];
strcpy(pair_style,str);
@@ -120,7 +120,7 @@ void Force::init()
create a pair style, called from input script or restart file
------------------------------------------------------------------------- */
-void Force::create_pair(char *style)
+void Force::create_pair(const char *style)
{
delete [] pair_style;
if (pair) delete pair;
@@ -135,7 +135,7 @@ void Force::create_pair(char *style)
generate a pair class
------------------------------------------------------------------------- */
-Pair *Force::new_pair(char *style)
+Pair *Force::new_pair(const char *style)
{
if (strcmp(style,"none") == 0) return NULL;
@@ -154,14 +154,21 @@ Pair *Force::new_pair(char *style)
else return NULL
------------------------------------------------------------------------- */
-Pair *Force::pair_match(char *word)
+Pair *Force::pair_match(const char *word)
{
if (strstr(pair_style,word)) return pair;
else if (strcmp(pair_style,"hybrid") == 0) {
- PairHybrid *pair_hybrid = (PairHybrid *) pair;
- for (int i = 0; i < pair_hybrid->nstyles; i++)
- if (strstr(pair_hybrid->keywords[i],word))
- return pair_hybrid->styles[i];
+ PairHybrid *hybrid = (PairHybrid *) pair;
+ for (int i = 0; i < hybrid->nstyles; i++) {
+ if (strstr(hybrid->keywords[i],word))
+ return hybrid->styles[i];
+ }
+ } else if (strcmp(pair_style,"hybrid/overlay") == 0) {
+ PairHybridOverlay *hybrid = (PairHybridOverlay *) pair;
+ for (int i = 0; i < hybrid->nstyles; i++) {
+ if (strstr(hybrid->keywords[i],word))
+ return hybrid->styles[i];
+ }
}
return NULL;
}
@@ -170,7 +177,7 @@ Pair *Force::pair_match(char *word)
create a bond style, called from input script or restart file
------------------------------------------------------------------------- */
-void Force::create_bond(char *style)
+void Force::create_bond(const char *style)
{
delete [] bond_style;
if (bond) delete bond;
@@ -185,7 +192,7 @@ void Force::create_bond(char *style)
generate a bond class
------------------------------------------------------------------------- */
-Bond *Force::new_bond(char *style)
+Bond *Force::new_bond(const char *style)
{
if (strcmp(style,"none") == 0) return NULL;
@@ -203,13 +210,13 @@ Bond *Force::new_bond(char *style)
return ptr to current bond class or hybrid sub-class if matches style
------------------------------------------------------------------------- */
-Bond *Force::bond_match(char *style)
+Bond *Force::bond_match(const char *style)
{
if (strcmp(bond_style,style) == 0) return bond;
else if (strcmp(bond_style,"hybrid") == 0) {
- BondHybrid *hbond = (BondHybrid *) bond;
- for (int i = 0; i < hbond->nstyles; i++)
- if (strcmp(hbond->keywords[i],style) == 0) return hbond->styles[i];
+ BondHybrid *hybrid = (BondHybrid *) bond;
+ for (int i = 0; i < hybrid->nstyles; i++)
+ if (strcmp(hybrid->keywords[i],style) == 0) return hybrid->styles[i];
}
return NULL;
}
@@ -218,7 +225,7 @@ Bond *Force::bond_match(char *style)
create an angle style, called from input script or restart file
------------------------------------------------------------------------- */
-void Force::create_angle(char *style)
+void Force::create_angle(const char *style)
{
delete [] angle_style;
if (angle) delete angle;
@@ -233,7 +240,7 @@ void Force::create_angle(char *style)
generate an angle class
------------------------------------------------------------------------- */
-Angle *Force::new_angle(char *style)
+Angle *Force::new_angle(const char *style)
{
if (strcmp(style,"none") == 0) return NULL;
@@ -251,7 +258,7 @@ Angle *Force::new_angle(char *style)
create a dihedral style, called from input script or restart file
------------------------------------------------------------------------- */
-void Force::create_dihedral(char *style)
+void Force::create_dihedral(const char *style)
{
delete [] dihedral_style;
if (dihedral) delete dihedral;
@@ -266,7 +273,7 @@ void Force::create_dihedral(char *style)
generate a dihedral class
------------------------------------------------------------------------- */
-Dihedral *Force::new_dihedral(char *style)
+Dihedral *Force::new_dihedral(const char *style)
{
if (strcmp(style,"none") == 0) return NULL;
@@ -284,7 +291,7 @@ Dihedral *Force::new_dihedral(char *style)
create an improper style, called from input script or restart file
------------------------------------------------------------------------- */
-void Force::create_improper(char *style)
+void Force::create_improper(const char *style)
{
delete [] improper_style;
if (improper) delete improper;
@@ -299,7 +306,7 @@ void Force::create_improper(char *style)
generate a improper class
------------------------------------------------------------------------- */
-Improper *Force::new_improper(char *style)
+Improper *Force::new_improper(const char *style)
{
if (strcmp(style,"none") == 0) return NULL;
diff --git a/src/force.h b/src/force.h
index a1ae61ddd1ce30d1ca8502f29958d02fb9307f32..7bf52ac7c52417417b285ade1f871e016a3286e6 100644
--- a/src/force.h
+++ b/src/force.h
@@ -56,22 +56,22 @@ class Force : protected Pointers {
~Force();
void init();
- void create_pair(char *);
- class Pair *new_pair(char *);
- class Pair *pair_match(char *);
+ void create_pair(const char *);
+ class Pair *new_pair(const char *);
+ class Pair *pair_match(const char *);
- void create_bond(char *);
- class Bond *new_bond(char *);
- class Bond *bond_match(char *);
+ void create_bond(const char *);
+ class Bond *new_bond(const char *);
+ class Bond *bond_match(const char *);
- void create_angle(char *);
- class Angle *new_angle(char *);
+ void create_angle(const char *);
+ class Angle *new_angle(const char *);
- void create_dihedral(char *);
- class Dihedral *new_dihedral(char *);
+ void create_dihedral(const char *);
+ class Dihedral *new_dihedral(const char *);
- void create_improper(char *);
- class Improper *new_improper(char *);
+ void create_improper(const char *);
+ class Improper *new_improper(const char *);
void create_kspace(int, char **);
diff --git a/src/group.cpp b/src/group.cpp
index 9b21a54f75bdd2505455a55b53d2e12874f486ad..9ea1cf2b07ed7ed6731bc430f2db53bfe38074cc 100644
--- a/src/group.cpp
+++ b/src/group.cpp
@@ -52,7 +52,7 @@ Group::Group(LAMMPS *lmp) : Pointers(lmp)
// create "all" group
- char *str = "all";
+ char *str = (char *) "all";
int n = strlen(str) + 1;
names[0] = (char *) memory->smalloc(n*sizeof(char),"group:names[]");
strcpy(names[0],str);
@@ -352,7 +352,7 @@ void Group::create(char *name, int *flag)
return group index if name matches existing group, -1 if no such group
------------------------------------------------------------------------- */
-int Group::find(char *name)
+int Group::find(const char *name)
{
for (int igroup = 0; igroup < ngroup; igroup++)
if (strcmp(name,names[igroup]) == 0) return igroup;
diff --git a/src/group.h b/src/group.h
index 34789e5c75a01eb40ad0e1549d5a27cb901a87d4..fc855ad5a1cd9d9d975ccb092c51615ee87fc123 100644
--- a/src/group.h
+++ b/src/group.h
@@ -31,7 +31,7 @@ class Group : protected Pointers {
~Group();
void assign(int, char **); // assign atoms to a group
void create(char *, int *); // add flagged atoms to a group
- int find(char *); // lookup name in list of groups
+ int find(const char *); // lookup name in list of groups
void write_restart(FILE *);
void read_restart(FILE *);
diff --git a/src/memory.cpp b/src/memory.cpp
index 430f7d8165a3ce9fb71f8ad1e3ce0c5237e8a3ac..caf553120a61f74d821beaa2ddf837c77b612eb2 100644
--- a/src/memory.cpp
+++ b/src/memory.cpp
@@ -28,7 +28,7 @@ Memory::Memory(LAMMPS *lmp) : Pointers(lmp) {}
safe malloc
------------------------------------------------------------------------- */
-void *Memory::smalloc(int n, char *name)
+void *Memory::smalloc(int n, const char *name)
{
if (n == 0) return NULL;
void *ptr = malloc(n);
@@ -54,7 +54,7 @@ void Memory::sfree(void *ptr)
safe realloc
------------------------------------------------------------------------- */
-void *Memory::srealloc(void *ptr, int n, char *name)
+void *Memory::srealloc(void *ptr, int n, const char *name)
{
if (n == 0) return NULL;
ptr = realloc(ptr,n);
@@ -70,7 +70,7 @@ void *Memory::srealloc(void *ptr, int n, char *name)
create a 1d double array with index from nlo to nhi inclusive
------------------------------------------------------------------------- */
-double *Memory::create_1d_double_array(int nlo, int nhi, char *name)
+double *Memory::create_1d_double_array(int nlo, int nhi, const char *name)
{
int n = nhi - nlo + 1;
double *array = (double *) smalloc(n*sizeof(double),name);
@@ -91,7 +91,7 @@ void Memory::destroy_1d_double_array(double *array, int offset)
create a 2d double array
------------------------------------------------------------------------- */
-double **Memory::create_2d_double_array(int n1, int n2, char *name)
+double **Memory::create_2d_double_array(int n1, int n2, const char *name)
{
double *data = (double *) smalloc(n1*n2*sizeof(double),name);
@@ -125,7 +125,7 @@ void Memory::destroy_2d_double_array(double **array)
------------------------------------------------------------------------- */
double **Memory::grow_2d_double_array(double **array,
- int n1, int n2, char *name)
+ int n1, int n2, const char *name)
{
if (array == NULL) return create_2d_double_array(n1,n2,name);
@@ -147,7 +147,7 @@ double **Memory::grow_2d_double_array(double **array,
if either dim is 0, return NULL
------------------------------------------------------------------------- */
-int **Memory::create_2d_int_array(int n1, int n2, char *name)
+int **Memory::create_2d_int_array(int n1, int n2, const char *name)
{
if (n1 == 0 || n2 == 0) return NULL;
@@ -182,7 +182,7 @@ void Memory::destroy_2d_int_array(int **array)
if either dim is 0, return NULL
------------------------------------------------------------------------- */
-int **Memory::grow_2d_int_array(int **array, int n1, int n2, char *name)
+int **Memory::grow_2d_int_array(int **array, int n1, int n2, const char *name)
{
if (n1 == 0 || n2 == 0) {
@@ -208,7 +208,8 @@ int **Memory::grow_2d_int_array(int **array, int n1, int n2, char *name)
create a 2d double array with 2nd index from n2lo to n2hi inclusive
------------------------------------------------------------------------- */
-double **Memory::create_2d_double_array(int n1, int n2lo, int n2hi, char *name)
+double **Memory::create_2d_double_array(int n1, int n2lo, int n2hi,
+ const char *name)
{
int n2 = n2hi - n2lo + 1;
double **array = create_2d_double_array(n1,n2,name);
@@ -232,7 +233,8 @@ void Memory::destroy_2d_double_array(double **array, int offset)
create a 3d double array
------------------------------------------------------------------------- */
-double ***Memory::create_3d_double_array(int n1, int n2, int n3, char *name)
+double ***Memory::create_3d_double_array(int n1, int n2, int n3,
+ const char *name)
{
int i,j;
@@ -271,7 +273,8 @@ void Memory::destroy_3d_double_array(double ***array)
------------------------------------------------------------------------- */
double ***Memory::grow_3d_double_array(double ***array,
- int n1, int n2, int n3, char *name)
+ int n1, int n2, int n3,
+ const char *name)
{
int i,j;
@@ -303,7 +306,7 @@ double ***Memory::grow_3d_double_array(double ***array,
------------------------------------------------------------------------- */
double ***Memory::create_3d_double_array(int n1lo, int n1hi,
- int n2, int n3, char *name)
+ int n2, int n3, const char *name)
{
int n1 = n1hi - n1lo + 1;
double ***array = create_3d_double_array(n1,n2,n3,name);
@@ -328,7 +331,7 @@ void Memory::destroy_3d_double_array(double ***array, int offset)
double ***Memory::create_3d_double_array(int n1lo, int n1hi,
int n2lo, int n2hi,
- int n3lo, int n3hi, char *name)
+ int n3lo, int n3hi, const char *name)
{
int n1 = n1hi - n1lo + 1;
int n2 = n2hi - n2lo + 1;
@@ -358,7 +361,7 @@ void Memory::destroy_3d_double_array(double ***array, int n1_offset,
create a 3d int array
------------------------------------------------------------------------- */
-int ***Memory::create_3d_int_array(int n1, int n2, int n3, char *name)
+int ***Memory::create_3d_int_array(int n1, int n2, int n3, const char *name)
{
int i,j;
@@ -394,7 +397,8 @@ void Memory::destroy_3d_int_array(int ***array)
create a 4d double array
------------------------------------------------------------------------- */
-double ****Memory::create_4d_double_array(int n1, int n2, int n3, int n4, char *name)
+double ****Memory::create_4d_double_array(int n1, int n2, int n3, int n4,
+ const char *name)
{
int i,j,k;
diff --git a/src/memory.h b/src/memory.h
index e5f2cf73daf81e9b9349b0bc7ca7e628049d00a9..39b79f7060a74def1569856bb8e6ea2b433955ff 100644
--- a/src/memory.h
+++ b/src/memory.h
@@ -22,38 +22,38 @@ class Memory : protected Pointers {
public:
Memory(class LAMMPS *);
- void *smalloc(int n, char *);
+ void *smalloc(int n, const char *);
void sfree(void *);
- void *srealloc(void *, int n, char *name);
+ void *srealloc(void *, int n, const char *name);
- double *create_1d_double_array(int, int, char *);
+ double *create_1d_double_array(int, int, const char *);
void destroy_1d_double_array(double *, int);
- double **create_2d_double_array(int, int, char *);
+ double **create_2d_double_array(int, int, const char *);
void destroy_2d_double_array(double **);
- double **grow_2d_double_array(double **, int, int, char *);
+ double **grow_2d_double_array(double **, int, int, const char *);
- int **create_2d_int_array(int, int, char *);
+ int **create_2d_int_array(int, int, const char *);
void destroy_2d_int_array(int **);
- int **grow_2d_int_array(int **, int, int, char *);
+ int **grow_2d_int_array(int **, int, int, const char *);
- double **create_2d_double_array(int, int, int, char *);
+ double **create_2d_double_array(int, int, int, const char *);
void destroy_2d_double_array(double **, int);
- double ***create_3d_double_array(int, int, int, char *);
+ double ***create_3d_double_array(int, int, int, const char *);
void destroy_3d_double_array(double ***);
- double ***grow_3d_double_array(double ***, int, int, int, char *);
+ double ***grow_3d_double_array(double ***, int, int, int, const char *);
- double ***create_3d_double_array(int, int, int, int, char *);
+ double ***create_3d_double_array(int, int, int, int, const char *);
void destroy_3d_double_array(double ***, int);
- double ***create_3d_double_array(int, int, int, int, int, int, char *);
+ double ***create_3d_double_array(int, int, int, int, int, int, const char *);
void destroy_3d_double_array(double ***, int, int, int);
- int ***create_3d_int_array(int, int, int, char *);
+ int ***create_3d_int_array(int, int, int, const char *);
void destroy_3d_int_array(int ***);
- double ****create_4d_double_array(int, int, int, int, char *);
+ double ****create_4d_double_array(int, int, int, int, const char *);
void destroy_4d_double_array(double ****);
};
diff --git a/src/min_cg.cpp b/src/min_cg.cpp
index 4390e27e5c9da6fa9fb5178c8c539194b2be9a24..ad0a74740e0e4db09d9798a3bbf282da4ee5797a 100644
--- a/src/min_cg.cpp
+++ b/src/min_cg.cpp
@@ -65,9 +65,9 @@ void MinCG::init()
// will delete it at end of run
char **fixarg = new char*[3];
- fixarg[0] = "MINIMIZE";
- fixarg[1] = "all";
- fixarg[2] = "MINIMIZE";
+ fixarg[0] = (char *) "MINIMIZE";
+ fixarg[1] = (char *) "all";
+ fixarg[2] = (char *) "MINIMIZE";
modify->add_fix(3,fixarg);
delete [] fixarg;
fix_minimize = (FixMinimize *) modify->fix[modify->nfix-1];
@@ -85,12 +85,9 @@ void MinCG::init()
// set flags for what arrays to clear in force_clear()
// need to clear torques if array exists
- // don't need to clear f_pair if atom_style is only granular (no virial)
torqueflag = 0;
if (atom->torque) torqueflag = 1;
- pairflag = 1;
- if (strcmp(atom->atom_style,"granular") == 0) pairflag = 0;
// orthogonal vs triclinic simulation box
@@ -115,11 +112,6 @@ void MinCG::init()
if (linestyle == SCAN) linemin = &MinCG::linemin_scan;
else if (linestyle == SECANT) linemin = &MinCG::linemin_secant;
-
- // local versions of Update quantities
-
- maxpair = update->maxpair;
- f_pair = update->f_pair;
}
/* ----------------------------------------------------------------------
@@ -233,6 +225,8 @@ void MinCG::setup()
int vflag = virial_thermo;
force_clear(vflag);
+ if (force->pair) force->pair->compute(eflag,vflag);
+
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
@@ -240,8 +234,6 @@ void MinCG::setup()
if (force->improper) force->improper->compute(eflag,vflag);
}
- if (force->pair) force->pair->compute(eflag,vflag);
-
if (force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
@@ -391,6 +383,12 @@ void MinCG::eng_force(int *pndof, double **px, double **ph, double *peng)
force_clear(vflag);
timer->stamp();
+
+ if (force->pair) {
+ force->pair->compute(eflag,vflag);
+ timer->stamp(TIME_PAIR);
+ }
+
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
@@ -399,11 +397,6 @@ void MinCG::eng_force(int *pndof, double **px, double **ph, double *peng)
timer->stamp(TIME_BOND);
}
- if (force->pair) {
- force->pair->compute(eflag,vflag);
- timer->stamp(TIME_PAIR);
- }
-
if (force->kspace) {
force->kspace->compute(eflag,vflag);
timer->stamp(TIME_KSPACE);
@@ -462,23 +455,6 @@ void MinCG::force_clear(int vflag)
torque[i][2] = 0.0;
}
}
-
- // clear f_pair array if using it this timestep to compute virial
-
- if (vflag == 2 && pairflag) {
- if (atom->nmax > maxpair) {
- maxpair = atom->nmax;
- memory->destroy_2d_double_array(f_pair);
- f_pair = memory->create_2d_double_array(maxpair,3,"min:f_pair");
- update->maxpair = maxpair;
- update->f_pair = f_pair;
- }
- for (i = 0; i < nall; i++) {
- f_pair[i][0] = 0.0;
- f_pair[i][1] = 0.0;
- f_pair[i][2] = 0.0;
- }
- }
}
/* ----------------------------------------------------------------------
diff --git a/src/modify.cpp b/src/modify.cpp
index 6d6c85da56a1fc14649b59b67a0f63e4432211be..7a53ea754122e036e75f90aab59c7bd8885c1f63 100644
--- a/src/modify.cpp
+++ b/src/modify.cpp
@@ -406,8 +406,8 @@ void Modify::add_fix(int narg, char **arg)
strcmp(style_restart_global[i],fix[ifix]->style) == 0) {
fix[ifix]->restart(state_restart_global[i]);
if (comm->me == 0) {
- char *str = "Resetting global state of Fix %s Style %s "
- "from restart file info\n";
+ char *str = (char *) ("Resetting global state of Fix %s Style %s "
+ "from restart file info\n");
if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
}
@@ -422,8 +422,8 @@ void Modify::add_fix(int narg, char **arg)
for (int j = 0; j < atom->nlocal; j++)
fix[ifix]->unpack_restart(j,index_restart_peratom[i]);
if (comm->me == 0) {
- char *str = "Resetting per-atom state of Fix %s Style %s "
- "from restart file info\n";
+ char *str = (char *) ("Resetting per-atom state of Fix %s Style %s "
+ "from restart file info\n");
if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
}
@@ -453,7 +453,7 @@ void Modify::modify_fix(int narg, char **arg)
Atom class must update indices in its list of callbacks to fixes
------------------------------------------------------------------------- */
-void Modify::delete_fix(char *id)
+void Modify::delete_fix(const char *id)
{
int ifix = find_fix(id);
if (ifix < 0) error->all("Could not find fix ID to delete");
@@ -472,7 +472,7 @@ void Modify::delete_fix(char *id)
return index of fix or -1 if not found
------------------------------------------------------------------------- */
-int Modify::find_fix(char *id)
+int Modify::find_fix(const char *id)
{
int ifix;
for (ifix = 0; ifix < nfix; ifix++)
diff --git a/src/modify.h b/src/modify.h
index e49bef7f740b99515a0602fae4314cde695c0bdd..88411fe11cd026de57a272092ed1da6701a949d9 100644
--- a/src/modify.h
+++ b/src/modify.h
@@ -58,8 +58,8 @@ class Modify : protected Pointers {
void add_fix(int, char **);
void modify_fix(int, char **);
- void delete_fix(char *);
- int find_fix(char *);
+ void delete_fix(const char *);
+ int find_fix(const char *);
void add_compute(int, char **);
void modify_compute(int, char **);
diff --git a/src/neigh_full.cpp b/src/neigh_full.cpp
index f5385e11e05a1563f9113d406bc843cb403e831e..878ab0819c8c5cc9b373b4b209ac29accd43c69f 100644
--- a/src/neigh_full.cpp
+++ b/src/neigh_full.cpp
@@ -12,6 +12,7 @@
------------------------------------------------------------------------- */
#include "neighbor.h"
+#include "neigh_list.h"
#include "atom.h"
#include "error.h"
@@ -22,7 +23,7 @@ using namespace LAMMPS_NS;
every neighbor pair appears in list of both atoms i and j
------------------------------------------------------------------------- */
-void Neighbor::full_nsq()
+void Neighbor::full_nsq(NeighList *list)
{
int i,j,n,itype,jtype,which;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
@@ -36,6 +37,12 @@ void Neighbor::full_nsq()
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ int **pages = list->pages;
+
+ int inum = 0;
int npage = 0;
int npnt = 0;
@@ -44,10 +51,10 @@ void Neighbor::full_nsq()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
- if (npage == maxpage_full) add_pages_full(npage);
+ if (npage == list->maxpage) pages = list->add_pages();
}
- neighptr = &pages_full[npage][npnt];
+ neighptr = &pages[npage][npnt];
n = 0;
itype = type[i];
@@ -60,9 +67,10 @@ void Neighbor::full_nsq()
for (j = 0; j < nall; j++) {
if (i == j) continue;
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@@ -75,12 +83,16 @@ void Neighbor::full_nsq()
}
}
- firstneigh_full[i] = neighptr;
- numneigh_full[i] = n;
+ ilist[inum] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
+
+ list->inum = inum;
}
/* ----------------------------------------------------------------------
@@ -88,7 +100,7 @@ void Neighbor::full_nsq()
every neighbor pair appears in list of both atoms i and j
------------------------------------------------------------------------- */
-void Neighbor::full_bin()
+void Neighbor::full_bin(NeighList *list)
{
int i,j,k,n,itype,jtype,ibin,which;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
@@ -108,6 +120,14 @@ void Neighbor::full_bin()
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ int **pages = list->pages;
+ int nstencil = list->nstencil;
+ int *stencil = list->stencil;
+
+ int inum = 0;
int npage = 0;
int npnt = 0;
@@ -116,10 +136,10 @@ void Neighbor::full_bin()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
- if (npage == maxpage_full) add_pages_full(npage);
+ if (npage == list->maxpage) pages = list->add_pages();
}
- neighptr = &pages_full[npage][npnt];
+ neighptr = &pages[npage][npnt];
n = 0;
itype = type[i];
@@ -132,12 +152,13 @@ void Neighbor::full_bin()
ibin = coord2bin(x[i]);
- for (k = 0; k < nstencil_full; k++) {
- for (j = binhead[ibin+stencil_full[k]]; j >= 0; j = bins[j]) {
+ for (k = 0; k < nstencil; k++) {
+ for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (i == j) continue;
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@@ -152,12 +173,16 @@ void Neighbor::full_bin()
}
}
- firstneigh_full[i] = neighptr;
- numneigh_full[i] = n;
+ ilist[inum] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
+
+ list->inum = inum;
}
/* ----------------------------------------------------------------------
@@ -166,7 +191,7 @@ void Neighbor::full_bin()
every neighbor pair appears in list of both atoms i and j
------------------------------------------------------------------------- */
-void Neighbor::full_bin_multi()
+void Neighbor::full_multi(NeighList *list)
{
int i,j,k,n,itype,jtype,ibin,which,ns;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
@@ -187,6 +212,15 @@ void Neighbor::full_bin_multi()
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ int **pages = list->pages;
+ int *nstencil_multi = list->nstencil_multi;
+ int **stencil_multi = list->stencil_multi;
+ double **distsq_multi = list->distsq_multi;
+
+ int inum = 0;
int npage = 0;
int npnt = 0;
@@ -195,10 +229,10 @@ void Neighbor::full_bin_multi()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
- if (npage == maxpage_full) add_pages_full(npage);
+ if (npage == list->maxpage) pages = list->add_pages();
}
- neighptr = &pages_full[npage][npnt];
+ neighptr = &pages[npage][npnt];
n = 0;
itype = type[i];
@@ -211,16 +245,17 @@ void Neighbor::full_bin_multi()
// skip i = j
ibin = coord2bin(x[i]);
- s = stencil_full_multi[itype];
- distsq = distsq_full_multi[itype];
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
cutsq = cutneighsq[itype];
- ns = nstencil_full_multi[itype];
+ ns = nstencil_multi[itype];
for (k = 0; k < ns; k++) {
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
jtype = type[j];
if (cutsq[jtype] < distsq[k]) continue;
if (i == j) continue;
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
+
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@@ -236,10 +271,14 @@ void Neighbor::full_bin_multi()
}
}
- firstneigh_full[i] = neighptr;
- numneigh_full[i] = n;
+ ilist[inum] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
+ inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
+
+ list->inum = inum;
}
diff --git a/src/neigh_gran.cpp b/src/neigh_gran.cpp
index ef12943b4070cdd60a438f034e86fee2599d051a..17c35fdb660d4e6d8fcf2e2f61da1ea3bac35aa2 100644
--- a/src/neigh_gran.cpp
+++ b/src/neigh_gran.cpp
@@ -12,8 +12,8 @@
------------------------------------------------------------------------- */
#include "neighbor.h"
+#include "neigh_list.h"
#include "atom.h"
-#include "modify.h"
#include "fix_shear_history.h"
#include "error.h"
@@ -27,22 +27,21 @@ using namespace LAMMPS_NS;
pair added if j is ghost (also stored by proc owning j)
------------------------------------------------------------------------- */
-void Neighbor::granular_nsq_no_newton()
+void Neighbor::granular_nsq_no_newton(NeighList *list)
{
int i,j,m,n,nn;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr,*touchptr;
double *shearptr;
- int *npartner;
- int **partner;
- double ***shearpartner;
- if (fix_history) {
- npartner = fix_history->npartner;
- partner = fix_history->partner;
- shearpartner = fix_history->shearpartner;
- }
+ NeighList *listgranhistory;
+ int *npartner,**partner;
+ double ***shearpartner;
+ int **firsttouch;
+ double **firstshear;
+ int **pages_touch;
+ double **pages_shear;
double **x = atom->x;
double *radius = atom->radius;
@@ -53,6 +52,26 @@ void Neighbor::granular_nsq_no_newton()
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ int **pages = list->pages;
+ int nstencil = list->nstencil;
+ int *stencil = list->stencil;
+
+ FixShearHistory *fix_history = list->fix_history;
+ if (fix_history) {
+ npartner = fix_history->npartner;
+ partner = fix_history->partner;
+ shearpartner = fix_history->shearpartner;
+ listgranhistory = list->listgranhistory;
+ firsttouch = listgranhistory->firstneigh;
+ firstshear = listgranhistory->firstdouble;
+ pages_touch = listgranhistory->pages;
+ pages_shear = listgranhistory->dpages;
+ }
+
+ int inum = 0;
int npage = 0;
int npnt = 0;
@@ -61,9 +80,12 @@ void Neighbor::granular_nsq_no_newton()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
- if (npage == maxpage) {
- add_pages(npage);
- if (fix_history) add_pages_history(npage);
+ if (npage == list->maxpage) {
+ pages = list->add_pages();
+ if (fix_history) {
+ pages_touch = listgranhistory->add_pages();
+ pages_shear = listgranhistory->dpages;
+ }
}
}
@@ -83,7 +105,7 @@ void Neighbor::granular_nsq_no_newton()
// loop over remaining atoms, owned and ghost
for (j = i+1; j < nall; j++) {
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@@ -122,16 +144,21 @@ void Neighbor::granular_nsq_no_newton()
}
}
+ ilist[inum] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
if (fix_history) {
firsttouch[i] = touchptr;
firstshear[i] = shearptr;
}
- firstneigh[i] = neighptr;
- numneigh[i] = n;
+
+ inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
+
+ list->inum = inum;
}
/* ----------------------------------------------------------------------
@@ -143,7 +170,7 @@ void Neighbor::granular_nsq_no_newton()
decision based on itag,jtag tests
------------------------------------------------------------------------- */
-void Neighbor::granular_nsq_newton()
+void Neighbor::granular_nsq_newton(NeighList *list)
{
int i,j,n,itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
@@ -159,6 +186,14 @@ void Neighbor::granular_nsq_newton()
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ int **pages = list->pages;
+ int nstencil = list->nstencil;
+ int *stencil = list->stencil;
+
+ int inum = 0;
int npage = 0;
int npnt = 0;
@@ -167,7 +202,7 @@ void Neighbor::granular_nsq_newton()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
- if (npage == maxpage) add_pages(npage);
+ if (npage == list->maxpage) pages = list->add_pages();
}
n = 0;
@@ -196,7 +231,7 @@ void Neighbor::granular_nsq_newton()
}
}
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@@ -208,12 +243,16 @@ void Neighbor::granular_nsq_newton()
if (rsq <= cutsq) neighptr[n++] = j;
}
+ ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
+ inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
+
+ list->inum = inum;
}
/* ----------------------------------------------------------------------
@@ -225,22 +264,21 @@ void Neighbor::granular_nsq_newton()
pair stored by me if j is ghost (also stored by proc owning j)
------------------------------------------------------------------------- */
-void Neighbor::granular_bin_no_newton()
+void Neighbor::granular_bin_no_newton(NeighList *list)
{
int i,j,k,m,n,nn,ibin;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double radi,radsum,cutsq;
int *neighptr,*touchptr;
double *shearptr;
- int *npartner;
- int **partner;
- double ***shearpartner;
- if (fix_history) {
- npartner = fix_history->npartner;
- partner = fix_history->partner;
- shearpartner = fix_history->shearpartner;
- }
+ NeighList *listgranhistory;
+ int *npartner,**partner;
+ double ***shearpartner;
+ int **firsttouch;
+ double **firstshear;
+ int **pages_touch;
+ double **pages_shear;
// bin local & ghost atoms
@@ -256,6 +294,26 @@ void Neighbor::granular_bin_no_newton()
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ int **pages = list->pages;
+ int nstencil = list->nstencil;
+ int *stencil = list->stencil;
+
+ FixShearHistory *fix_history = list->fix_history;
+ if (fix_history) {
+ npartner = fix_history->npartner;
+ partner = fix_history->partner;
+ shearpartner = fix_history->shearpartner;
+ listgranhistory = list->listgranhistory;
+ firsttouch = listgranhistory->firstneigh;
+ firstshear = listgranhistory->firstdouble;
+ pages_touch = listgranhistory->pages;
+ pages_shear = listgranhistory->dpages;
+ }
+
+ int inum = 0;
int npage = 0;
int npnt = 0;
@@ -264,9 +322,12 @@ void Neighbor::granular_bin_no_newton()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
- if (npage == maxpage) {
- add_pages(npage);
- if (fix_history) add_pages_history(npage);
+ if (npage == list->maxpage) {
+ pages = list->add_pages();
+ if (fix_history) {
+ pages_touch = listgranhistory->add_pages();
+ pages_shear = listgranhistory->dpages;
+ }
}
}
@@ -292,7 +353,7 @@ void Neighbor::granular_bin_no_newton()
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (j <= i) continue;
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@@ -332,16 +393,21 @@ void Neighbor::granular_bin_no_newton()
}
}
+ ilist[inum] = i;
+ firstneigh[i] = neighptr;
+ numneigh[i] = n;
if (fix_history) {
firsttouch[i] = touchptr;
firstshear[i] = shearptr;
}
- firstneigh[i] = neighptr;
- numneigh[i] = n;
+
+ inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
+
+ list->inum = inum;
}
/* ----------------------------------------------------------------------
@@ -352,7 +418,7 @@ void Neighbor::granular_bin_no_newton()
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
-void Neighbor::granular_bin_newton()
+void Neighbor::granular_bin_newton(NeighList *list)
{
int i,j,k,n,ibin;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
@@ -372,6 +438,14 @@ void Neighbor::granular_bin_newton()
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ int **pages = list->pages;
+ int nstencil = list->nstencil;
+ int *stencil = list->stencil;
+
+ int inum = 0;
int npage = 0;
int npnt = 0;
@@ -380,7 +454,7 @@ void Neighbor::granular_bin_newton()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
- if (npage == maxpage) add_pages(npage);
+ if (npage == list->maxpage) pages = list->add_pages();
}
n = 0;
@@ -400,7 +474,7 @@ void Neighbor::granular_bin_newton()
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
}
delx = xtmp - x[j][0];
@@ -418,7 +492,7 @@ void Neighbor::granular_bin_newton()
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@@ -431,12 +505,16 @@ void Neighbor::granular_bin_newton()
}
}
+ ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
+ inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
+
+ list->inum = inum;
}
/* ----------------------------------------------------------------------
@@ -447,7 +525,7 @@ void Neighbor::granular_bin_newton()
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
-void Neighbor::granular_bin_newton_tri()
+void Neighbor::granular_bin_newton_tri(NeighList *list)
{
int i,j,k,n,ibin;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
@@ -467,6 +545,14 @@ void Neighbor::granular_bin_newton_tri()
int *molecule = atom->molecule;
int nlocal = atom->nlocal;
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ int **pages = list->pages;
+ int nstencil = list->nstencil;
+ int *stencil = list->stencil;
+
+ int inum = 0;
int npage = 0;
int npnt = 0;
@@ -475,7 +561,7 @@ void Neighbor::granular_bin_newton_tri()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
- if (npage == maxpage) add_pages(npage);
+ if (npage == list->maxpage) pages = list->add_pages();
}
n = 0;
@@ -497,7 +583,7 @@ void Neighbor::granular_bin_newton_tri()
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] <= xtmp) continue;
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
+ if (exclude && exclusion(i,j,type[i],type[j],mask,molecule)) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
@@ -510,10 +596,14 @@ void Neighbor::granular_bin_newton_tri()
}
}
+ ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
+ inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
+
+ list->inum = inum;
}
diff --git a/src/neigh_half.cpp b/src/neigh_half.cpp
deleted file mode 100644
index 63f1edff7ec432cf76c599199f88727ff0086810..0000000000000000000000000000000000000000
--- a/src/neigh_half.cpp
+++ /dev/null
@@ -1,820 +0,0 @@
-/* ----------------------------------------------------------------------
- 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.
-------------------------------------------------------------------------- */
-
-#include "neighbor.h"
-#include "atom.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-/* ----------------------------------------------------------------------
- N^2 / 2 search for neighbor pairs with partial Newton's 3rd law
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::half_nsq_no_newton()
-{
- int i,j,n,itype,jtype,which;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- int *molecule = atom->molecule;
- int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
- int molecular = atom->molecular;
-
- int npage = 0;
- int npnt = 0;
-
- for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == maxpage) add_pages(npage);
- }
-
- neighptr = &pages[npage][npnt];
- n = 0;
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
-
- // loop over remaining atoms, owned and ghost
-
- for (j = i+1; j < nall; j++) {
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
-
- jtype = type[j];
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = which*nall + j;
- }
- }
-
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- npnt += n;
- if (npnt >= pgsize)
- error->one("Neighbor list overflow, boost neigh_modify one or page");
- }
-}
-
-/* ----------------------------------------------------------------------
- N^2 / 2 search for neighbor pairs with full Newton's 3rd law
- every pair stored exactly once by some processor
- decision on ghost atoms based on itag,jtag tests
-------------------------------------------------------------------------- */
-
-void Neighbor::half_nsq_newton()
-{
- int i,j,n,itype,jtype,itag,jtag,which;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- double **x = atom->x;
- int *tag = atom->tag;
- int *type = atom->type;
- int *mask = atom->mask;
- int *molecule = atom->molecule;
- int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
- int molecular = atom->molecular;
-
- int npage = 0;
- int npnt = 0;
-
- for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == maxpage) add_pages(npage);
- }
-
- neighptr = &pages[npage][npnt];
- n = 0;
-
- itag = tag[i];
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
-
- // loop over remaining atoms, owned and ghost
- // itag = jtag is possible for long cutoffs that include images of self
-
- for (j = i+1; j < nall; j++) {
- if (j >= nlocal) {
- jtag = tag[j];
- if (itag > jtag) {
- if ((itag+jtag) % 2 == 0) continue;
- } else if (itag < jtag) {
- if ((itag+jtag) % 2 == 1) continue;
- } else {
- if (x[j][2] < ztmp) continue;
- else if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
- else if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp)
- continue;
- }
- }
-
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
-
- jtype = type[j];
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = which*nall + j;
- }
- }
-
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- npnt += n;
- if (npnt >= pgsize)
- error->one("Neighbor list overflow, boost neigh_modify one or page");
- }
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with partial Newton's 3rd law
- each owned atom i checks own bin and other bins in stencil
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::half_bin_no_newton()
-{
- int i,j,k,n,itype,jtype,ibin,which;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- // bin local & ghost atoms
-
- bin_atoms();
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- int *molecule = atom->molecule;
- int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
- int molecular = atom->molecular;
-
- int npage = 0;
- int npnt = 0;
-
- for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == maxpage) add_pages(npage);
- }
-
- neighptr = &pages[npage][npnt];
- n = 0;
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
-
- // loop over all atoms in other bins in stencil including self
- // only store pair if i < j
- // stores own/own pairs only once
- // stores own/ghost pairs on both procs
-
- ibin = coord2bin(x[i]);
-
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
-
- jtype = type[j];
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = which*nall + j;
- }
- }
- }
-
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- npnt += n;
- if (npnt >= pgsize)
- error->one("Neighbor list overflow, boost neigh_modify one or page");
- }
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with partial Newton's 3rd law
- each owned atom i checks own bin and other bins in stencil
- multi-type stencil is itype dependent and is distance checked
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::half_bin_no_newton_multi()
-{
- int i,j,k,n,itype,jtype,ibin,which,ns;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*s;
- double *cutsq,*distsq;
-
- // bin local & ghost atoms
-
- bin_atoms();
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- int *molecule = atom->molecule;
- int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
- int molecular = atom->molecular;
-
- int npage = 0;
- int npnt = 0;
-
- for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == maxpage) add_pages(npage);
- }
-
- neighptr = &pages[npage][npnt];
- n = 0;
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
-
- // loop over all atoms in other bins in stencil including self
- // only store pair if i < j
- // skip if i,j neighbor cutoff is less than bin distance
- // stores own/own pairs only once
- // stores own/ghost pairs on both procs
-
- ibin = coord2bin(x[i]);
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- cutsq = cutneighsq[itype];
- ns = nstencil_multi[itype];
- for (k = 0; k < ns; k++) {
- for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- if (j <= i) continue;
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = which*nall + j;
- }
- }
- }
-
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- npnt += n;
- if (npnt >= pgsize)
- error->one("Neighbor list overflow, boost neigh_modify one or page");
- }
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with full Newton's 3rd law
- each owned atom i checks its own bin and other bins in Newton stencil
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::half_bin_newton()
-{
- int i,j,k,n,itype,jtype,ibin,which;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- // bin local & ghost atoms
-
- bin_atoms();
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- int *molecule = atom->molecule;
- int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
- int molecular = atom->molecular;
-
- int npage = 0;
- int npnt = 0;
-
- for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == maxpage) add_pages(npage);
- }
-
- neighptr = &pages[npage][npnt];
- n = 0;
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
-
- // loop over rest of atoms in i's bin, ghosts are at end of linked list
- // if j is owned atom, store it, since j is beyond i in linked list
- // if j is ghost, only store if j coords are "above and to the right" of i
-
- for (j = bins[i]; j >= 0; j = bins[j]) {
- if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
- if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
-
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
-
- jtype = type[j];
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = which*nall + j;
- }
- }
-
- // loop over all atoms in other bins in stencil, store every pair
-
- ibin = coord2bin(x[i]);
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
-
- jtype = type[j];
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = which*nall + j;
- }
- }
- }
-
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- npnt += n;
- if (npnt >= pgsize)
- error->one("Neighbor list overflow, boost neigh_modify one or page");
- }
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with full Newton's 3rd law
- each owned atom i checks its own bin and other bins in Newton stencil
- multi-type stencil is itype dependent and is distance checked
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::half_bin_newton_multi()
-{
- int i,j,k,n,itype,jtype,ibin,which,ns;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*s;
- double *cutsq,*distsq;
-
- // bin local & ghost atoms
-
- bin_atoms();
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- int *molecule = atom->molecule;
- int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
- int molecular = atom->molecular;
-
- int npage = 0;
- int npnt = 0;
-
- for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == maxpage) add_pages(npage);
- }
-
- neighptr = &pages[npage][npnt];
- n = 0;
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
-
- // loop over rest of atoms in i's bin, ghosts are at end of linked list
- // if j is owned atom, store it, since j is beyond i in linked list
- // if j is ghost, only store if j coords are "above and to the right" of i
-
- for (j = bins[i]; j >= 0; j = bins[j]) {
- if (j >= nlocal) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
- if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
-
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
-
- jtype = type[j];
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = which*nall + j;
- }
- }
-
- // loop over all atoms in other bins in stencil, store every pair
- // skip if i,j neighbor cutoff is less than bin distance
-
- ibin = coord2bin(x[i]);
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- cutsq = cutneighsq[itype];
- ns = nstencil_multi[itype];
- for (k = 0; k < ns; k++) {
- for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = which*nall + j;
- }
- }
- }
-
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- npnt += n;
- if (npnt >= pgsize)
- error->one("Neighbor list overflow, boost neigh_modify one or page");
- }
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with Newton's 3rd law for triclinic
- each owned atom i checks its own bin and other bins in triclinic stencil
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::half_bin_newton_tri()
-{
- int i,j,k,n,itype,jtype,ibin,which;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr;
-
- // bin local & ghost atoms
-
- bin_atoms();
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- int *molecule = atom->molecule;
- int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
- int molecular = atom->molecular;
-
- int npage = 0;
- int npnt = 0;
-
- for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == maxpage) add_pages(npage);
- }
-
- neighptr = &pages[npage][npnt];
- n = 0;
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
-
- // loop over all atoms in bins in stencil
- // pairs for atoms j "below" i are excluded
- // below = lower z or (equal z and lower y) or (equal zy and <= x)
- // this excludes self-self interaction
-
- ibin = coord2bin(x[i]);
- for (k = 0; k < nstencil; k++) {
- for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
- if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] <= xtmp) continue;
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
-
- jtype = type[j];
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = which*nall + j;
- }
- }
- }
-
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- npnt += n;
- if (npnt >= pgsize)
- error->one("Neighbor list overflow, boost neigh_modify one or page");
- }
-}
-
-/* ----------------------------------------------------------------------
- binned neighbor list construction with Newton's 3rd law for triclinic
- each owned atom i checks its own bin and other bins in triclinic stencil
- multi-type stencil is itype dependent and is distance checked
- every pair stored exactly once by some processor
-------------------------------------------------------------------------- */
-
-void Neighbor::half_bin_newton_multi_tri()
-{
- int i,j,k,n,itype,jtype,ibin,which,ns;
- double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr,*s;
- double *cutsq,*distsq;
-
- // bin local & ghost atoms
-
- bin_atoms();
-
- // loop over each atom, storing neighbors
-
- double **x = atom->x;
- int *type = atom->type;
- int *mask = atom->mask;
- int *molecule = atom->molecule;
- int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
- int molecular = atom->molecular;
-
- int npage = 0;
- int npnt = 0;
-
- for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == maxpage) add_pages(npage);
- }
-
- neighptr = &pages[npage][npnt];
- n = 0;
-
- itype = type[i];
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
-
- // loop over all atoms in bins, including self, in stencil
- // skip if i,j neighbor cutoff is less than bin distance
- // bins below self are excluded from stencil
- // pairs for atoms j below i are excluded
-
- ibin = coord2bin(x[i]);
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- cutsq = cutneighsq[itype];
- ns = nstencil_multi[itype];
- for (k = 0; k < ns; k++) {
- for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
- jtype = type[j];
- if (cutsq[jtype] < distsq[k]) continue;
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
- if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] <= xtmp) continue;
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
-
- delx = xtmp - x[j][0];
- dely = ytmp - x[j][1];
- delz = ztmp - x[j][2];
- rsq = delx*delx + dely*dely + delz*delz;
-
- if (rsq <= cutneighsq[itype][jtype]) {
- if (molecular) which = find_special(i,j);
- else which = 0;
- if (which == 0) neighptr[n++] = j;
- else if (which > 0) neighptr[n++] = which*nall + j;
- }
- }
- }
-
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- npnt += n;
- if (npnt >= pgsize)
- error->one("Neighbor list overflow, boost neigh_modify one or page");
- }
-}
-
-/* ----------------------------------------------------------------------
- build half list from full list
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::half_full_no_newton()
-{
- int i,j,k,n,nfull;
- int *neighptr,*neighs;
-
- int nlocal = atom->nlocal;
-
- int npage = 0;
- int npnt = 0;
-
- for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == maxpage) add_pages(npage);
- }
-
- neighptr = &pages[npage][npnt];
- n = 0;
-
- // loop over full neighbor list
-
- neighs = firstneigh_full[i];
- nfull = numneigh_full[i];
-
- for (k = 0; k < nfull; k++) {
- j = neighs[k];
- if (j > i) neighptr[n++] = j;
- }
-
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- npnt += n;
- if (npnt >= pgsize)
- error->one("Neighbor list overflow, boost neigh_modify one or page");
- }
-}
-
-/* ----------------------------------------------------------------------
- build half list from full list
- pair stored once if i,j are both owned and i < j
- pair stored by me if j is ghost (also stored by proc owning j)
-------------------------------------------------------------------------- */
-
-void Neighbor::half_full_newton()
-{
- int i,j,k,n,nfull;
- int *neighptr,*neighs;
- double xtmp,ytmp,ztmp;
-
- double **x = atom->x;
- int nlocal = atom->nlocal;
-
- int npage = 0;
- int npnt = 0;
-
- for (i = 0; i < nlocal; i++) {
-
- if (pgsize - npnt < oneatom) {
- npnt = 0;
- npage++;
- if (npage == maxpage) add_pages(npage);
- }
-
- neighptr = &pages[npage][npnt];
- n = 0;
-
- xtmp = x[i][0];
- ytmp = x[i][1];
- ztmp = x[i][2];
-
- // loop over full neighbor list
-
- neighs = firstneigh_full[i];
- nfull = numneigh_full[i];
-
- for (k = 0; k < nfull; k++) {
- j = neighs[k];
- if (j < nlocal) {
- if (i > j) continue;
- } else {
- if (x[j][2] < ztmp) continue;
- if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
- if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
- }
- neighptr[n++] = j;
- }
-
- firstneigh[i] = neighptr;
- numneigh[i] = n;
- npnt += n;
- if (npnt >= pgsize)
- error->one("Neighbor list overflow, boost neigh_modify one or page");
- }
-}
diff --git a/src/neigh_respa.cpp b/src/neigh_respa.cpp
index a37275f37b5ae0a7c1e00ed841a75e315e2df5bb..38bb3232e7fb03286609b49e6a83d90ef5a404f4 100644
--- a/src/neigh_respa.cpp
+++ b/src/neigh_respa.cpp
@@ -12,6 +12,7 @@
------------------------------------------------------------------------- */
#include "neighbor.h"
+#include "neigh_list.h"
#include "atom.h"
#include "error.h"
@@ -24,14 +25,11 @@ using namespace LAMMPS_NS;
pair added if j is ghost (also stored by proc owning j)
------------------------------------------------------------------------- */
-void Neighbor::respa_nsq_no_newton()
+void Neighbor::respa_nsq_no_newton(NeighList *list)
{
- int i,j,itype,jtype,which;
- int n_inner,n_middle,n;
+ int i,j,n,itype,jtype,which,n_inner,n_middle;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr_inner;
- int *neighptr_middle;
- int *neighptr;
+ int *neighptr,*neighptr_inner,*neighptr_middle;
double **x = atom->x;
int *type = atom->type;
@@ -41,6 +39,27 @@ void Neighbor::respa_nsq_no_newton()
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ int **pages = list->pages;
+
+ NeighList *listinner = list->listinner;
+ int *numneigh_inner = listinner->numneigh;
+ int **firstneigh_inner = listinner->firstneigh;
+ int **pages_inner = listinner->pages;
+
+ NeighList *listmiddle;
+ int *numneigh_middle,**firstneigh_middle,**pages_middle;
+ int respamiddle = list->respamiddle;
+ if (respamiddle) {
+ listmiddle = list->listmiddle;
+ numneigh_middle = listmiddle->numneigh;
+ firstneigh_middle = listmiddle->firstneigh;
+ pages_middle = listmiddle->pages;
+ }
+
+ int inum = 0;
int npage = 0;
int npnt = 0;
int npage_inner = 0;
@@ -53,7 +72,7 @@ void Neighbor::respa_nsq_no_newton()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
- if (npage == maxpage) add_pages(npage);
+ if (npage == list->maxpage) pages = list->add_pages();
}
neighptr = &pages[npage][npnt];
n = 0;
@@ -61,16 +80,18 @@ void Neighbor::respa_nsq_no_newton()
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner++;
- if (npage_inner == maxpage_inner) add_pages_inner(npage_inner);
+ if (npage_inner == listinner->maxpage)
+ pages_inner = listinner->add_pages();
}
neighptr_inner = &pages_inner[npage_inner][npnt_inner];
n_inner = 0;
- if (respa == 2) {
+ if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle++;
- if (npage_middle == maxpage_middle) add_pages_middle(npage_middle);
+ if (npage_middle == listmiddle->maxpage)
+ pages_middle = listmiddle->add_pages();
}
neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
@@ -84,9 +105,9 @@ void Neighbor::respa_nsq_no_newton()
// loop over remaining atoms, owned and ghost
for (j = i+1; j < nall; j++) {
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
-
jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@@ -103,15 +124,17 @@ void Neighbor::respa_nsq_no_newton()
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
}
- if (respa == 2 && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (respamiddle && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
}
}
}
+ ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
+ inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -122,7 +145,7 @@ void Neighbor::respa_nsq_no_newton()
if (npnt_inner >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
- if (respa == 2) {
+ if (respamiddle) {
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
@@ -130,6 +153,8 @@ void Neighbor::respa_nsq_no_newton()
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
}
+
+ list->inum = inum;
}
/* ----------------------------------------------------------------------
@@ -140,14 +165,11 @@ void Neighbor::respa_nsq_no_newton()
decision based on itag,jtag tests
------------------------------------------------------------------------- */
-void Neighbor::respa_nsq_newton()
+void Neighbor::respa_nsq_newton(NeighList *list)
{
- int i,j,itype,jtype,itag,jtag,which;
- int n_inner,n_middle,n;
+ int i,j,n,itype,jtype,itag,jtag,which,n_inner,n_middle;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr_inner;
- int *neighptr_middle;
- int *neighptr;
+ int *neighptr,*neighptr_inner,*neighptr_middle;
double **x = atom->x;
int *tag = atom->tag;
@@ -158,6 +180,27 @@ void Neighbor::respa_nsq_newton()
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ int **pages = list->pages;
+
+ NeighList *listinner = list->listinner;
+ int *numneigh_inner = listinner->numneigh;
+ int **firstneigh_inner = listinner->firstneigh;
+ int **pages_inner = listinner->pages;
+
+ NeighList *listmiddle;
+ int *numneigh_middle,**firstneigh_middle,**pages_middle;
+ int respamiddle = list->respamiddle;
+ if (respamiddle) {
+ listmiddle = list->listmiddle;
+ numneigh_middle = listmiddle->numneigh;
+ firstneigh_middle = listmiddle->firstneigh;
+ pages_middle = listmiddle->pages;
+ }
+
+ int inum = 0;
int npage = 0;
int npnt = 0;
int npage_inner = 0;
@@ -170,7 +213,7 @@ void Neighbor::respa_nsq_newton()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
- if (npage == maxpage) add_pages(npage);
+ if (npage == list->maxpage) pages = list->add_pages();
}
neighptr = &pages[npage][npnt];
n = 0;
@@ -178,16 +221,18 @@ void Neighbor::respa_nsq_newton()
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner++;
- if (npage_inner == maxpage_inner) add_pages_inner(npage_inner);
+ if (npage_inner == listinner->maxpage)
+ pages_inner = listinner->add_pages();
}
neighptr_inner = &pages_inner[npage_inner][npnt_inner];
n_inner = 0;
- if (respa == 2) {
+ if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle++;
- if (npage_middle == maxpage_middle) add_pages_middle(npage_middle);
+ if (npage_middle == listmiddle->maxpage)
+ pages_middle = listmiddle->add_pages();
}
neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
@@ -216,9 +261,9 @@ void Neighbor::respa_nsq_newton()
}
}
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
-
jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@@ -235,15 +280,18 @@ void Neighbor::respa_nsq_newton()
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
}
- if (respa == 2 && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
}
}
}
+ ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
+ inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -254,7 +302,7 @@ void Neighbor::respa_nsq_newton()
if (npnt_inner >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
- if (respa == 2) {
+ if (respamiddle) {
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
@@ -262,6 +310,8 @@ void Neighbor::respa_nsq_newton()
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
}
+
+ list->inum = inum;
}
/* ----------------------------------------------------------------------
@@ -272,14 +322,11 @@ void Neighbor::respa_nsq_newton()
pair stored by me if j is ghost (also stored by proc owning j)
------------------------------------------------------------------------- */
-void Neighbor::respa_bin_no_newton()
+void Neighbor::respa_bin_no_newton(NeighList *list)
{
- int i,j,k,itype,jtype,ibin,which;
- int n_inner,n_middle,n;
+ int i,j,k,n,itype,jtype,ibin,which,n_inner,n_middle;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr_inner;
- int *neighptr_middle;
- int *neighptr;
+ int *neighptr,*neighptr_inner,*neighptr_middle;
// bin local & ghost atoms
@@ -295,6 +342,29 @@ void Neighbor::respa_bin_no_newton()
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ int **pages = list->pages;
+ int nstencil = list->nstencil;
+ int *stencil = list->stencil;
+
+ NeighList *listinner = list->listinner;
+ int *numneigh_inner = listinner->numneigh;
+ int **firstneigh_inner = listinner->firstneigh;
+ int **pages_inner = listinner->pages;
+
+ NeighList *listmiddle;
+ int *numneigh_middle,**firstneigh_middle,**pages_middle;
+ int respamiddle = list->respamiddle;
+ if (respamiddle) {
+ listmiddle = list->listmiddle;
+ numneigh_middle = listmiddle->numneigh;
+ firstneigh_middle = listmiddle->firstneigh;
+ pages_middle = listmiddle->pages;
+ }
+
+ int inum = 0;
int npage = 0;
int npnt = 0;
int npage_inner = 0;
@@ -307,7 +377,7 @@ void Neighbor::respa_bin_no_newton()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
- if (npage == maxpage) add_pages(npage);
+ if (npage == list->maxpage) pages = list->add_pages();
}
neighptr = &pages[npage][npnt];
n = 0;
@@ -315,16 +385,18 @@ void Neighbor::respa_bin_no_newton()
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner++;
- if (npage_inner == maxpage_inner) add_pages_inner(npage_inner);
+ if (npage_inner == listinner->maxpage)
+ pages_inner = listinner->add_pages();
}
neighptr_inner = &pages_inner[npage_inner][npnt_inner];
n_inner = 0;
- if (respa == 2) {
+ if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle++;
- if (npage_middle == maxpage_middle) add_pages_middle(npage_middle);
+ if (npage_middle == listmiddle->maxpage)
+ pages_middle = listmiddle->add_pages();
}
neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
@@ -344,9 +416,10 @@ void Neighbor::respa_bin_no_newton()
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
if (j <= i) continue;
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@@ -363,7 +436,8 @@ void Neighbor::respa_bin_no_newton()
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
}
- if (respa == 2 && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
}
@@ -371,8 +445,10 @@ void Neighbor::respa_bin_no_newton()
}
}
+ ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
+ inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -383,7 +459,7 @@ void Neighbor::respa_bin_no_newton()
if (npnt_inner >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
- if (respa == 2) {
+ if (respamiddle) {
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
@@ -391,6 +467,8 @@ void Neighbor::respa_bin_no_newton()
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
}
+
+ list->inum = inum;
}
/* ----------------------------------------------------------------------
@@ -400,14 +478,11 @@ void Neighbor::respa_bin_no_newton()
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
-void Neighbor::respa_bin_newton()
+void Neighbor::respa_bin_newton(NeighList *list)
{
- int i,j,k,itype,jtype,ibin,which;
- int n_inner,n_middle,n;
+ int i,j,k,n,itype,jtype,ibin,which,n_inner,n_middle;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr_inner;
- int *neighptr_middle;
- int *neighptr;
+ int *neighptr,*neighptr_inner,*neighptr_middle;
// bin local & ghost atoms
@@ -423,6 +498,29 @@ void Neighbor::respa_bin_newton()
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ int **pages = list->pages;
+ int nstencil = list->nstencil;
+ int *stencil = list->stencil;
+
+ NeighList *listinner = list->listinner;
+ int *numneigh_inner = listinner->numneigh;
+ int **firstneigh_inner = listinner->firstneigh;
+ int **pages_inner = listinner->pages;
+
+ NeighList *listmiddle;
+ int *numneigh_middle,**firstneigh_middle,**pages_middle;
+ int respamiddle = list->respamiddle;
+ if (respamiddle) {
+ listmiddle = list->listmiddle;
+ numneigh_middle = listmiddle->numneigh;
+ firstneigh_middle = listmiddle->firstneigh;
+ pages_middle = listmiddle->pages;
+ }
+
+ int inum = 0;
int npage = 0;
int npnt = 0;
int npage_inner = 0;
@@ -435,7 +533,7 @@ void Neighbor::respa_bin_newton()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
- if (npage == maxpage) add_pages(npage);
+ if (npage == list->maxpage) pages = list->add_pages();
}
neighptr = &pages[npage][npnt];
n = 0;
@@ -443,16 +541,18 @@ void Neighbor::respa_bin_newton()
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner++;
- if (npage_inner == maxpage_inner) add_pages_inner(npage_inner);
+ if (npage_inner == listinner->maxpage)
+ pages_inner = listinner->add_pages();
}
neighptr_inner = &pages_inner[npage_inner][npnt_inner];
n_inner = 0;
- if (respa == 2) {
+ if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle++;
- if (npage_middle == maxpage_middle) add_pages_middle(npage_middle);
+ if (npage_middle == listmiddle->maxpage)
+ pages_middle = listmiddle->add_pages();
}
neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
@@ -472,10 +572,11 @@ void Neighbor::respa_bin_newton()
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
}
jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@@ -492,7 +593,8 @@ void Neighbor::respa_bin_newton()
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
}
- if (respa == 2 && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
}
@@ -504,9 +606,9 @@ void Neighbor::respa_bin_newton()
ibin = coord2bin(x[i]);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin+stencil[k]]; j >= 0; j = bins[j]) {
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
-
jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@@ -523,7 +625,8 @@ void Neighbor::respa_bin_newton()
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
}
- if (respa == 2 && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
}
@@ -531,8 +634,10 @@ void Neighbor::respa_bin_newton()
}
}
+ ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
+ inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -543,7 +648,7 @@ void Neighbor::respa_bin_newton()
if (npnt_inner >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
- if (respa == 2) {
+ if (respamiddle) {
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
@@ -551,6 +656,8 @@ void Neighbor::respa_bin_newton()
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
}
+
+ list->inum = inum;
}
/* ----------------------------------------------------------------------
@@ -560,14 +667,11 @@ void Neighbor::respa_bin_newton()
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
-void Neighbor::respa_bin_newton_tri()
+void Neighbor::respa_bin_newton_tri(NeighList *list)
{
- int i,j,k,itype,jtype,ibin,which;
- int n_inner,n_middle,n;
+ int i,j,k,n,itype,jtype,ibin,which,n_inner,n_middle;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
- int *neighptr_inner;
- int *neighptr_middle;
- int *neighptr;
+ int *neighptr,*neighptr_inner,*neighptr_middle;
// bin local & ghost atoms
@@ -583,6 +687,29 @@ void Neighbor::respa_bin_newton_tri()
int nall = atom->nlocal + atom->nghost;
int molecular = atom->molecular;
+ int *ilist = list->ilist;
+ int *numneigh = list->numneigh;
+ int **firstneigh = list->firstneigh;
+ int **pages = list->pages;
+ int nstencil = list->nstencil;
+ int *stencil = list->stencil;
+
+ NeighList *listinner = list->listinner;
+ int *numneigh_inner = listinner->numneigh;
+ int **firstneigh_inner = listinner->firstneigh;
+ int **pages_inner = listinner->pages;
+
+ NeighList *listmiddle;
+ int *numneigh_middle,**firstneigh_middle,**pages_middle;
+ int respamiddle = list->respamiddle;
+ if (respamiddle) {
+ listmiddle = list->listmiddle;
+ numneigh_middle = listmiddle->numneigh;
+ firstneigh_middle = listmiddle->firstneigh;
+ pages_middle = listmiddle->pages;
+ }
+
+ int inum = 0;
int npage = 0;
int npnt = 0;
int npage_inner = 0;
@@ -595,7 +722,7 @@ void Neighbor::respa_bin_newton_tri()
if (pgsize - npnt < oneatom) {
npnt = 0;
npage++;
- if (npage == maxpage) add_pages(npage);
+ if (npage == list->maxpage) pages = list->add_pages();
}
neighptr = &pages[npage][npnt];
n = 0;
@@ -603,16 +730,18 @@ void Neighbor::respa_bin_newton_tri()
if (pgsize - npnt_inner < oneatom) {
npnt_inner = 0;
npage_inner++;
- if (npage_inner == maxpage_inner) add_pages_inner(npage_inner);
+ if (npage_inner == listinner->maxpage)
+ pages_inner = listinner->add_pages();
}
neighptr_inner = &pages_inner[npage_inner][npnt_inner];
n_inner = 0;
- if (respa == 2) {
+ if (respamiddle) {
if (pgsize - npnt_middle < oneatom) {
npnt_middle = 0;
npage_middle++;
- if (npage_middle == maxpage_middle) add_pages_middle(npage_middle);
+ if (npage_middle == listmiddle->maxpage)
+ pages_middle = listmiddle->add_pages();
}
neighptr_middle = &pages_middle[npage_middle][npnt_middle];
n_middle = 0;
@@ -634,9 +763,10 @@ void Neighbor::respa_bin_newton_tri()
if (x[j][2] < ztmp) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] <= xtmp) continue;
- if (exclude && exclusion(i,j,type,mask,molecule)) continue;
jtype = type[j];
+ if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
+
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
@@ -653,7 +783,8 @@ void Neighbor::respa_bin_newton_tri()
else if (which > 0) neighptr_inner[n_inner++] = which*nall + j;
}
- if (respa == 2 && rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
+ if (respamiddle &&
+ rsq < cut_middle_sq && rsq > cut_middle_inside_sq) {
if (which == 0) neighptr_middle[n_middle++] = j;
else if (which > 0) neighptr_middle[n_middle++] = which*nall + j;
}
@@ -661,8 +792,10 @@ void Neighbor::respa_bin_newton_tri()
}
}
+ ilist[inum] = i;
firstneigh[i] = neighptr;
numneigh[i] = n;
+ inum++;
npnt += n;
if (npnt >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
@@ -673,7 +806,7 @@ void Neighbor::respa_bin_newton_tri()
if (npnt_inner >= pgsize)
error->one("Neighbor list overflow, boost neigh_modify one or page");
- if (respa == 2) {
+ if (respamiddle) {
firstneigh_middle[i] = neighptr_middle;
numneigh_middle[i] = n_middle;
npnt_middle += n_middle;
@@ -681,4 +814,6 @@ void Neighbor::respa_bin_newton_tri()
error->one("Neighbor list overflow, boost neigh_modify one or page");
}
}
+
+ list->inum = inum;
}
diff --git a/src/neigh_stencil.cpp b/src/neigh_stencil.cpp
index 89f8895c27f0042dd9c502ebd48df9f194db27bb..7f2170a022e1c9a7138c1ca6f0ba12546a0b5f78 100644
--- a/src/neigh_stencil.cpp
+++ b/src/neigh_stencil.cpp
@@ -12,29 +12,29 @@
------------------------------------------------------------------------- */
#include "neighbor.h"
+#include "neigh_list.h"
#include "atom.h"
#include "memory.h"
using namespace LAMMPS_NS;
-enum{NSQ,BIN,MULTI}; // also in neighbor.cpp
-
/* ----------------------------------------------------------------------
routines to create a stencil = list of bin offsets
stencil = bins whose closest corner to central bin is within cutoff
sx,sy,sz = bin bounds = furthest the stencil could possibly extend
3d creates xyz stencil, 2d creates xy stencil
- for half neigh list with partial Newton:
+ for half list with newton off:
stencil is all surrounding bins
stencil includes self
- for half neigh list with full Newton:
+ regardless of triclinic
+ for half list with newton on:
stencil is bins to the "upper right" of central bin
stencil does not include self
- for half neigh list with triclinic:
+ for half list with triclinic:
stencil is all bins in z-plane of self and above, but not below
in 2d is all bins in y-plane of self and above, but not below
stencil includes self
- for full neigh list:
+ for full list:
stencil is all surrounding bins including self
regardless of newton on/off or triclinic
for multi:
@@ -45,139 +45,65 @@ enum{NSQ,BIN,MULTI}; // also in neighbor.cpp
/* ---------------------------------------------------------------------- */
-void Neighbor::stencil_allocate(int sx, int sy, int sz)
+void Neighbor::stencil_half_bin_2d_no_newton(NeighList *list,
+ int sx, int sy, int sz)
{
- int i;
-
- // for 2d, sz = 0
-
- int nmax = (2*sz+1) * (2*sy+1) * (2*sx+1);
-
- if (half) {
- if (style == BIN) {
- if (nmax > maxstencil) {
- maxstencil = nmax;
- memory->sfree(stencil);
- stencil = (int *) memory->smalloc(nmax*sizeof(int),"neigh:stencil");
- }
-
- } else {
- int n = atom->ntypes;
- if (nstencil_multi == NULL) {
- maxstencil_multi = 0;
- nstencil_multi = new int[n+1];
- stencil_multi = new int*[n+1];
- distsq_multi = new double*[n+1];
- for (i = 1; i <= n; i++) {
- nstencil_multi[i] = 0;
- stencil_multi[i] = NULL;
- distsq_multi[i] = NULL;
- }
- }
- if (nmax > maxstencil_multi) {
- maxstencil_multi = nmax;
- for (int i = 1; i <= n; i++) {
- memory->sfree(stencil_multi[i]);
- memory->sfree(distsq_multi[i]);
- stencil_multi[i] = (int *)
- memory->smalloc(nmax*sizeof(int),"neigh:stencil_multi");
- distsq_multi[i] = (double *) memory->smalloc(nmax*sizeof(double),
- "neigh:distsq_multi");
- }
- }
- }
- }
+ int i,j;
+ int *stencil = list->stencil;
+ int nstencil = 0;
- if (full) {
- if (style == BIN) {
- if (nmax > maxstencil_full) {
- maxstencil_full = nmax;
- memory->sfree(stencil_full);
- stencil_full = (int *) memory->smalloc(nmax*sizeof(int),
- "neigh:stencil_full");
- }
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (bin_distance(i,j,0) < cutneighmaxsq)
+ stencil[nstencil++] = j*mbinx + i;
- } else {
- int n = atom->ntypes;
- if (nstencil_full_multi == NULL) {
- maxstencil_full_multi = 0;
- nstencil_full_multi = new int[n+1];
- stencil_full_multi = new int*[n+1];
- distsq_full_multi = new double*[n+1];
- for (i = 1; i <= n; i++) {
- nstencil_full_multi[i] = 0;
- stencil_full_multi[i] = NULL;
- distsq_full_multi[i] = NULL;
- }
- }
- if (nmax > maxstencil_full_multi) {
- maxstencil_full_multi = nmax;
- for (int i = 1; i <= n; i++) {
- memory->sfree(stencil_full_multi[i]);
- memory->sfree(distsq_full_multi[i]);
- stencil_full_multi[i] = (int *)
- memory->smalloc(nmax*sizeof(int),"neigh:stencil_full_multi");
- distsq_full_multi[i] =
- (double *) memory->smalloc(nmax*sizeof(double),
- "neigh:distsq_full_multi");
- }
- }
- }
- }
+ list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
-void Neighbor::stencil_none(int sx, int sy, int sz) {}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_3d_no_newton(int sx, int sy, int sz)
+void Neighbor::stencil_half_bin_3d_no_newton(NeighList *list,
+ int sx, int sy, int sz)
{
int i,j,k;
- nstencil = 0;
+ int *stencil = list->stencil;
+ int nstencil = 0;
for (k = -sz; k <= sz; k++)
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (bin_distance(i,j,k) < cutneighmaxsq)
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
+
+ list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
-void Neighbor::stencil_half_3d_no_newton_multi(int sx, int sy, int sz)
+void Neighbor::stencil_half_bin_2d_newton(NeighList *list,
+ int sx, int sy, int sz)
{
- int i,j,k,n;
- double rsq,typesq;
- int *s;
- double *distsq;
+ int i,j;
+ int *stencil = list->stencil;
+ int nstencil = 0;
- int ntypes = atom->ntypes;
- for (int itype = 1; itype <= ntypes; itype++) {
- typesq = cuttypesq[itype];
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- n = 0;
- for (k = -sz; k <= sz; k++)
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++) {
- rsq = bin_distance(i,j,k);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = k*mbiny*mbinx + j*mbinx + i;
- }
- }
- nstencil_multi[itype] = n;
- }
+ for (j = 0; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (j > 0 || (j == 0 && i > 0))
+ if (bin_distance(i,j,0) < cutneighmaxsq)
+ stencil[nstencil++] = j*mbinx + i;
+
+ list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
-void Neighbor::stencil_half_3d_newton(int sx, int sy, int sz)
+void Neighbor::stencil_half_bin_3d_newton(NeighList *list,
+ int sx, int sy, int sz)
{
int i,j,k;
- nstencil = 0;
+ int *stencil = list->stencil;
+ int nstencil = 0;
for (k = 0; k <= sz; k++)
for (j = -sy; j <= sy; j++)
@@ -185,142 +111,124 @@ void Neighbor::stencil_half_3d_newton(int sx, int sy, int sz)
if (k > 0 || j > 0 || (j == 0 && i > 0))
if (bin_distance(i,j,k) < cutneighmaxsq)
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
+
+ list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
-void Neighbor::stencil_half_3d_newton_multi(int sx, int sy, int sz)
+void Neighbor::stencil_half_bin_2d_newton_tri(NeighList *list,
+ int sx, int sy, int sz)
{
- int i,j,k,n;
- double rsq,typesq;
- int *s;
- double *distsq;
+ int i,j;
+ int *stencil = list->stencil;
+ int nstencil = 0;
- int ntypes = atom->ntypes;
- for (int itype = 1; itype <= ntypes; itype++) {
- typesq = cuttypesq[itype];
- s = stencil_multi[itype];
- distsq = distsq_multi[itype];
- n = 0;
- for (k = 0; k <= sz; k++)
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (k > 0 || j > 0 || (j == 0 && i > 0)) {
- rsq = bin_distance(i,j,k);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = k*mbiny*mbinx + j*mbinx + i;
- }
- }
- nstencil_multi[itype] = n;
- }
+ for (j = 0; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (bin_distance(i,j,0) < cutneighmaxsq)
+ stencil[nstencil++] = j*mbinx + i;
+
+ list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
-void Neighbor::stencil_half_3d_newton_tri(int sx, int sy, int sz)
+void Neighbor::stencil_half_bin_3d_newton_tri(NeighList *list,
+ int sx, int sy, int sz)
{
int i,j,k;
- nstencil = 0;
+ int *stencil = list->stencil;
+ int nstencil = 0;
for (k = 0; k <= sz; k++)
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (bin_distance(i,j,k) < cutneighmaxsq)
stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
+
+ list->nstencil = nstencil;
}
/* ---------------------------------------------------------------------- */
-void Neighbor::stencil_half_3d_newton_multi_tri(int sx, int sy, int sz)
+void Neighbor::stencil_half_multi_2d_no_newton(NeighList *list,
+ int sx, int sy, int sz)
{
- int i,j,k,n;
+ int i,j,n;
double rsq,typesq;
int *s;
double *distsq;
+ int *nstencil_multi = list->nstencil_multi;
+ int **stencil_multi = list->stencil_multi;
+ double **distsq_multi = list->distsq_multi;
+
int ntypes = atom->ntypes;
for (int itype = 1; itype <= ntypes; itype++) {
typesq = cuttypesq[itype];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
n = 0;
- for (k = 0; k <= sz; k++)
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++) {
- rsq = bin_distance(i,j,k);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = k*mbiny*mbinx + j*mbinx + i;
- }
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++) {
+ rsq = bin_distance(i,j,0);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = j*mbinx + i;
}
+ }
nstencil_multi[itype] = n;
}
}
/* ---------------------------------------------------------------------- */
-void Neighbor::stencil_half_2d_no_newton(int sx, int sy, int sz)
+void Neighbor::stencil_half_multi_3d_no_newton(NeighList *list,
+ int sx, int sy, int sz)
{
- int i,j;
- nstencil = 0;
-
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (bin_distance(i,j,0) < cutneighmaxsq)
- stencil[nstencil++] = j*mbinx + i;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_2d_no_newton_multi(int sx, int sy, int sz)
-{
- int i,j,n;
+ int i,j,k,n;
double rsq,typesq;
int *s;
double *distsq;
+ int *nstencil_multi = list->nstencil_multi;
+ int **stencil_multi = list->stencil_multi;
+ double **distsq_multi = list->distsq_multi;
+
int ntypes = atom->ntypes;
for (int itype = 1; itype <= ntypes; itype++) {
typesq = cuttypesq[itype];
s = stencil_multi[itype];
distsq = distsq_multi[itype];
n = 0;
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++) {
- rsq = bin_distance(i,j,0);
- if (rsq < typesq) {
- distsq[n] = rsq;
- s[n++] = j*mbinx + i;
+ for (k = -sz; k <= sz; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++) {
+ rsq = bin_distance(i,j,k);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = k*mbiny*mbinx + j*mbinx + i;
+ }
}
- }
nstencil_multi[itype] = n;
}
}
/* ---------------------------------------------------------------------- */
-void Neighbor::stencil_half_2d_newton(int sx, int sy, int sz)
-{
- int i,j;
- nstencil = 0;
-
- for (j = 0; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (j > 0 || (j == 0 && i > 0))
- if (bin_distance(i,j,0) < cutneighmaxsq)
- stencil[nstencil++] = j*mbinx + i;
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_half_2d_newton_multi(int sx, int sy, int sz)
+void Neighbor::stencil_half_multi_2d_newton(NeighList *list,
+ int sx, int sy, int sz)
{
int i,j,n;
double rsq,typesq;
int *s;
double *distsq;
+ int *nstencil_multi = list->nstencil_multi;
+ int **stencil_multi = list->stencil_multi;
+ double **distsq_multi = list->distsq_multi;
+
int ntypes = atom->ntypes;
for (int itype = 1; itype <= ntypes; itype++) {
typesq = cuttypesq[itype];
@@ -342,26 +250,52 @@ void Neighbor::stencil_half_2d_newton_multi(int sx, int sy, int sz)
/* ---------------------------------------------------------------------- */
-void Neighbor::stencil_half_2d_newton_tri(int sx, int sy, int sz)
+void Neighbor::stencil_half_multi_3d_newton(NeighList *list,
+ int sx, int sy, int sz)
{
- int i,j;
- nstencil = 0;
+ int i,j,k,n;
+ double rsq,typesq;
+ int *s;
+ double *distsq;
- for (j = 0; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (bin_distance(i,j,0) < cutneighmaxsq)
- stencil[nstencil++] = j*mbinx + i;
+ int *nstencil_multi = list->nstencil_multi;
+ int **stencil_multi = list->stencil_multi;
+ double **distsq_multi = list->distsq_multi;
+
+ int ntypes = atom->ntypes;
+ for (int itype = 1; itype <= ntypes; itype++) {
+ typesq = cuttypesq[itype];
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ n = 0;
+ for (k = 0; k <= sz; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (k > 0 || j > 0 || (j == 0 && i > 0)) {
+ rsq = bin_distance(i,j,k);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = k*mbiny*mbinx + j*mbinx + i;
+ }
+ }
+ nstencil_multi[itype] = n;
+ }
}
/* ---------------------------------------------------------------------- */
-void Neighbor::stencil_half_2d_newton_multi_tri(int sx, int sy, int sz)
+void Neighbor::stencil_half_multi_2d_newton_tri(NeighList *list,
+ int sx, int sy, int sz)
{
int i,j,n;
double rsq,typesq;
int *s;
double *distsq;
+ int *nstencil_multi = list->nstencil_multi;
+ int **stencil_multi = list->stencil_multi;
+ double **distsq_multi = list->distsq_multi;
+
int ntypes = atom->ntypes;
for (int itype = 1; itype <= ntypes; itype++) {
typesq = cuttypesq[itype];
@@ -380,36 +314,28 @@ void Neighbor::stencil_half_2d_newton_multi_tri(int sx, int sy, int sz)
}
}
-/* ---------------------------------------------------------------------- */
-
-void Neighbor::stencil_full_3d(int sx, int sy, int sz)
-{
- int i,j,k;
- nstencil_full = 0;
-
- for (k = -sz; k <= sz; k++)
- for (j = -sy; j <= sy; j++)
- for (i = -sx; i <= sx; i++)
- if (bin_distance(i,j,k) < cutneighmaxsq)
- stencil_full[nstencil_full++] = k*mbiny*mbinx + j*mbinx + i;
-}
/* ---------------------------------------------------------------------- */
-void Neighbor::stencil_full_3d_multi(int sx, int sy, int sz)
+void Neighbor::stencil_half_multi_3d_newton_tri(NeighList *list,
+ int sx, int sy, int sz)
{
int i,j,k,n;
double rsq,typesq;
int *s;
double *distsq;
+ int *nstencil_multi = list->nstencil_multi;
+ int **stencil_multi = list->stencil_multi;
+ double **distsq_multi = list->distsq_multi;
+
int ntypes = atom->ntypes;
for (int itype = 1; itype <= ntypes; itype++) {
typesq = cuttypesq[itype];
- s = stencil_full_multi[itype];
- distsq = distsq_full_multi[itype];
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
n = 0;
- for (k = -sz; k <= sz; k++)
+ for (k = 0; k <= sz; k++)
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++) {
rsq = bin_distance(i,j,k);
@@ -418,37 +344,65 @@ void Neighbor::stencil_full_3d_multi(int sx, int sy, int sz)
s[n++] = k*mbiny*mbinx + j*mbinx + i;
}
}
- nstencil_full_multi[itype] = n;
+ nstencil_multi[itype] = n;
}
}
/* ---------------------------------------------------------------------- */
-void Neighbor::stencil_full_2d(int sx, int sy, int sz)
+void Neighbor::stencil_full_bin_2d(NeighList *list,
+ int sx, int sy, int sz)
{
int i,j;
- nstencil_full = 0;
+ int *stencil = list->stencil;
+ int nstencil = 0;
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++)
if (bin_distance(i,j,0) < cutneighmaxsq)
- stencil_full[nstencil_full++] = j*mbinx + i;
+ stencil[nstencil++] = j*mbinx + i;
+
+ list->nstencil = nstencil;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Neighbor::stencil_full_bin_3d(NeighList *list,
+ int sx, int sy, int sz)
+{
+ int i,j,k;
+ int *stencil = list->stencil;
+ int nstencil = 0;
+
+ for (k = -sz; k <= sz; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++)
+ if (bin_distance(i,j,k) < cutneighmaxsq)
+ stencil[nstencil++] = k*mbiny*mbinx + j*mbinx + i;
+
+ list->nstencil = nstencil;
}
+
/* ---------------------------------------------------------------------- */
-void Neighbor::stencil_full_2d_multi(int sx, int sy, int sz)
+void Neighbor::stencil_full_multi_2d(NeighList *list,
+ int sx, int sy, int sz)
{
int i,j,n;
double rsq,typesq;
int *s;
double *distsq;
+ int *nstencil_multi = list->nstencil_multi;
+ int **stencil_multi = list->stencil_multi;
+ double **distsq_multi = list->distsq_multi;
+
int ntypes = atom->ntypes;
for (int itype = 1; itype <= ntypes; itype++) {
typesq = cuttypesq[itype];
- s = stencil_full_multi[itype];
- distsq = distsq_full_multi[itype];
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
n = 0;
for (j = -sy; j <= sy; j++)
for (i = -sx; i <= sx; i++) {
@@ -458,6 +412,39 @@ void Neighbor::stencil_full_2d_multi(int sx, int sy, int sz)
s[n++] = j*mbinx + i;
}
}
- nstencil_full_multi[itype] = n;
+ nstencil_multi[itype] = n;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Neighbor::stencil_full_multi_3d(NeighList *list,
+ int sx, int sy, int sz)
+{
+ int i,j,k,n;
+ double rsq,typesq;
+ int *s;
+ double *distsq;
+
+ int *nstencil_multi = list->nstencil_multi;
+ int **stencil_multi = list->stencil_multi;
+ double **distsq_multi = list->distsq_multi;
+
+ int ntypes = atom->ntypes;
+ for (int itype = 1; itype <= ntypes; itype++) {
+ typesq = cuttypesq[itype];
+ s = stencil_multi[itype];
+ distsq = distsq_multi[itype];
+ n = 0;
+ for (k = -sz; k <= sz; k++)
+ for (j = -sy; j <= sy; j++)
+ for (i = -sx; i <= sx; i++) {
+ rsq = bin_distance(i,j,k);
+ if (rsq < typesq) {
+ distsq[n] = rsq;
+ s[n++] = k*mbiny*mbinx + j*mbinx + i;
+ }
+ }
+ nstencil_multi[itype] = n;
}
}
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index dc42db9d52679301249be4e78686b79ac99dba39..4e562b7affd5d949c6ea32822377d58d8d057228 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -21,6 +21,8 @@
#include "string.h"
#include "limits.h"
#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
@@ -39,17 +41,18 @@
using namespace LAMMPS_NS;
-#define PGDELTA 1
+#define RQDELTA 1
+#define EXDELTA 1
+
#define LB_FACTOR 1.5
#define SMALL 1.0e-6
-#define EXDELTA 1
#define BIG 1.0e20
#define CUT2BIN_RATIO 100
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
-enum{NSQ,BIN,MULTI}; // also in neigh_stencil.cpp
+enum{NSQ,BIN,MULTI}; // also in neigh_list.cpp
/* ---------------------------------------------------------------------- */
@@ -65,18 +68,23 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
pgsize = 10000;
oneatom = 2000;
- maxlocal = 0;
-
cutneighsq = NULL;
cuttype = NULL;
cuttypesq = NULL;
fixchecklist = NULL;
- // last neighbor info
+ // coords at last neighboring
maxhold = 0;
xhold = NULL;
+ // binning
+
+ maxhead = 0;
+ binhead = NULL;
+ maxbin = 0;
+ bins = NULL;
+
// pair exclusion list info
nex_type = maxex_type = 0;
@@ -89,66 +97,24 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
nex_mol = maxex_mol = 0;
ex_mol_group = ex_mol_bit = NULL;
- // bin info
-
- maxhead = 0;
- binhead = NULL;
- maxbin = 0;
- bins = NULL;
-
- nstencil = maxstencil = 0;
- stencil = NULL;
- nstencil_full = maxstencil_full = 0;
- stencil_full = NULL;
-
- maxstencil_multi = 0;
- nstencil_multi = NULL;
- stencil_multi = NULL;
- distsq_multi = NULL;
-
- maxstencil_full_multi = 0;
- nstencil_full_multi = NULL;
- stencil_full_multi = NULL;
- distsq_full_multi = NULL;
-
- // half neighbor list info
+ // pair lists
- half = half_command = 0;
- numneigh = NULL;
- firstneigh = NULL;
- maxpage = 0;
- pages = NULL;
-
- // full neighbor list info
-
- full = 0;
- numneigh_full = NULL;
- firstneigh_full = NULL;
- maxpage_full = 0;
- pages_full = NULL;
-
- // shear history neighbor list info
+ maxlocal = 0;
- fix_history = NULL;
- firsttouch = NULL;
- firstshear = NULL;
- maxpage_history = 0;
- pages_touch = NULL;
- pages_shear = NULL;
+ nlist = 0;
+ lists = NULL;
+ pair_build = NULL;
+ stencil_create = NULL;
+ blist = glist = slist = NULL;
- // multiple respa neighbor list info
+ nrequest = maxrequest = 0;
+ requests = NULL;
- respa = 0;
- numneigh_inner = NULL;
- firstneigh_inner = NULL;
- numneigh_middle = NULL;
- firstneigh_middle = NULL;
- maxpage_inner = 0;
- maxpage_middle = 0;
- pages_inner = NULL;
- pages_middle = NULL;
+ old_style = BIN;
+ old_nrequest = 0;
+ old_requests = NULL;
- // bond list info
+ // bond lists
maxbond = 0;
bondlist = NULL;
@@ -167,10 +133,13 @@ Neighbor::~Neighbor()
memory->destroy_2d_double_array(cutneighsq);
delete [] cuttype;
delete [] cuttypesq;
-
delete [] fixchecklist;
+
memory->destroy_2d_double_array(xhold);
+ memory->sfree(binhead);
+ memory->sfree(bins);
+
memory->sfree(ex1_type);
memory->sfree(ex2_type);
memory->destroy_2d_int_array(ex_type);
@@ -183,54 +152,23 @@ Neighbor::~Neighbor()
memory->sfree(ex_mol_group);
delete [] ex_mol_bit;
- memory->sfree(binhead);
- memory->sfree(bins);
-
- memory->sfree(stencil);
- memory->sfree(stencil_full);
+ for (int i = 0; i < nlist; i++) delete lists[i];
+ delete [] lists;
+ delete [] pair_build;
+ delete [] stencil_create;
+ delete [] blist;
+ delete [] glist;
+ delete [] slist;
- if (nstencil_multi) {
- for (int i = 1; i <= atom->ntypes; i++) {
- memory->sfree(stencil_multi[i]);
- memory->sfree(distsq_multi[i]);
- }
- delete [] nstencil_multi;
- delete [] stencil_multi;
- delete [] distsq_multi;
- }
- if (nstencil_full_multi) {
- for (int i = 1; i <= atom->ntypes; i++) {
- memory->sfree(stencil_full_multi[i]);
- memory->sfree(distsq_full_multi[i]);
- }
- delete [] nstencil_full_multi;
- delete [] stencil_full_multi;
- delete [] distsq_full_multi;
- }
+ for (int i = 0; i < nrequest; i++) delete requests[i];
+ memory->sfree(requests);
+ for (int i = 0; i < old_nrequest; i++) delete old_requests[i];
+ memory->sfree(old_requests);
memory->destroy_2d_int_array(bondlist);
memory->destroy_2d_int_array(anglelist);
memory->destroy_2d_int_array(dihedrallist);
memory->destroy_2d_int_array(improperlist);
-
- memory->sfree(numneigh);
- memory->sfree(firstneigh);
- clear_pages();
-
- memory->sfree(numneigh_full);
- memory->sfree(firstneigh_full);
- clear_pages_full();
-
- memory->sfree(firsttouch);
- memory->sfree(firstshear);
- clear_pages_history();
-
- memory->sfree(numneigh_inner);
- memory->sfree(firstneigh_inner);
- memory->sfree(numneigh_middle);
- memory->sfree(firstneigh_middle);
- clear_pages_inner();
- clear_pages_middle();
}
/* ---------------------------------------------------------------------- */
@@ -242,6 +180,7 @@ void Neighbor::init()
ncalls = ndanger = 0;
dimension = domain->dimension;
triclinic = domain->triclinic;
+ newton_pair = force->newton_pair;
// error check
@@ -335,8 +274,23 @@ void Neighbor::init()
if (force->kspace) special_flag[1] = special_flag[2] = special_flag[3] = 2;
+ // rRESPA cutoffs
+
+ int respa = 0;
+ if (update->whichflag == 0 && strcmp(update->integrate_style,"respa") == 0) {
+ if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
+ if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
+ }
+
+ if (respa) {
+ double *cut_respa = ((Respa *) update->integrate)->cutoff;
+ cut_inner_sq = (cut_respa[1] + skin) * (cut_respa[1] + skin);
+ cut_middle_sq = (cut_respa[3] + skin) * (cut_respa[3] + skin);
+ cut_middle_inside_sq = (cut_respa[0] - skin) * (cut_respa[0] - skin);
+ }
+
// ------------------------------------------------------------------
- // memory management
+ // xhold, bins, exclusion lists
// free xhold and bins if not needed for this run
@@ -349,9 +303,7 @@ void Neighbor::init()
if (style == NSQ) {
memory->sfree(bins);
memory->sfree(binhead);
- memory->sfree(stencil);
- memory->sfree(stencil_full);
- maxbin = maxhead = maxstencil = maxstencil_full = 0;
+ maxbin = maxhead = 0;
binhead = NULL;
bins = NULL;
}
@@ -417,252 +369,275 @@ void Neighbor::init()
}
// ------------------------------------------------------------------
- // neighbor list flags and memory allocation/deallocation
+ // pairwise lists
- // determine whether to build half and full lists
- // query pair,fix,compute for their requirements
+ // test if pairwise lists need to be re-created
+ // no need to re-create if:
+ // neigh style has not changed and current requests = old requests
- half_once = full_once = 0;
- half_every = full_every = 0;
- if (force->pair) half_every = force->pair->neigh_half_every;
- if (force->pair) full_every = force->pair->neigh_full_every;
+ int same = 1;
+ if (style != old_style) same = 0;
+ if (nrequest != old_nrequest) same = 0;
+ else
+ for (i = 0; i < nrequest; i++)
+ if (requests[i]->identical(old_requests[i]) == 0) same = 0;
- for (i = 0; i < modify->nfix; i++) {
- if (modify->fix[i]->neigh_half_every) half_every = 1;
- if (modify->fix[i]->neigh_full_every) full_every = 1;
- if (modify->fix[i]->neigh_half_once) half_once = 1;
- if (modify->fix[i]->neigh_full_once) full_once = 1;
- }
+ printf("SAME %d\n",same);
- 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;
- }
+ // if old and new are not the same, create new pairwise lists
- half = full = 0;
- if (half_every || half_once || half_command) half = 1;
- if (full_every || full_once) full = 1;
+ if (!same) {
- // determine whether to build granular history lists
- // fix_history = granular shear history fix
-
- 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)
- fix_history = (FixShearHistory *) modify->fix[i];
+ // delete old lists and create new ones
- // determine whether to build extra rRESPA lists
- // respa = 1,2 if rRESPA requires inner,middle neighbor lists
- // set neighbor cutoffs for multiple lists
+ for (i = 0; i < nlist; i++) delete lists[i];
+ delete [] lists;
+ delete [] pair_build;
+ delete [] stencil_create;
- respa = 0;
- if (update->whichflag == 0 && strcmp(update->integrate_style,"respa") == 0) {
- if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
- if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
- }
+ nlist = nrequest;
+ lists = new NeighList*[nlist];
+ pair_build = new PairPtr[nlist];
+ stencil_create = new StencilPtr[nlist];
- if (respa && half_every == 0)
- error->all("Cannot use rRESPA with full neighbor lists");
+ // create individual lists, one per request
+ // copy dnum setting from request to list
+ // pass list ptr back to requestor (except for Command class)
- if (respa) {
- double *cut_respa = ((Respa *) update->integrate)->cutoff;
- cut_inner_sq = (cut_respa[1] + skin) * (cut_respa[1] + skin);
- cut_middle_sq = (cut_respa[3] + skin) * (cut_respa[3] + skin);
- cut_middle_inside_sq = (cut_respa[0] - skin) * (cut_respa[0] - skin);
- }
+ for (i = 0; i < nlist; i++) {
+ lists[i] = new NeighList(lmp,pgsize);
+ lists[i]->index = i;
+ lists[i]->dnum = requests[i]->dnum;
+
+ if (requests[i]->pair) {
+ Pair *pair = (Pair *) requests[i]->requestor;
+ pair->init_list(requests[i]->id,lists[i]);
+ } else if (requests[i]->fix) {
+ Fix *fix = (Fix *) requests[i]->requestor;
+ fix->init_list(requests[i]->id,lists[i]);
+ } else if (requests[i]->compute) {
+ Compute *compute = (Compute *) requests[i]->requestor;
+ compute->init_list(requests[i]->id,lists[i]);
+ }
+ }
- // zero atom-length numneigh and firstneigh arrays
- // will be (re)allocated on first build()
+ // detect lists that are connected to other lists
+ // skip: point this list at request->otherlist, copy skip ptrs from request
+ // copy: point this list at request->otherlist
+ // half_from_full: point this list at preceeding full list
+ // granhistory: set preceeding list's listgranhistory to this list
+ // also set precedding list's ptr to FixShearHistory
+ // respaouter: point this list at preceeding 1/2 inner/middle lists
+ // pair and half and non-skip: if there is a pair full non-skip list,
+ // change this list to half_from_full and point at the full list
+ // fix/compute requests:
+ // kind of request = half or full
+ // occasional or not doesn't matter
+ // if non-skip pair list of same kind exists, become copy of that list
+ // else if request is half and non-skip pair full exists,
+ // become half_from_full of that list
+ // else do nothing and the fix/compute list will be built directly
+
+ for (i = 0; i < nlist; i++) {
+ if (requests[i]->skip) {
+ lists[i]->listskip = lists[requests[i]->otherlist];
+ lists[i]->iskip = requests[i]->iskip;
+ lists[i]->ijskip = requests[i]->ijskip;
+ }
- maxlocal = 0;
+ if (requests[i]->copy)
+ lists[i]->listcopy = lists[requests[i]->otherlist];
- memory->sfree(numneigh);
- memory->sfree(firstneigh);
- memory->sfree(numneigh_full);
- memory->sfree(firstneigh_full);
- memory->sfree(firsttouch);
- memory->sfree(firstshear);
- memory->sfree(numneigh_inner);
- memory->sfree(firstneigh_inner);
- memory->sfree(numneigh_middle);
- memory->sfree(firstneigh_middle);
-
- numneigh = numneigh_full = numneigh_inner = numneigh_middle = NULL;
- firstneigh = firstneigh_full = NULL;
- firsttouch = NULL;
- firstshear = NULL;
- firstneigh_inner = firstneigh_middle = NULL;
-
- // clear old neighbor lists if no longer needed (whether exist or not)
-
- if (half == 0) clear_pages();
- if (full == 0) clear_pages_full();
- if (fix_history == NULL) clear_pages_history();
- if (respa == 0) clear_pages_inner();
- if (respa == 0 || respa == 1) clear_pages_middle();
-
- // setup new neighbor lists
- // only if they don't exist so memory will persist from run to run
-
- if (half && pages == NULL) add_pages(0);
- if (full && pages_full == NULL) add_pages_full(0);
- if (fix_history && pages_touch == NULL) add_pages_history(0);
- if (respa >= 1 && pages_inner == NULL) add_pages_inner(0);
- if (respa == 2 && pages_middle == NULL) add_pages_middle(0);
-
- // set ptrs to half/full/multi/triclinic build & stencil functions
-
- if (half) {
- if (fix_history) {
- if (style == NSQ) {
- if (force->newton_pair == 0)
- half_build = &Neighbor::granular_nsq_no_newton;
- else half_build = &Neighbor::granular_nsq_newton;
- } else if (style == BIN) {
- if (force->newton_pair == 0) {
- half_build = &Neighbor::granular_bin_no_newton;
- if (dimension == 3)
- half_stencil = &Neighbor::stencil_half_3d_no_newton;
- else
- half_stencil = &Neighbor::stencil_half_2d_no_newton;
- } else if (triclinic) {
- half_build = &Neighbor::granular_bin_newton_tri;
- if (dimension == 3)
- half_stencil = &Neighbor::stencil_half_3d_newton_tri;
- else
- half_stencil = &Neighbor::stencil_half_2d_newton_tri;
+ if (requests[i]->half_from_full) lists[i]->listfull = lists[i-1];
+
+ if (requests[i]->granhistory) {
+ lists[i-1]->listgranhistory = lists[i];
+ for (int ifix = 0; ifix < modify->nfix; ifix++)
+ if (strcmp(modify->fix[ifix]->style,"SHEAR_HISTORY") == 0)
+ lists[i-1]->fix_history = (FixShearHistory *) modify->fix[ifix];
+ }
+
+ if (requests[i]->respaouter) {
+ if (requests[i-1]->respainner) {
+ lists[i]->respamiddle = 0;
+ lists[i]->listinner = lists[i-1];
} else {
- half_build = &Neighbor::granular_bin_newton;
- if (dimension == 3)
- half_stencil = &Neighbor::stencil_half_3d_newton;
- else
- half_stencil = &Neighbor::stencil_half_2d_newton;
+ lists[i]->respamiddle = 1;
+ lists[i]->listmiddle = lists[i-1];
+ lists[i]->listinner = lists[i-2];
}
- } else error->all("Neighbor multi not allowed with granular");
-
- } else if (respa) {
- if (style == NSQ) {
- if (force->newton_pair == 0)
- half_build = &Neighbor::respa_nsq_no_newton;
- else half_build = &Neighbor::respa_nsq_newton;
- } else if (style == BIN) {
- if (force->newton_pair == 0) {
- half_build = &Neighbor::respa_bin_no_newton;
- if (dimension == 3)
- half_stencil = &Neighbor::stencil_half_3d_no_newton;
- else
- half_stencil = &Neighbor::stencil_half_2d_no_newton;
- } else if (triclinic) {
- half_build = &Neighbor::respa_bin_newton_tri;
- if (dimension == 3)
- half_stencil = &Neighbor::stencil_half_3d_newton_tri;
- else
- half_stencil = &Neighbor::stencil_half_2d_newton_tri;
- } else {
- half_build = &Neighbor::respa_bin_newton;
- if (dimension == 3)
- half_stencil = &Neighbor::stencil_half_3d_newton;
- else
- half_stencil = &Neighbor::stencil_half_2d_newton;
+ }
+
+ if (requests[i]->pair && requests[i]->half && requests[i]->skip == 0) {
+ for (j = 0; j < nlist; j++)
+ if (requests[i]->pair && requests[j]->full &&
+ requests[j]->skip == 0) break;
+ if (j < nlist) {
+ requests[i]->half = 0;
+ requests[i]->half_from_full = 1;
+ lists[i]->listfull = lists[j];
}
- } else error->all("Neighbor multi not allowed with rRESPA");
+ }
- } else {
- if (style == NSQ) {
- if (force->newton_pair == 0) {
- if (full_every) half_build = &Neighbor::half_full_no_newton;
- else half_build = &Neighbor::half_nsq_no_newton;
- } else {
- if (full_every) half_build = &Neighbor::half_full_newton;
- else half_build = &Neighbor::half_nsq_newton;
+ if (requests[i]->fix || requests[i]->compute) {
+ for (j = 0; j < nlist; j++) {
+ if (requests[j]->pair && requests[j]->skip == 0 &&
+ requests[j]->half && requests[i]->half) break;
+ if (requests[j]->pair && requests[j]->skip == 0 &&
+ requests[j]->full && requests[i]->full) break;
}
- } else if (style == BIN) {
- if (force->newton_pair == 0) {
- if (full_every) {
- half_build = &Neighbor::half_full_no_newton;
- half_stencil = &Neighbor::stencil_none;
- } else {
- half_build = &Neighbor::half_bin_no_newton;
- if (dimension == 3)
- half_stencil = &Neighbor::stencil_half_3d_no_newton;
- else
- half_stencil = &Neighbor::stencil_half_2d_no_newton;
- }
+ if (j < nlist) {
+ requests[i]->copy = 1;
+ lists[i]->listcopy = lists[j];
} else {
- if (full_every) {
- half_build = &Neighbor::half_full_newton;
- half_stencil = &Neighbor::stencil_none;
- } else if (triclinic) {
- half_build = &Neighbor::half_bin_newton_tri;
- if (dimension == 3)
- half_stencil = &Neighbor::stencil_half_3d_newton_tri;
- else
- half_stencil = &Neighbor::stencil_half_2d_newton_tri;
- } else {
- half_build = &Neighbor::half_bin_newton;
- if (dimension == 3)
- half_stencil = &Neighbor::stencil_half_3d_newton;
- else
- half_stencil = &Neighbor::stencil_half_2d_newton;
- }
- }
- } else if (style == MULTI) {
- if (force->newton_pair == 0) {
- if (full_every) {
- half_build = &Neighbor::half_full_no_newton;
- half_stencil = &Neighbor::stencil_none;
- } else {
- half_build = &Neighbor::half_bin_no_newton_multi;
- if (dimension == 3)
- half_stencil = &Neighbor::stencil_half_3d_no_newton_multi;
- else
- half_stencil = &Neighbor::stencil_half_2d_no_newton_multi;
+ for (j = 0; j < nlist; j++) {
+ if (requests[j]->pair && requests[j]->skip == 0 &&
+ requests[j]->full && requests[i]->half) break;
}
- } else {
- if (full_every) {
- half_build = &Neighbor::half_full_newton;
- half_stencil = &Neighbor::stencil_none;
- } else if (triclinic) {
- half_build = &Neighbor::half_bin_newton_multi_tri;
- if (dimension == 3)
- half_stencil = &Neighbor::stencil_half_3d_newton_multi_tri;
- else
- half_stencil = &Neighbor::stencil_half_2d_newton_multi_tri;
- } else {
- half_build = &Neighbor::half_bin_newton_multi;
- if (dimension == 3)
- half_stencil = &Neighbor::stencil_half_3d_newton_multi;
- else
- half_stencil = &Neighbor::stencil_half_2d_newton_multi;
+ if (j < nlist) {
+ requests[i]->half = 0;
+ requests[i]->half_from_full = 1;
+ lists[i]->listfull = lists[j];
}
}
}
}
- } else half_build = NULL;
-
- if (full) {
- if (style == NSQ) full_build = &Neighbor::full_nsq;
- else if (style == BIN) {
- full_build = &Neighbor::full_bin;
- if (dimension == 3)
- full_stencil = &Neighbor::stencil_full_3d;
- else
- full_stencil = &Neighbor::stencil_full_2d;
- } else {
- full_build = &Neighbor::full_bin_multi;
- if (dimension == 3)
- full_stencil = &Neighbor::stencil_full_3d_multi;
- else
- full_stencil = &Neighbor::stencil_full_2d_multi;
+ // set ptrs to pair_build and stencil_create functions for each list
+ // ptrs set to NULL if not set explicitly
+
+ for (i = 0; i < nlist; i++) {
+ choose_build(i,requests[i]);
+ if (style != NSQ) choose_stencil(i,requests[i]);
+ else stencil_create[i] = NULL;
+ }
+
+ // set each list's build/grow/stencil flags based on neigh request
+ // buildflag = 1 if its pair_build() invoked every reneighbor
+ // growflag = 1 if it stores atom-based arrays and pages
+ // stencilflag = 1 if it stores stencil arrays
+
+ for (i = 0; i < nlist; i++) {
+ lists[i]->buildflag = 1;
+ if (pair_build[i] == NULL) lists[i]->buildflag = 0;
+ if (requests[i]->occasional) lists[i]->buildflag = 0;
+
+ lists[i]->growflag = 1;
+ if (requests[i]->copy) lists[i]->growflag = 0;
+
+ lists[i]->stencilflag = 1;
+ if (style == NSQ) lists[i]->stencilflag = 0;
+ if (stencil_create[i] == NULL) lists[i]->stencilflag = 0;
+ }
+
+ // DEBUG: print list attributes
+
+ for (i = 0; i < nlist; i++) lists[i]->print_attributes();
+
+ // allocate atom arrays and 1st pages of lists that store them
+
+ for (i = 0; i < nlist; i++)
+ if (lists[i]->growflag) {
+ lists[i]->grow(maxlocal);
+ lists[i]->add_pages();
+ }
+
+ // setup 3 vectors of pairwise neighbor lists
+ // blist = lists whose pair_build() is invoked every reneighbor
+ // glist = lists who store atom arrays which are used every reneighbor
+ // slist = lists who store stencil arrays which are used every reneighbor
+ // blist and glist vectors are used by neighbor::build()
+ // slist vector is used by neighbor::setup_bins()
+
+ nblist = nglist = nslist = 0;
+ delete [] blist;
+ delete [] glist;
+ delete [] slist;
+ blist = new int[nlist];
+ glist = new int[nlist];
+ slist = new int[nlist];
+
+ for (i = 0; i < nlist; i++) {
+ if (lists[i]->buildflag) blist[nblist++] = i;
+ if (lists[i]->growflag && requests[i]->occasional == 0)
+ glist[nglist++] = i;
+ if (lists[i]->stencilflag && requests[i]->occasional == 0)
+ slist[nslist++] = i;
+ }
+
+ // DEBUG: print lists of lists
+
+ if (comm->me == 0) {
+ printf("Build lists = %d: ",nblist);
+ for (i = 0; i < nblist; i++) printf("%d ",blist[i]);
+ printf("\n");
+ printf("Grow lists = %d: ",nglist);
+ for (i = 0; i < nglist; i++) printf("%d ",glist[i]);
+ printf("\n");
+ printf("Stencil lists = %d: ",nslist);
+ for (i = 0; i < nslist; i++) printf("%d ",slist[i]);
+ printf("\n");
+ }
+
+ // reorder build vector if necessary
+ // relevant for lists that copy/skip/half-full from parent
+ // the derived lst must appear in blist after the parent list
+ // no occasional lists are in build vector
+ // swap two lists within blist when dependency is mis-ordered
+ // done when entire pass thru blist results in no swaps
+
+ int done = 0;
+ while (!done) {
+ done = 1;
+ for (i = 0; i < nblist; i++) {
+ NeighList *ptr = NULL;
+ if (lists[blist[i]]->listfull) ptr = lists[blist[i]]->listfull;
+ if (lists[blist[i]]->listcopy) ptr = lists[blist[i]]->listcopy;
+ if (lists[blist[i]]->listskip) ptr = lists[blist[i]]->listskip;
+ if (ptr == NULL) continue;
+ for (m = 0; m < nlist; m++)
+ if (ptr == lists[m]) break;
+ for (j = 0; j < nblist; j++)
+ if (m == blist[j]) break;
+ if (j < i) continue;
+ int tmp = blist[i];
+ blist[i] = blist[j];
+ blist[j] = tmp;
+ done = 0;
+ break;
+ }
+ }
+
+ // DEBUG: print lists of lists
+
+ if (comm->me == 0) {
+ printf("Build lists = %d: ",nblist);
+ for (i = 0; i < nblist; i++) printf("%d ",blist[i]);
+ printf("\n");
+ printf("Grow lists = %d: ",nglist);
+ for (i = 0; i < nglist; i++) printf("%d ",glist[i]);
+ printf("\n");
+ printf("Stencil lists = %d: ",nslist);
+ for (i = 0; i < nslist; i++) printf("%d ",slist[i]);
+ printf("\n");
}
- } else full_build = NULL;
+ }
+
+ // delete old requests
+ // copy current requests and style to old for next run
+
+ for (i = 0; i < old_nrequest; i++) delete old_requests[i];
+ memory->sfree(old_requests);
+ old_nrequest = nrequest;
+ old_requests = requests;
+ nrequest = maxrequest = 0;
+ requests = NULL;
+ old_style = style;
// ------------------------------------------------------------------
- // bond neighbor lists
+ // topology lists
- // 1st time allocation of bond lists
+ // 1st time allocation of topology lists
if (atom->molecular && atom->nbonds && maxbond == 0) {
if (nprocs == 1) maxbond = atom->nbonds;
@@ -692,7 +667,7 @@ void Neighbor::init()
memory->create_2d_int_array(maximproper,5,"neigh:improperlist");
}
- // set flags that determine which bond neighboring routines to use
+ // set flags that determine which topology neighboring routines to use
// SHAKE sets bonds and angles negative
// bond_quartic sets bonds to 0
// delete_bonds sets all interactions negative
@@ -738,7 +713,7 @@ void Neighbor::init()
}
}
- // set ptrs to intra-molecular build functions
+ // set ptrs to topology build functions
if (bond_off) bond_build = &Neighbor::bond_partial;
else bond_build = &Neighbor::bond_all;
@@ -752,7 +727,7 @@ void Neighbor::init()
if (improper_off) improper_build = &Neighbor::improper_partial;
else improper_build = &Neighbor::improper_all;
- // set intra-molecular neighbor list counts to 0
+ // set topology neighbor list counts to 0
// in case all are turned off but potential is still defined
nbondlist = nanglelist = ndihedrallist = nimproperlist = 0;
@@ -760,6 +735,149 @@ void Neighbor::init()
/* ---------------------------------------------------------------------- */
+int Neighbor::request(void *requestor)
+{
+ if (nrequest == maxrequest) {
+ maxrequest += RQDELTA;
+ requests = (NeighRequest **)
+ memory->srealloc(requests,maxrequest*sizeof(NeighRequest *),
+ "neighbor:requests");
+ }
+
+ requests[nrequest] = new NeighRequest(lmp);
+ requests[nrequest]->requestor = requestor;
+ nrequest++;
+ return nrequest-1;
+}
+
+
+/* ----------------------------------------------------------------------
+ determine which pair_build function each neigh list needs
+ based on settings of neigh request
+ skip or copy -> single function
+ half_from_full, half, full, gran, respaouter -> choose by newton and tri
+ style NSQ options = newton off, newton on
+ style BIN options = newton off, newton on and not tri, newton on and tri
+ stlye MULTI options = same options as BIN
+ if none of these, ptr = NULL since pair_build is not invoked for this list
+ use "else if" b/c skip,copy can be set in addition to half,full,etc
+------------------------------------------------------------------------- */
+
+void Neighbor::choose_build(int index, NeighRequest *rq)
+{
+ PairPtr pb = NULL;
+
+ if (rq->skip) pb = &Neighbor::skip_from;
+
+ else if (rq->copy) pb = &Neighbor::copy_from;
+
+ else if (rq->half_from_full) {
+ if (newton_pair == 0) pb = &Neighbor::half_full_no_newton;
+ else if (newton_pair == 1) pb = &Neighbor::half_full_newton;
+
+ } else if (rq->half) {
+ if (style == NSQ) {
+ if (newton_pair == 0) pb = &Neighbor::half_nsq_no_newton;
+ else if (newton_pair == 1) pb = &Neighbor::half_nsq_newton;
+ } else if (style == BIN) {
+ if (newton_pair == 0) pb = &Neighbor::half_bin_no_newton;
+ else if (triclinic == 0) pb = &Neighbor::half_bin_newton;
+ else if (triclinic == 1) pb = &Neighbor::half_bin_newton_tri;
+ } else if (style == MULTI) {
+ if (newton_pair == 0) pb = &Neighbor::half_multi_no_newton;
+ else if (triclinic == 0) pb = &Neighbor::half_multi_newton;
+ else if (triclinic == 1) pb = &Neighbor::half_multi_newton_tri;
+ }
+
+ } else if (rq->full) {
+ if (style == NSQ) pb = &Neighbor::full_nsq;
+ else if (style == BIN) pb = &Neighbor::full_bin;
+ else if (style == MULTI) pb = &Neighbor::full_multi;
+
+ } else if (rq->gran) {
+ if (style == NSQ) {
+ if (newton_pair == 0) pb = &Neighbor::granular_nsq_no_newton;
+ else if (newton_pair == 1) pb = &Neighbor::granular_nsq_newton;
+ } else if (style == BIN) {
+ if (newton_pair == 0) pb = &Neighbor::granular_bin_no_newton;
+ else if (triclinic == 0) pb = &Neighbor::granular_bin_newton;
+ else if (triclinic == 1) pb = &Neighbor::granular_bin_newton_tri;
+ } else if (style == MULTI)
+ error->all("Neighbor multi not yet enabled for granular");
+
+ } else if (rq->respaouter) {
+ if (style == NSQ) {
+ if (newton_pair == 0) pb = &Neighbor::respa_nsq_no_newton;
+ else if (newton_pair == 1) pb = &Neighbor::respa_nsq_newton;
+ } else if (style == BIN) {
+ if (newton_pair == 0) pb = &Neighbor::respa_bin_no_newton;
+ else if (triclinic == 0) pb = &Neighbor::respa_bin_newton;
+ else if (triclinic == 1) pb = &Neighbor::respa_bin_newton_tri;
+ } else if (style == MULTI)
+ error->all("Neighbor multi not yet enabled for rRESPA");
+ }
+
+ pair_build[index] = pb;
+}
+
+/* ----------------------------------------------------------------------
+ determine which stencil_create function each neigh list needs
+ based on settings of neigh request, only called if style != NSQ
+ skip or copy or half_from_full -> no stencil
+ half, gran, respaouter, full -> choose by newton and tri and dimension
+ if none of these, ptr = NULL since this list needs no stencils
+ use "else if" b/c skip,copy can be set in addition to half,full,etc
+------------------------------------------------------------------------- */
+
+void Neighbor::choose_stencil(int index, NeighRequest *rq)
+{
+ StencilPtr sc = NULL;
+
+ if (rq->skip || rq->copy || rq->half_from_full) sc = NULL;
+
+ else if (rq->half || rq->gran || rq->respaouter) {
+ if (style == BIN) {
+ if (newton_pair == 0) {
+ if (dimension == 2) sc = &Neighbor::stencil_half_bin_2d_no_newton;
+ else if (dimension == 3) sc = &Neighbor::stencil_half_bin_3d_no_newton;
+ } else if (triclinic == 0) {
+ if (dimension == 2) sc = &Neighbor::stencil_half_bin_2d_newton;
+ else if (dimension == 3) sc = &Neighbor::stencil_half_bin_3d_newton;
+ } else if (triclinic == 1) {
+ if (dimension == 2) sc = &Neighbor::stencil_half_bin_2d_newton_tri;
+ else if (dimension == 3)
+ sc = &Neighbor::stencil_half_bin_3d_newton_tri;
+ }
+ } else if (style == MULTI) {
+ if (newton_pair == 0) {
+ if (dimension == 2) sc = &Neighbor::stencil_half_multi_2d_no_newton;
+ else if (dimension == 3)
+ sc = &Neighbor::stencil_half_multi_3d_no_newton;
+ } else if (triclinic == 0) {
+ if (dimension == 2) sc = &Neighbor::stencil_half_multi_2d_newton;
+ else if (dimension == 3) sc = &Neighbor::stencil_half_multi_3d_newton;
+ } else if (triclinic == 1) {
+ if (dimension == 2) sc = &Neighbor::stencil_half_multi_2d_newton_tri;
+ else if (dimension == 3)
+ sc = &Neighbor::stencil_half_multi_3d_newton_tri;
+ }
+ }
+
+ } else if (rq->full) {
+ if (style == BIN) {
+ if (dimension == 2) sc = &Neighbor::stencil_full_bin_2d;
+ else if (dimension == 3) sc = &Neighbor::stencil_full_bin_3d;
+ } else if (style == MULTI) {
+ if (dimension == 2) sc = &Neighbor::stencil_full_multi_2d;
+ else if (dimension == 3) sc = &Neighbor::stencil_full_multi_3d;
+ }
+ }
+
+ stencil_create[index] = sc;
+}
+
+/* ---------------------------------------------------------------------- */
+
int Neighbor::decide()
{
if (must_check) {
@@ -800,19 +918,17 @@ int Neighbor::check_distance()
}
/* ----------------------------------------------------------------------
- build all needed neighbor lists every few timesteps
- half, full, bond lists are created as needed
+ build all perpetual neighbor lists every few timesteps
+ pairwise & topology lists are created as needed
------------------------------------------------------------------------- */
void Neighbor::build()
{
+ int i;
+
ago = 0;
ncalls++;
- // store current nlocal used on this build (used by fix shear/history)
-
- nlocal_neighbor = atom->nlocal;
-
// store current atom positions if needed
if (dist_check) {
@@ -823,66 +939,22 @@ void Neighbor::build()
memory->destroy_2d_double_array(xhold);
xhold = memory->create_2d_double_array(maxhold,3,"neigh:xhold");
}
- for (int i = 0; i < nlocal; i++) {
+ for (i = 0; i < nlocal; i++) {
xhold[i][0] = x[i][0];
xhold[i][1] = x[i][1];
xhold[i][2] = x[i][2];
}
}
- // extend atom arrays if necessary
- // check half/full instead of half_every/full_every so memory will be
- // allocated correctly whenever build_half() and build_full() are called
+ // if necessary, extend atom arrays in pairwise lists
+ // only done for lists with growflag set which are used every reneighbor
if (atom->nlocal > maxlocal) {
maxlocal = atom->nmax;
-
- if (half) {
- memory->sfree(numneigh);
- memory->sfree(firstneigh);
- numneigh = (int *)
- memory->smalloc(maxlocal*sizeof(int),"neigh:numneigh");
- firstneigh = (int **)
- memory->smalloc(maxlocal*sizeof(int *),"neigh:firstneigh");
- }
-
- if (full) {
- memory->sfree(numneigh_full);
- memory->sfree(firstneigh_full);
- numneigh_full = (int *)
- memory->smalloc(maxlocal*sizeof(int),"neigh:numneigh_full");
- firstneigh_full = (int **)
- memory->smalloc(maxlocal*sizeof(int *),"neigh:firstneigh_full");
- }
-
- if (fix_history) {
- memory->sfree(firsttouch);
- memory->sfree(firstshear);
- firsttouch = (int **)
- memory->smalloc(maxlocal*sizeof(int *),"neigh:firsttouch");
- firstshear = (double **)
- memory->smalloc(maxlocal*sizeof(double *),"neigh:firstshear");
- }
-
- if (respa) {
- memory->sfree(numneigh_inner);
- memory->sfree(firstneigh_inner);
- numneigh_inner = (int *)
- memory->smalloc(maxlocal*sizeof(int),"neigh:numneigh_inner");
- firstneigh_inner = (int **)
- memory->smalloc(maxlocal*sizeof(int *),"neigh:firstneigh_inner");
- if (respa == 2) {
- memory->sfree(numneigh_middle);
- memory->sfree(firstneigh_middle);
- numneigh_middle = (int *)
- memory->smalloc(maxlocal*sizeof(int),"neigh:numneigh_middle");
- firstneigh_middle = (int **)
- memory->smalloc(maxlocal*sizeof(int *),"neigh:firstneigh_middle");
- }
- }
+ for (i = 0; i < nglist; i++) lists[glist[i]]->grow(maxlocal);
}
- // extend bin list if necessary
+ // extend atom bin list if necessary
if (style != NSQ && atom->nmax > maxbin) {
maxbin = atom->nmax;
@@ -890,11 +962,22 @@ void Neighbor::build()
bins = (int *) memory->smalloc(maxbin*sizeof(int),"bins");
}
- // list construction for pairs and bonds
- // full comes first in case half is built from full
+ // invoke building of pair and molecular neighbor lists
+ // only done for pairwise lists with buildflag set
- if (full_every) (this->*full_build)();
- if (half_every) (this->*half_build)();
+ for (i = 0; i < nblist; i++)
+ (this->*pair_build[blist[i]])(lists[blist[i]]);
+
+ /*
+ if (comm->me == 0) {
+ for (int m = 0; m < nlist; m++) {
+ int num = 0;
+ for (i = 0; i < lists[m]->inum; i++)
+ num += lists[m]->numneigh[lists[m]->ilist[i]];
+ printf("List %d length = %d\n",m,num);
+ }
+ }
+ */
if (atom->molecular) {
if (atom->nbonds) (this->*bond_build)();
@@ -905,21 +988,21 @@ void Neighbor::build()
}
/* ----------------------------------------------------------------------
- one-time call to build a half neighbor list made by other classes
+ build a single non-active pairwise neighbor list indexed by I
+ called by other classes when needed occasionally
------------------------------------------------------------------------- */
-void Neighbor::build_half()
+void Neighbor::build_one(int i)
{
- (this->*half_build)();
-}
+ // grow atom arrays and update stencils depending on growflag & stencilflag
-/* ----------------------------------------------------------------------
- one-time call to build a full neighbor list made by other classes
-------------------------------------------------------------------------- */
+ if (lists[i]->growflag) lists[i]->grow(maxlocal);
+ if (lists[i]->stencilflag) {
+ lists[i]->stencil_allocate(smax,style);
+ (this->*stencil_create[i])(lists[i],sx,sy,sz);
+ }
-void Neighbor::build_full()
-{
- (this->*full_build)();
+ (this->*pair_build[i])(lists[i]);
}
/* ----------------------------------------------------------------------
@@ -941,8 +1024,6 @@ void Neighbor::build_full()
mbinlo = lowest global bin any of my ghost atoms could fall into
mbinhi = highest global bin any of my ghost atoms could fall into
mbin = number of bins I need in a dimension
- stencil() = bin offsets in 1d sense for stencil of surrounding bins
- stencil_full() = bin offsets in 1d sense for stencil for full neighbor list
------------------------------------------------------------------------- */
void Neighbor::setup_bins()
@@ -1089,23 +1170,25 @@ void Neighbor::setup_bins()
// create stencil of bins to search over in neighbor list construction
// sx,sy,sz = max range of stencil extent
+ // smax =
// stencil is empty if cutneighmax = 0.0
- int sx = static_cast<int> (cutneighmax*bininvx);
+ sx = static_cast<int> (cutneighmax*bininvx);
if (sx*binsizex < cutneighmax) sx++;
- int sy = static_cast<int> (cutneighmax*bininvy);
+ sy = static_cast<int> (cutneighmax*bininvy);
if (sy*binsizey < cutneighmax) sy++;
- int sz = static_cast<int> (cutneighmax*bininvz);
+ sz = static_cast<int> (cutneighmax*bininvz);
if (sz*binsizez < cutneighmax) sz++;
if (dimension == 2) sz = 0;
+ smax = (2*sx+1) * (2*sy+1) * (2*sz+1);
- // allocate stencil memory and create stencil(s)
- // check half/full instead of half_every/full_every so stencils will be
- // allocated correctly whenever build_half() and build_full() are called
+ // create stencils for pairwise neighbor lists
+ // only done for lists with stencilflag and buildflag set
- stencil_allocate(sx,sy,sz);
- if (half) (this->*half_stencil)(sx,sy,sz);
- if (full) (this->*full_stencil)(sx,sy,sz);
+ for (int i = 0; i < nslist; i++) {
+ lists[slist[i]]->stencil_allocate(smax,style);
+ (this->*stencil_create[slist[i]])(lists[slist[i]],sx,sy,sz);
+ }
}
/* ----------------------------------------------------------------------
@@ -1218,7 +1301,7 @@ 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 =
+ char *str = (char *)
"Must use molecular atom style with neigh_modify exclude molecule";
error->all(str);
}
@@ -1243,170 +1326,6 @@ void Neighbor::modify_params(int narg, char **arg)
}
}
-/* ----------------------------------------------------------------------
- return # of bytes of allocated memory
-------------------------------------------------------------------------- */
-
-int Neighbor::memory_usage()
-{
- int bytes = 0;
-
- bytes += maxhold*3 * sizeof(double);
-
- if (style == NSQ) {
- bytes += maxbin * sizeof(int);
- bytes += maxhead * sizeof(int);
- bytes += maxstencil * sizeof(int);
- bytes += maxstencil_full * sizeof(int);
- }
-
- if (half) {
- bytes += maxlocal * sizeof(int);
- bytes += maxlocal * sizeof(int *);
- bytes += maxpage*pgsize * sizeof(int);
- }
-
- if (full) {
- bytes += maxlocal * sizeof(int);
- bytes += maxlocal * sizeof(int *);
- bytes += maxpage_full*pgsize * sizeof(int);
- }
-
- if (fix_history) {
- bytes += maxlocal * sizeof(int *);
- bytes += maxlocal * sizeof(double *);
- bytes += maxpage_history*pgsize * sizeof(int);
- bytes += maxpage_history*pgsize*3 * sizeof(double);
- }
-
- if (respa) {
- bytes += maxlocal * sizeof(int);
- bytes += maxlocal * sizeof(int *);
- bytes += maxpage_inner*pgsize * sizeof(int);
- if (respa == 2) {
- bytes += maxlocal * sizeof(int);
- bytes += maxlocal * sizeof(int *);
- bytes += maxpage_middle*pgsize * sizeof(int);
- }
- }
-
- bytes += maxbond*3 * sizeof(int);
- bytes += maxangle*4 * sizeof(int);
- bytes += maxdihedral*5 * sizeof(int);
- bytes += maximproper*5 * sizeof(int);
-
- return bytes;
-}
-
-/* ----------------------------------------------------------------------
- add pages to half/full/granular/rRESPA neighbor lists, starting at npage
-------------------------------------------------------------------------- */
-
-void Neighbor::add_pages(int npage)
-{
- maxpage += PGDELTA;
- pages = (int **)
- memory->srealloc(pages,maxpage*sizeof(int *),"neigh:pages");
- for (int i = npage; i < maxpage; i++)
- pages[i] = (int *) memory->smalloc(pgsize*sizeof(int),"neigh:pages[i]");
-}
-
-void Neighbor::add_pages_full(int npage)
-{
- maxpage_full += PGDELTA;
- pages_full = (int **)
- memory->srealloc(pages_full,maxpage_full*sizeof(int *),"neigh:pages_full");
- for (int i = npage; i < maxpage_full; i++)
- pages_full[i] =
- (int *) memory->smalloc(pgsize*sizeof(int),"neigh:pages_full[i]");
-}
-
-void Neighbor::add_pages_history(int npage)
-{
- maxpage_history += PGDELTA;
- pages_touch = (int **)
- memory->srealloc(pages_touch,maxpage_history*sizeof(int *),
- "neigh:pages_touch");
- pages_shear = (double **)
- memory->srealloc(pages_shear,maxpage_history*sizeof(double *),
- "neigh:pages_shear");
- for (int i = npage; i < maxpage_history; i++) {
- pages_touch[i] = (int *)
- memory->smalloc(pgsize*sizeof(int),"neigh:pages_touch[i]");
- pages_shear[i] = (double *)
- memory->smalloc(3*pgsize*sizeof(double),"neigh:pages_shear[i]");
- }
-}
-
-void Neighbor::add_pages_inner(int npage_inner)
-{
- maxpage_inner += PGDELTA;
- pages_inner = (int **)
- memory->srealloc(pages_inner,maxpage_inner*sizeof(int *),
- "neigh:pages_inner");
- for (int i = npage_inner; i < maxpage_inner; i++)
- pages_inner[i] =
- (int *) memory->smalloc(pgsize*sizeof(int),"neigh:pages_inner[i]");
-}
-
-void Neighbor::add_pages_middle(int npage_middle)
-{
- maxpage_middle += PGDELTA;
- pages_middle = (int **)
- memory->srealloc(pages_middle,maxpage_middle*sizeof(int *),
- "neigh:pages_middle");
- for (int i = npage_middle; i < maxpage_middle; i++)
- pages_middle[i] =
- (int *) memory->smalloc(pgsize*sizeof(int),"neigh:pages_middle[i]");
-}
-
-/* ----------------------------------------------------------------------
- clear half/full/granular/rRESPA neighbor lists
-------------------------------------------------------------------------- */
-
-void Neighbor::clear_pages()
-{
- for (int i = 0; i < maxpage; i++) memory->sfree(pages[i]);
- memory->sfree(pages);
- pages = NULL;
- maxpage = 0;
-}
-
-void Neighbor::clear_pages_full()
-{
- for (int i = 0; i < maxpage_full; i++) memory->sfree(pages_full[i]);
- memory->sfree(pages_full);
- pages_full = NULL;
- maxpage_full = 0;
-}
-
-void Neighbor::clear_pages_history()
-{
- for (int i = 0; i < maxpage_history; i++) memory->sfree(pages_touch[i]);
- for (int i = 0; i < maxpage_history; i++) memory->sfree(pages_shear[i]);
- memory->sfree(pages_touch);
- memory->sfree(pages_shear);
- pages_touch = NULL;
- pages_shear = NULL;
- maxpage_history = 0;
-}
-
-void Neighbor::clear_pages_inner()
-{
- for (int i = 0; i < maxpage_inner; i++) memory->sfree(pages_inner[i]);
- memory->sfree(pages_inner);
- pages_inner = NULL;
- maxpage_inner = 0;
-}
-
-void Neighbor::clear_pages_middle()
-{
- for (int i = 0; i < maxpage_middle; i++) memory->sfree(pages_middle[i]);
- memory->sfree(pages_middle);
- pages_middle = NULL;
- maxpage_middle = 0;
-}
-
/* ----------------------------------------------------------------------
determine if atom j is in special list of atom i
if it is not, return 0
@@ -1526,11 +1445,12 @@ int Neighbor::coord2bin(double *x)
return 1 if should be excluded, 0 if included
------------------------------------------------------------------------- */
-int Neighbor::exclusion(int i, int j, int *type, int *mask, int *molecule)
+int Neighbor::exclusion(int i, int j, int itype, int jtype,
+ int *mask, int *molecule)
{
int m;
- if (nex_type && ex_type[type[i]][type[j]]) return 1;
+ if (nex_type && ex_type[itype][jtype]) return 1;
if (nex_group) {
for (m = 0; m < nex_group; m++) {
@@ -1547,3 +1467,28 @@ int Neighbor::exclusion(int i, int j, int *type, int *mask, int *molecule)
return 0;
}
+
+/* ----------------------------------------------------------------------
+ return # of bytes of allocated memory
+------------------------------------------------------------------------- */
+
+int Neighbor::memory_usage()
+{
+ int bytes = 0;
+
+ bytes += maxhold*3 * sizeof(double);
+
+ if (style != NSQ) {
+ bytes += maxbin * sizeof(int);
+ bytes += maxhead * sizeof(int);
+ }
+
+ for (int i = 0; i < nlist; i++) bytes += lists[i]->memory_usage();
+
+ bytes += maxbond*3 * sizeof(int);
+ bytes += maxangle*4 * sizeof(int);
+ bytes += maxdihedral*5 * sizeof(int);
+ bytes += maximproper*5 * sizeof(int);
+
+ return bytes;
+}
diff --git a/src/neighbor.h b/src/neighbor.h
index 4766f5cb2c5e907e9ac3c8c441075e3e76aef191..a4b8d2b8b714d81c6b4b58a20e8f9d186ddba0ce 100644
--- a/src/neighbor.h
+++ b/src/neighbor.h
@@ -20,7 +20,7 @@ namespace LAMMPS_NS {
class Neighbor : protected Pointers {
public:
- int style; // 0 = nsq, 1 = binned
+ int style; // 0,1,2 = nsq, bin, multi
int every; // build every this many steps
int delay; // delay build for this many steps
int dist_check; // 0 = always build, 1 = only if 1/2 dist
@@ -34,54 +34,38 @@ class Neighbor : protected Pointers {
int ncalls; // # of times build has been called
int ndanger; // # of dangerous builds
- int nlocal_neighbor; // nlocal at last build
- int half; // 0/1 if half pair list ever built
- int full; // 0/1 if full pair list ever built
- int half_every; // 0/1 if half list built every step
- int full_every; // 0/1 if full list built every step
- int half_once; // 0/1 if half pair list built occasionally
- int full_once; // 0/1 if full pair list built occasionally
- int half_command; // 0/1 if command requires half list
+ int nrequest; // requests for pairwise neighbor lists
+ class NeighRequest **requests; // from Pair, Fix, Compute, Command classes
+ int maxrequest;
- int *numneigh; // # of half neighbors for each atom
- int **firstneigh; // ptr to 1st half neighbor of each atom
-
- int *numneigh_full; // # of full neighbors for each atom
- int **firstneigh_full; // ptr to 1st full neighbor of each atom
+ int old_style; // previous run info to avoid
+ int old_nrequest; // re-creation of pairwise neighbor lists
+ class NeighRequest **old_requests;
+
+ int nlist; // pairwise neighbor lists
+ class NeighList **lists;
int nbondlist; // list of bonds to compute
int **bondlist;
-
int nanglelist; // list of angles to compute
int **anglelist;
-
int ndihedrallist; // list of dihedrals to compute
int **dihedrallist;
-
int nimproperlist; // list of impropers to compute
int **improperlist;
- // granular neighbor list
- int **firsttouch; // ptr to first touch flag for each atom
- double **firstshear; // ptr to first shear values for each atom
-
- // rRESPA neighbor lists
- int *numneigh_inner; // # of inner pair neighbors for each atom
- int **firstneigh_inner; // ptr to inner 1st neigh of each atom
- int *numneigh_middle; // # of middle pair neighbors for each atom
- int **firstneigh_middle; // ptr to middle 1st neigh of each atom
Neighbor(class LAMMPS *);
~Neighbor();
void init();
+ int request(void *); // another class requests a neighbor list
int decide(); // decide whether to build or not
int check_distance(); // check max distance moved since last build
void setup_bins(); // setup bins based on box and cutoff
- void build(); // create all neighbor lists (half,full,bond)
- void build_half(); // one-time creation of half neighbor list
- void build_full(); // one-time creation of full neighbor list
+ void build(); // create all neighbor lists (pair,bond)
+ void build_one(int); // create a single neighbor list
void set(int, char **); // set neighbor style and skin distance
- void modify_params(int, char**); // modify parameters of neighbor build
+ void modify_params(int, char**); // modify parameters that control builds
int memory_usage(); // tally memory usage
private:
@@ -120,55 +104,19 @@ class Neighbor : protected Pointers {
double binsizex,binsizey,binsizez; // bin sizes and inverse sizes
double bininvx,bininvy,bininvz;
+ int sx,sy,sz,smax; // bin stencil extents
+
int dimension; // 2/3 for 2d/3d
int triclinic; // 0 if domain is orthog, 1 if triclinic
+ int newton_pair; // 0 if newton off, 1 if on for pairwise
+
double *bboxlo,*bboxhi; // copy of full domain bounding box
- int nstencil; // # of bins in half neighbor stencil
- int *stencil; // list of bin offsets
- int maxstencil; // max size of stencil
-
- int nstencil_full; // # of bins in full neighbor stencil
- int *stencil_full; // list of bin offsets
- int maxstencil_full; // max size of stencil
-
- int *nstencil_multi; // # bins in each type-based multi stencil
- int **stencil_multi; // list of bin offsets in each stencil
- double **distsq_multi; // sq distances to bins in each stencil
- int maxstencil_multi; // max sizes of stencils
-
- int *nstencil_full_multi; // # bins in full type-based multi stencil
- int **stencil_full_multi; // list of bin offsets in each stencil
- double **distsq_full_multi; // sq distances to bins in each stencil
- int maxstencil_full_multi; // max sizes of stencils
-
- int **pages; // half neighbor list pages
- int maxpage; // # of half pages currently allocated
-
- int **pages_full; // full neighbor list pages
- int maxpage_full; // # of full pages currently allocated
-
- // granular neighbor list
- class FixShearHistory *fix_history; // NULL if history not needed
- // else is ptr to fix shear history
- int **pages_touch; // pages of touch flags
- double **pages_shear; // pages of shear values
- int maxpage_history; // # of history pages currently allocated
-
- // rRESPA neighbor lists
- int respa; // 0 = single neighbor list
- // 1 = additional inner list
- // 2 = additional inner and middle list
double inner[2],middle[2]; // rRESPA cutoffs for extra lists
double cut_inner_sq; // outer cutoff for inner neighbor list
double cut_middle_sq; // outer cutoff for middle neighbor list
double cut_middle_inside_sq; // inner cutoff for middle neighbor list
- int **pages_inner; // inner neighbor list pages
- int maxpage_inner; // # of inner pages currently allocated
- int **pages_middle; // middle neighbor list pages
- int maxpage_middle; // # of middle pages currently allocated
-
int special_flag[4]; // flags for 1-2, 1-3, 1-4 neighbors
int exclude; // 0 if no type/group exclusions, 1 if yes
@@ -188,100 +136,100 @@ class Neighbor : protected Pointers {
int *ex_mol_group; // molecule group #'s to exclude
int *ex_mol_bit; // molecule group bits to exclude
- typedef void (Neighbor::*FnPtr)();
- FnPtr half_build; // ptr to half pair list functions
- FnPtr full_build; // ptr to full pair list functions
+ int nblist,nglist,nslist; // # of pairwise neigh lists of various kinds
+ int *blist; // lists to build every reneighboring
+ int *glist; // lists to grow atom arrays every reneigh
+ int *slist; // lists to grow stencil arrays every reneigh
- void half_nsq_no_newton(); // fns for half neighbor lists
- void half_nsq_newton();
+ void bin_atoms(); // bin all atoms
+ double bin_distance(int, int, int); // distance between binx
+ int coord2bin(double *); // mapping atom coord to a bin
+ int find_special(int, int); // look for special neighbor
+ int exclusion(int, int, int, int, int *, int *); // test for pair exclusion
+ void choose_build(int, class NeighRequest *);
+ void choose_stencil(int, class NeighRequest *);
- void half_bin_no_newton();
- void half_bin_no_newton_multi();
- void half_bin_newton();
- void half_bin_newton_multi();
- void half_bin_newton_tri();
- void half_bin_newton_multi_tri();
+ // pairwise build functions
- void half_full_no_newton();
- void half_full_newton();
+ typedef void (Neighbor::*PairPtr)(class NeighList *);
+ PairPtr *pair_build;
- void full_nsq(); // fns for full neighbor lists
- void full_bin();
- void full_bin_multi();
+ void half_nsq_no_newton(class NeighList *);
+ void half_nsq_newton(class NeighList *);
- void granular_nsq_no_newton(); // fns for granular neighbor lists
- void granular_nsq_newton();
- void granular_bin_no_newton();
- void granular_bin_newton();
- void granular_bin_newton_tri();
+ void half_bin_no_newton(class NeighList *);
+ void half_bin_newton(class NeighList *);
+ void half_bin_newton_tri(class NeighList *);
- void respa_nsq_no_newton(); // fns for respa neighbor lists
- void respa_nsq_newton();
- void respa_bin_no_newton();
- void respa_bin_newton();
- void respa_bin_newton_tri();
+ void half_multi_no_newton(class NeighList *);
+ void half_multi_newton(class NeighList *);
+ void half_multi_newton_tri(class NeighList *);
- FnPtr bond_build; // ptr to bond list functions
- void bond_all(); // bond list with all bonds
- void bond_partial(); // exclude certain bonds
+ void full_nsq(class NeighList *);
+ void full_bin(class NeighList *);
+ void full_multi(class NeighList *);
- FnPtr angle_build; // ptr to angle list functions
- void angle_all(); // angle list with all angles
- void angle_partial(); // exclude certain angles
+ void half_full_no_newton(class NeighList *);
+ void half_full_newton(class NeighList *);
+ void skip_from(class NeighList *);
+ void copy_from(class NeighList *);
- FnPtr dihedral_build; // ptr to dihedral list functions
- void dihedral_all(); // dihedral list with all dihedrals
- void dihedral_partial(); // exclude certain dihedrals
+ void granular_nsq_no_newton(class NeighList *);
+ void granular_nsq_newton(class NeighList *);
+ void granular_bin_no_newton(class NeighList *);
+ void granular_bin_newton(class NeighList *);
+ void granular_bin_newton_tri(class NeighList *);
- FnPtr improper_build; // ptr to improper list functions
- void improper_all(); // improper list with all impropers
- void improper_partial(); // exclude certain impropers
+ void respa_nsq_no_newton(class NeighList *);
+ void respa_nsq_newton(class NeighList *);
+ void respa_bin_no_newton(class NeighList *);
+ void respa_bin_newton(class NeighList *);
+ void respa_bin_newton_tri(class NeighList *);
- void add_pages(int); // add neigh list pages
- void add_pages_full(int);
- void add_pages_history(int);
- void add_pages_inner(int);
- void add_pages_middle(int);
+ // pairwise stencil creation functions
- void clear_pages(); // clear all neigh list pages
- void clear_pages_full();
- void clear_pages_history();
- void clear_pages_inner();
- void clear_pages_middle();
+ typedef void (Neighbor::*StencilPtr)(class NeighList *, int, int, int);
+ StencilPtr *stencil_create;
- void bin_atoms(); // bin all atoms
- double bin_distance(int, int, int); // distance between binx
- int coord2bin(double *); // mapping atom coord to a bin
- int find_special(int, int); // look for special neighbor
- int exclusion(int, int, int *, int *, int *); // test for pair exclusion
+ void stencil_half_bin_2d_no_newton(class NeighList *, int, int, int);
+ void stencil_half_bin_3d_no_newton(class NeighList *, int, int, int);
+ void stencil_half_bin_2d_newton(class NeighList *, int, int, int);
+ void stencil_half_bin_3d_newton(class NeighList *, int, int, int);
+ void stencil_half_bin_2d_newton_tri(class NeighList *, int, int, int);
+ void stencil_half_bin_3d_newton_tri(class NeighList *, int, int, int);
- typedef void (Neighbor::*SFnPtr)(int, int, int);
- SFnPtr half_stencil; // ptr to half stencil functions
- SFnPtr full_stencil; // ptr to full stencil functions
+ void stencil_half_multi_2d_no_newton(class NeighList *, int, int, int);
+ void stencil_half_multi_3d_no_newton(class NeighList *, int, int, int);
+ void stencil_half_multi_2d_newton(class NeighList *, int, int, int);
+ void stencil_half_multi_3d_newton(class NeighList *, int, int, int);
+ void stencil_half_multi_2d_newton_tri(class NeighList *, int, int, int);
+ void stencil_half_multi_3d_newton_tri(class NeighList *, int, int, int);
- void stencil_allocate(int, int, int);
+ void stencil_full_bin_2d(class NeighList *, int, int, int);
+ void stencil_full_bin_3d(class NeighList *, int, int, int);
+ void stencil_full_multi_2d(class NeighList *, int, int, int);
+ void stencil_full_multi_3d(class NeighList *, int, int, int);
- void stencil_none(int, int, int); // fns for stencil creation
+ // topology build functions
- void stencil_half_3d_no_newton(int, int, int);
- void stencil_half_3d_no_newton_multi(int, int, int);
- void stencil_half_3d_newton(int, int, int);
- void stencil_half_3d_newton_multi(int, int, int);
- void stencil_half_3d_newton_tri(int, int, int);
- void stencil_half_3d_newton_multi_tri(int, int, int);
+ typedef void (Neighbor::*BondPtr)(); // ptrs to topology build functions
- void stencil_half_2d_no_newton(int, int, int);
- void stencil_half_2d_no_newton_multi(int, int, int);
- void stencil_half_2d_newton(int, int, int);
- void stencil_half_2d_newton_multi(int, int, int);
- void stencil_half_2d_newton_tri(int, int, int);
- void stencil_half_2d_newton_multi_tri(int, int, int);
+ BondPtr bond_build; // ptr to bond list functions
+ void bond_all(); // bond list with all bonds
+ void bond_partial(); // exclude certain bonds
- void stencil_full_3d(int, int, int);
- void stencil_full_3d_multi(int, int, int);
+ BondPtr angle_build; // ptr to angle list functions
+ void angle_all(); // angle list with all angles
+ void angle_partial(); // exclude certain angles
+
+ BondPtr dihedral_build; // ptr to dihedral list functions
+ void dihedral_all(); // dihedral list with all dihedrals
+ void dihedral_partial(); // exclude certain dihedrals
+
+ BondPtr improper_build; // ptr to improper list functions
+ void improper_all(); // improper list with all impropers
+ void improper_partial(); // exclude certain impropers
- void stencil_full_2d(int, int, int);
- void stencil_full_2d_multi(int, int, int);
};
}
diff --git a/src/output.cpp b/src/output.cpp
index fd5d765c11131ae8b07d9d929a41659af39f5049..4e850d903ac5c80bfc6121274655da45edd3f14a 100644
--- a/src/output.cpp
+++ b/src/output.cpp
@@ -49,21 +49,21 @@ Output::Output(LAMMPS *lmp) : Pointers(lmp)
// create 2 default computes for temp and pressure
char **newarg = new char*[4];
- newarg[0] = "thermo_temp";
- newarg[1] = "all";
- newarg[2] = "temp";
+ newarg[0] = (char *) "thermo_temp";
+ newarg[1] = (char *) "all";
+ newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
- newarg[0] = "thermo_pressure";
- newarg[1] = "all";
- newarg[2] = "pressure";
- newarg[3] = "thermo_temp";
+ newarg[0] = (char *) "thermo_pressure";
+ newarg[1] = (char *) "all";
+ newarg[2] = (char *) "pressure";
+ newarg[3] = (char *) "thermo_temp";
modify->add_compute(4,newarg);
delete [] newarg;
// create default Thermo class
newarg = new char*[1];
- newarg[0] = "one";
+ newarg[0] = (char *) "one";
thermo = new Thermo(lmp,1,newarg);
delete [] newarg;
diff --git a/src/pair.cpp b/src/pair.cpp
index b7278c634b80e53a1bc0898ad74f739f53789df9..02a9ec576274602300a4e5b719ae20d31d4ff715 100644
--- a/src/pair.cpp
+++ b/src/pair.cpp
@@ -25,6 +25,8 @@
#include "pair.h"
#include "pair_soft.h"
#include "atom.h"
+#include "neighbor.h"
+#include "neigh_list.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
@@ -46,8 +48,6 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp)
eng_vdwl = eng_coul = 0.0;
comm_forward = comm_reverse = 0;
- neigh_half_every = 1;
- neigh_full_every = 0;
single_enable = 1;
respa_enable = 0;
@@ -123,11 +123,21 @@ void Pair::init()
error->warning("Using pair tail corrections with nonperiodic system");
if (!allocated) error->all("All pair coeffs are not set");
+
+ // I,I coeffs must be set
+ // init_one() will check if I,J is set explicitly or inferred by mixing
+
for (i = 1; i <= atom->ntypes; i++)
if (setflag[i][i] == 0) error->all("All pair coeffs are not set");
+ // style-specific initialization
+
init_style();
+ // call init_one() for each I,J
+ // set cutsq for each I,J, used to neighbor
+ // cutforce = max of all I,J cutoffs
+
double cut;
cutforce = 0.0;
etail = ptail = 0.0;
@@ -147,6 +157,29 @@ void Pair::init()
}
}
+/* ----------------------------------------------------------------------
+ init specific to a pair style
+ specific pair style can override this function
+ if needs its own error checks
+ if needs another kind of neighbor list
+ request default neighbor list = half list
+------------------------------------------------------------------------- */
+
+void Pair::init_style()
+{
+ int irequest = neighbor->request(this);
+}
+
+/* ----------------------------------------------------------------------
+ neighbor callback to inform pair style of neighbor list to use
+ specific pair style can override this function
+------------------------------------------------------------------------- */
+
+void Pair::init_list(int which, NeighList *ptr)
+{
+ list = ptr;
+}
+
/* ----------------------------------------------------------------------
mixing of pair potential prefactors (epsilon)
------------------------------------------------------------------------- */
@@ -181,34 +214,25 @@ double Pair::mix_distance(double sig1, double sig2)
}
/* ----------------------------------------------------------------------
- compute pair virial via pair own/ghost forces
+ compute pair virial via own/ghost forces
+ at this point, only pairwise forces have been accumulated in atom->f
------------------------------------------------------------------------- */
void Pair::virial_compute()
{
double **x = atom->x;
- double **f_pair = update->f_pair;
+ double **f = atom->f;
int nall = atom->nlocal + atom->nghost;
// sum over own & ghost atoms
for (int i = 0; i < nall; i++) {
- virial[0] += f_pair[i][0]*x[i][0];
- virial[1] += f_pair[i][1]*x[i][1];
- virial[2] += f_pair[i][2]*x[i][2];
- virial[3] += f_pair[i][1]*x[i][0];
- virial[4] += f_pair[i][2]*x[i][0];
- virial[5] += f_pair[i][2]*x[i][1];
- }
-
- // add pair forces into total force
-
- double **f = atom->f;
-
- for (int i = 0; i < nall; i++) {
- f[i][0] += f_pair[i][0];
- f[i][1] += f_pair[i][1];
- f[i][2] += f_pair[i][2];
+ virial[0] += f[i][0]*x[i][0];
+ virial[1] += f[i][1]*x[i][1];
+ virial[2] += f[i][2]*x[i][2];
+ virial[3] += f[i][1]*x[i][0];
+ virial[4] += f[i][2]*x[i][0];
+ virial[5] += f[i][2]*x[i][1];
}
}
diff --git a/src/pair.h b/src/pair.h
index 00f10c03972e5b0ccf3605809ac33b90ef597dcf..342c844e9bac1119736873566ffb7aa6223e973e 100644
--- a/src/pair.h
+++ b/src/pair.h
@@ -29,8 +29,6 @@ class Pair : protected Pointers {
int comm_forward; // size of forward communication (0 if none)
int comm_reverse; // size of reverse communication (0 if none)
- int neigh_half_every; // 0/1 = if needs half neighbor list
- int neigh_full_every; // 0/1 = if needs full neighbor list
int single_enable; // 1 if single() routine exists
int respa_enable; // 1 if inner/middle/outer rRESPA routines
@@ -40,11 +38,17 @@ class Pair : protected Pointers {
double etail,ptail; // energy/pressure tail corrections
double etail_ij,ptail_ij;
+ class NeighList *list; // standard neighbor list used by most pairs
+ class NeighList *listhalf; // half list used by some pairs
+ class NeighList *listfull; // full list used by some pairs
+ class NeighList *listgranhistory; // granular history list used by some
+ class NeighList *listinner; // rRESPA lists used by some pairs
+ class NeighList *listmiddle;
+ class NeighList *listouter;
+
struct One { // single interaction between 2 atoms
double fforce;
double eng_vdwl,eng_coul;
- double fx,fy,fz;
- double tix,tiy,tiz,tjx,tjy,tjz;
};
Pair(class LAMMPS *);
@@ -63,17 +67,20 @@ class Pair : protected Pointers {
// general child-class methods
virtual void compute(int, int) = 0;
- virtual void settings(int, char **) = 0;
- virtual void coeff(int, char **) = 0;
-
- virtual double init_one(int, int) {return 0.0;}
- virtual void init_style() {}
virtual void compute_inner() {}
virtual void compute_middle() {}
virtual void compute_outer(int, int) {}
+
virtual void single(int, int, int, int,
double, double, double, int, One &) {}
+ virtual void settings(int, char **) = 0;
+ virtual void coeff(int, char **) = 0;
+
+ virtual void init_style();
+ virtual void init_list(int, class NeighList *);
+ virtual double init_one(int, int) {return 0.0;}
+
virtual void write_restart(FILE *) {}
virtual void read_restart(FILE *) {}
virtual void write_restart_settings(FILE *) {}
@@ -88,6 +95,9 @@ class Pair : protected Pointers {
// specific child-class methods for certain Pair styles
virtual void single_embed(int, int, double &) {}
+
+ virtual void *extract_ptr(char *) {return NULL;}
+
virtual void extract_charmm(double ***, double ***,
double ***, double ***, int *) {}
virtual void extract_dipole(double ***) {}
diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp
index 5fe48f4189d81e3245def0fef088e06a9dd11135..67d919177b1902bd99c964a80ae7b183bca2ae20 100644
--- a/src/pair_buck.cpp
+++ b/src/pair_buck.cpp
@@ -18,9 +18,8 @@
#include "atom.h"
#include "comm.h"
#include "force.h"
-#include "update.h"
+#include "neigh_list.h"
#include "memory.h"
-#include "neighbor.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -55,37 +54,41 @@ PairBuck::~PairBuck()
void PairBuck::compute(int eflag, int vflag)
{
- int i,j,k,numneigh,itype,jtype;
+ int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcebuck,fforce,factor_lj;
double phibuck,r,rexp;
- int *neighs;
- double **f;
+ int *ilist,*jlist,*numneigh,**firstneigh;
eng_vdwl = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
- if (vflag == 2) f = update->f_pair;
- else f = atom->f;
double **x = atom->x;
+ double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
// loop over neighbors of my atoms
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
- neighs = neighbor->firstneigh[i];
- numneigh = neighbor->numneigh[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp
index 9348c0f693dd1757c4531b744fdf98c359877608..955b98c7cd4a505166cde1fae7abf12bd90f08cc 100644
--- a/src/pair_buck_coul_cut.cpp
+++ b/src/pair_buck_coul_cut.cpp
@@ -22,9 +22,9 @@
#include "atom.h"
#include "comm.h"
#include "force.h"
-#include "update.h"
-#include "memory.h"
#include "neighbor.h"
+#include "neigh_list.h"
+#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -62,19 +62,17 @@ PairBuckCoulCut::~PairBuckCoulCut()
void PairBuckCoulCut::compute(int eflag, int vflag)
{
- int i,j,k,numneigh,itype,jtype;
+ int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcecoul,forcebuck,fforce,factor_coul,factor_lj;
double factor,phicoul,phibuck,r,rexp;
- int *neighs;
- double **f;
+ int *ilist,*jlist,*numneigh,**firstneigh;
eng_vdwl = eng_coul = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
- if (vflag == 2) f = update->f_pair;
- else f = atom->f;
double **x = atom->x;
+ double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
@@ -84,19 +82,25 @@ void PairBuckCoulCut::compute(int eflag, int vflag)
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
// loop over neighbors of my atoms
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
- neighs = neighbor->firstneigh[i];
- numneigh = neighbor->numneigh[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
@@ -258,6 +262,18 @@ void PairBuckCoulCut::coeff(int narg, char **arg)
if (count == 0) error->all("Incorrect args for pair coefficients");
}
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairBuckCoulCut::init_style()
+{
+ if (!atom->q_flag)
+ error->all("Pair style buck/coul/cut requires atom attribute q");
+
+ int irequest = neighbor->request(this);
+}
+
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
@@ -291,16 +307,6 @@ double PairBuckCoulCut::init_one(int i, int j)
return cut;
}
-/* ----------------------------------------------------------------------
- init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairBuckCoulCut::init_style()
-{
- if (!atom->q_flag)
- error->all("Pair style buck/coul/cut requires atom attribute q");
-}
-
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
diff --git a/src/pair_buck_coul_cut.h b/src/pair_buck_coul_cut.h
index 6bf81731f7e5db25aaec6a1f302d52c696889467..06fd27c7819dd4699b4dbf001f854d6373384324 100644
--- a/src/pair_buck_coul_cut.h
+++ b/src/pair_buck_coul_cut.h
@@ -25,8 +25,8 @@ class PairBuckCoulCut : public Pair {
void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
- double init_one(int, int);
void init_style();
+ double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..ba5f6a44eff3f0aa32c782b8ed070aeb76134375
--- /dev/null
+++ b/src/pair_coul_cut.cpp
@@ -0,0 +1,313 @@
+/* ----------------------------------------------------------------------
+ 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.
+------------------------------------------------------------------------- */
+
+#include "math.h"
+#include "stdio.h"
+#include "stdlib.h"
+#include "string.h"
+#include "pair_coul_cut.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define MIN(a,b) ((a) < (b) ? (a) : (b))
+#define MAX(a,b) ((a) > (b) ? (a) : (b))
+
+/* ---------------------------------------------------------------------- */
+
+PairCoulCut::PairCoulCut(LAMMPS *lmp) : Pair(lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+PairCoulCut::~PairCoulCut()
+{
+ if (allocated) {
+ memory->destroy_2d_int_array(setflag);
+ memory->destroy_2d_double_array(cutsq);
+
+ memory->destroy_2d_double_array(cut);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairCoulCut::compute(int eflag, int vflag)
+{
+ int i,j,ii,jj,inum,jnum,itype,jtype;
+ double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
+ double rsq,r2inv,rinv,forcecoul,fforce,factor_coul,phicoul;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ eng_coul = 0.0;
+ if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ double *q = atom->q;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ int nall = atom->nlocal + atom->nghost;
+ double *special_coul = force->special_coul;
+ int newton_pair = force->newton_pair;
+ double qqrd2e = force->qqrd2e;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ // loop over neighbors of my atoms
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ qtmp = q[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+
+ if (j < nall) factor_coul = 1.0;
+ else {
+ factor_coul = special_coul[j/nall];
+ j %= nall;
+ }
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ jtype = type[j];
+
+ if (rsq < cutsq[itype][jtype]) {
+ r2inv = 1.0/rsq;
+ rinv = sqrt(r2inv);
+ forcecoul = qqrd2e * qtmp*q[j]*rinv;
+ fforce = factor_coul*forcecoul * r2inv;
+
+ f[i][0] += delx*fforce;
+ f[i][1] += dely*fforce;
+ f[i][2] += delz*fforce;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fforce;
+ f[j][1] -= dely*fforce;
+ f[j][2] -= delz*fforce;
+ }
+
+ if (eflag) {
+ phicoul = qqrd2e * qtmp*q[j]*rinv;
+ if (newton_pair || j < nlocal) eng_coul += factor_coul*phicoul;
+ else eng_coul += 0.5*factor_coul*phicoul;
+ }
+
+ if (vflag == 1) {
+ if (newton_pair == 0 && j >= nlocal) fforce *= 0.5;
+ virial[0] += delx*delx*fforce;
+ virial[1] += dely*dely*fforce;
+ virial[2] += delz*delz*fforce;
+ virial[3] += delx*dely*fforce;
+ virial[4] += delx*delz*fforce;
+ virial[5] += dely*delz*fforce;
+ }
+ }
+ }
+ }
+ if (vflag == 2) virial_compute();
+}
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairCoulCut::allocate()
+{
+ allocated = 1;
+ int n = atom->ntypes;
+
+ setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
+
+ cut = memory->create_2d_double_array(n+1,n+1,"pair:cut");
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+------------------------------------------------------------------------- */
+
+void PairCoulCut::settings(int narg, char **arg)
+{
+ if (narg != 1) error->all("Illegal pair_style command");
+
+ cut_global = atof(arg[0]);
+
+ // reset cutoffs that have been explicitly set
+
+ if (allocated) {
+ int i,j;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i+1; j <= atom->ntypes; j++)
+ if (setflag[i][j]) cut[i][j] = cut_global;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairCoulCut::coeff(int narg, char **arg)
+{
+ if (narg < 2 || narg > 3) error->all("Incorrect args for pair coefficients");
+ if (!allocated) allocate();
+
+ int ilo,ihi,jlo,jhi;
+ force->bounds(arg[0],atom->ntypes,ilo,ihi);
+ force->bounds(arg[1],atom->ntypes,jlo,jhi);
+
+ double cut_one = cut_global;
+ if (narg == 3) cut_one = atof(arg[2]);
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ for (int j = MAX(jlo,i); j <= jhi; j++) {
+ cut[i][j] = cut_one;
+ setflag[i][j] = 1;
+ count++;
+ }
+ }
+
+ if (count == 0) error->all("Incorrect args for pair coefficients");
+}
+
+
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairCoulCut::init_style()
+{
+ if (!atom->q_flag)
+ error->all("Pair style coul/cut requires atom attribute q");
+
+ int irequest = neighbor->request(this);
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairCoulCut::init_one(int i, int j)
+{
+ if (setflag[i][j] == 0)
+ cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
+
+ return cut[i][j];
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairCoulCut::write_restart(FILE *fp)
+{
+ write_restart_settings(fp);
+
+ int i,j;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++) {
+ fwrite(&setflag[i][j],sizeof(int),1,fp);
+ if (setflag[i][j]) fwrite(&cut[i][j],sizeof(double),1,fp);
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairCoulCut::read_restart(FILE *fp)
+{
+ read_restart_settings(fp);
+ allocate();
+
+ int i,j;
+ int me = comm->me;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++) {
+ if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+ MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+ if (setflag[i][j]) {
+ if (me == 0) fread(&cut[i][j],sizeof(double),1,fp);
+ MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairCoulCut::write_restart_settings(FILE *fp)
+{
+ fwrite(&cut_global,sizeof(double),1,fp);
+ fwrite(&offset_flag,sizeof(int),1,fp);
+ fwrite(&mix_flag,sizeof(int),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairCoulCut::read_restart_settings(FILE *fp)
+{
+ if (comm->me == 0) {
+ fread(&cut_global,sizeof(double),1,fp);
+ fread(&offset_flag,sizeof(int),1,fp);
+ fread(&mix_flag,sizeof(int),1,fp);
+ }
+ MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
+ MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairCoulCut::single(int i, int j, int itype, int jtype,
+ double rsq, double factor_coul, double factor_lj,
+ int eflag, One &one)
+{
+ double r2inv,rinv,forcecoul,phicoul;
+
+ r2inv = 1.0/rsq;
+ rinv = sqrt(r2inv);
+ forcecoul = force->qqrd2e * atom->q[i]*atom->q[j]*rinv;
+ one.fforce = factor_coul*forcecoul * r2inv;
+
+ if (eflag) {
+ phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*rinv;
+ one.eng_coul = factor_coul*phicoul;
+ one.eng_vdwl = 0.0;
+ }
+}
diff --git a/src/compute_etotal_atom.h b/src/pair_coul_cut.h
similarity index 55%
rename from src/compute_etotal_atom.h
rename to src/pair_coul_cut.h
index b5c171e2ac74850a2ca2aa7264e8a5a4eab9b8a5..9b6a0fca4927ea5cd5e8d20cabbf5e292bbaa710 100644
--- a/src/compute_etotal_atom.h
+++ b/src/pair_coul_cut.h
@@ -11,25 +11,33 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-#ifndef COMPUTE_ETOTAL_ATOM_H
-#define COMPUTE_ETOTAL_ATOM_H
+#ifndef PAIR_COUL_CUT_H
+#define PAIR_COUL_CUT_H
-#include "compute.h"
+#include "pair.h"
namespace LAMMPS_NS {
-class ComputeEtotalAtom : public Compute {
+class PairCoulCut : public Pair {
public:
- ComputeEtotalAtom(class LAMMPS *, int, char **);
- ~ComputeEtotalAtom();
- void init();
- void compute_peratom();
- int memory_usage();
+ PairCoulCut(class LAMMPS *);
+ ~PairCoulCut();
+ void compute(int, int);
+ void settings(int, char **);
+ void coeff(int, char **);
+ void init_style();
+ double init_one(int, int);
+ void write_restart(FILE *);
+ void read_restart(FILE *);
+ void write_restart_settings(FILE *);
+ void read_restart_settings(FILE *);
+ void single(int, int, int, int, double, double, double, int, One &);
private:
- int nmax;
- double *etotal;
- Compute *compute_epair;
+ double cut_global;
+ double **cut;
+
+ void allocate();
};
}
diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp
index 80f77a74dee94bfd2ded1940ab082f3b04f50f9f..df69770d7776f5d60000185f77cd05fcaacb13be 100644
--- a/src/pair_hybrid.cpp
+++ b/src/pair_hybrid.cpp
@@ -11,13 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
-/* ----------------------------------------------------------------------
- Contributing authors:
- James Fischer (High Performance Technologies, Inc)
- Vincent Natoli (Stone Ridge Technology)
- David Richie (Stone Ridge Technology)
-------------------------------------------------------------------------- */
-
#include "math.h"
#include "string.h"
#include "ctype.h"
@@ -26,6 +19,7 @@
#include "force.h"
#include "pair.h"
#include "neighbor.h"
+#include "neigh_request.h"
#include "update.h"
#include "comm.h"
#include "memory.h"
@@ -33,8 +27,6 @@
using namespace LAMMPS_NS;
-#define NEIGHEXTRA 10000
-
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
@@ -58,265 +50,32 @@ PairHybrid::~PairHybrid()
if (allocated) {
memory->destroy_2d_int_array(setflag);
- memory->destroy_2d_int_array(map);
memory->destroy_2d_double_array(cutsq);
-
- delete [] nnlist;
- delete [] maxneigh;
- for (int m = 0; m < nstyles; m++) memory->sfree(nlist[m]);
- delete [] nlist;
-
- delete [] nnlist_full;
- delete [] maxneigh_full;
- for (int m = 0; m < nstyles; m++) memory->sfree(nlist_full[m]);
- delete [] nlist_full;
-
- for (int m = 0; m < nstyles; m++) delete [] firstneigh[m];
- delete [] firstneigh;
- for (int m = 0; m < nstyles; m++) delete [] numneigh[m];
- delete [] numneigh;
-
- for (int m = 0; m < nstyles; m++) delete [] firstneigh_full[m];
- delete [] firstneigh_full;
- for (int m = 0; m < nstyles; m++) delete [] numneigh_full[m];
- delete [] numneigh_full;
+ memory->destroy_2d_int_array(nmap);
+ memory->destroy_3d_int_array(map);
}
}
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+ call each sub-style's compute function
+ accumulate sub-style energy/virial in hybrid's energy/virial
+ for vflag = 1:
+ each sub-style computes own virial[6]
+ sum sub-style virial[6] to hybrid's virial[6]
+ for vflag = 2:
+ call sub-style compute() with vflag % 2
+ to prevent sub-style from calling virial_compute()
+ hybrid calls virial_compute() on final accumulated f
+------------------------------------------------------------------------- */
void PairHybrid::compute(int eflag, int vflag)
{
- int i,j,k,m,n,jfull,nneigh;
- int *neighs,*mapi;
- double **f_original;
-
- // save ptrs to original neighbor lists
-
- int **firstneigh_original = neighbor->firstneigh;
- int *numneigh_original = neighbor->numneigh;
- int **firstneigh_full_original = neighbor->firstneigh_full;
- int *numneigh_full_original = neighbor->numneigh_full;
-
- // if this is re-neighbor step, create sub-style lists
-
- if (neighbor->ago == 0) {
- int *type = atom->type;
- int nlocal = atom->nlocal;
- int nall = atom->nlocal + atom->nghost;
-
- // realloc per-atom per-style firstneigh/numneigh half/full if necessary
-
- if (nlocal > maxlocal) {
- maxlocal = nlocal;
- if (neigh_half_every) {
- for (m = 0; m < nstyles; m++) {
- delete [] firstneigh[m];
- delete [] numneigh[m];
- }
- for (m = 0; m < nstyles; m++) {
- firstneigh[m] = new int*[maxlocal];
- numneigh[m] = new int[maxlocal];
- }
- }
- if (neigh_full_every) {
- for (m = 0; m < nstyles; m++) {
- delete [] firstneigh_full[m];
- delete [] numneigh_full[m];
- }
- for (m = 0; m < nstyles; m++) {
- firstneigh_full[m] = new int*[maxlocal];
- numneigh_full[m] = new int[maxlocal];
- }
- }
- }
-
- // nnlist[] = length of each sub-style half list
- // nnlist_full[] = length of each sub-style full list
- // count from half and/or full list depending on what sub-styles use
-
- for (m = 0; m < nstyles; m++) nnlist[m] = nnlist_full[m] = 0;
-
- if (neigh_half_every && neigh_full_every) {
- for (i = 0; i < nlocal; i++) {
- mapi = map[type[i]];
- neighs = firstneigh_original[i];
- nneigh = numneigh_original[i];
- for (k = 0; k < nneigh; k++) {
- j = neighs[k];
- if (j >= nall) j %= nall;
- m = mapi[type[j]];
- if (styles[m] && styles[m]->neigh_half_every) nnlist[m]++;
- }
- neighs = firstneigh_full_original[i];
- nneigh = numneigh_full_original[i];
- for (k = 0; k < nneigh; k++) {
- j = neighs[k];
- if (j >= nall) j %= nall;
- m = mapi[type[j]];
- if (styles[m] && styles[m]->neigh_full_every) nnlist_full[m]++;
- }
- }
-
- } else if (neigh_half_every) {
- for (i = 0; i < nlocal; i++) {
- mapi = map[type[i]];
- neighs = firstneigh_original[i];
- nneigh = numneigh_original[i];
- for (k = 0; k < nneigh; k++) {
- j = neighs[k];
- if (j >= nall) j %= nall;
- nnlist[mapi[type[j]]]++;
- }
- }
-
- } else if (neigh_full_every) {
- for (i = 0; i < nlocal; i++) {
- mapi = map[type[i]];
- neighs = firstneigh_full_original[i];
- nneigh = numneigh_full_original[i];
- for (k = 0; k < nneigh; k++) {
- j = neighs[k];
- if (j >= nall) j %= nall;
- nnlist_full[mapi[type[j]]]++;
- }
- }
- }
-
- // realloc sub-style nlist and nlist_full if necessary
-
- if (neigh_half_every) {
- for (m = 0; m < nstyles; m++) {
- if (nnlist[m] > maxneigh[m]) {
- memory->sfree(nlist[m]);
- maxneigh[m] = nnlist[m] + NEIGHEXTRA;
- nlist[m] = (int *)
- memory->smalloc(maxneigh[m]*sizeof(int),"pair_hybrid:nlist");
- }
- nnlist[m] = 0;
- }
- }
- if (neigh_full_every) {
- for (m = 0; m < nstyles; m++) {
- if (nnlist_full[m] > maxneigh_full[m]) {
- memory->sfree(nlist_full[m]);
- maxneigh_full[m] = nnlist_full[m] + NEIGHEXTRA;
- nlist_full[m] = (int *)
- memory->smalloc(maxneigh_full[m]*sizeof(int),
- "pair_hybrid:nlist_full");
- }
- nnlist_full[m] = 0;
- }
- }
-
- // load sub-style half/full list with values from original lists
- // load from half and/or full list depending on what sub-styles use
-
- if (neigh_half_every && neigh_full_every) {
- for (i = 0; i < nlocal; i++) {
- for (m = 0; m < nstyles; m++) {
- firstneigh[m][i] = &nlist[m][nnlist[m]];
- numneigh[m][i] = nnlist[m];
- firstneigh_full[m][i] = &nlist_full[m][nnlist_full[m]];
- numneigh_full[m][i] = nnlist_full[m];
- }
- mapi = map[type[i]];
- neighs = firstneigh_original[i];
- nneigh = numneigh_original[i];
- for (k = 0; k < nneigh; k++) {
- j = jfull = neighs[k];
- if (j >= nall) j %= nall;
- m = mapi[type[j]];
- if (styles[m] && styles[m]->neigh_half_every)
- nlist[m][nnlist[m]++] = jfull;
- }
- neighs = firstneigh_full_original[i];
- nneigh = numneigh_full_original[i];
- for (k = 0; k < nneigh; k++) {
- j = jfull = neighs[k];
- if (j >= nall) j %= nall;
- m = mapi[type[j]];
- if (styles[m] && styles[m]->neigh_full_every)
- nlist_full[m][nnlist_full[m]++] = jfull;
- }
- for (m = 0; m < nstyles; m++) {
- numneigh[m][i] = nnlist[m] - numneigh[m][i];
- numneigh_full[m][i] = nnlist_full[m] - numneigh_full[m][i];
- }
- }
-
- } else if (neigh_half_every) {
- for (i = 0; i < nlocal; i++) {
- for (m = 0; m < nstyles; m++) {
- firstneigh[m][i] = &nlist[m][nnlist[m]];
- numneigh[m][i] = nnlist[m];
- }
- mapi = map[type[i]];
- neighs = firstneigh_original[i];
- nneigh = numneigh_original[i];
- for (k = 0; k < nneigh; k++) {
- j = jfull = neighs[k];
- if (j >= nall) j %= nall;
- m = mapi[type[j]];
- nlist[m][nnlist[m]++] = jfull;
- }
- for (m = 0; m < nstyles; m++)
- numneigh[m][i] = nnlist[m] - numneigh[m][i];
- }
-
- } else if (neigh_full_every) {
- for (i = 0; i < nlocal; i++) {
- for (m = 0; m < nstyles; m++) {
- firstneigh_full[m][i] = &nlist_full[m][nnlist_full[m]];
- numneigh_full[m][i] = nnlist_full[m];
- }
- mapi = map[type[i]];
- neighs = firstneigh_full_original[i];
- nneigh = numneigh_full_original[i];
- for (k = 0; k < nneigh; k++) {
- j = jfull = neighs[k];
- if (j >= nall) j %= nall;
- m = mapi[type[j]];
- nlist_full[m][nnlist_full[m]++] = jfull;
- }
- for (m = 0; m < nstyles; m++)
- numneigh_full[m][i] = nnlist_full[m] - numneigh_full[m][i];
- }
- }
- }
-
- // call each sub-style's compute function
- // set neighbor->firstneigh/numneigh to sub-style lists before call
- // set half or full or both depending on what sub-style uses
- // for vflag = 1:
- // sub-style accumulates in its virial[6]
- // sum sub-style virial[6] to hybrid's virial[6]
- // for vflag = 2:
- // set atom->f to update->f_pair so sub-style will sum its f to f_pair
- // call sub-style compute() with vflag % 2 to prevent sub-style
- // from calling virial_compute()
- // reset atom->f to stored f_original
- // call hybrid virial_compute() which will use update->f_pair
- // accumulate sub-style energy,virial in hybrid's energy,virial
+ int m,n;
eng_vdwl = eng_coul = 0.0;
if (vflag) for (n = 0; n < 6; n++) virial[n] = 0.0;
- if (vflag == 2) {
- f_original = atom->f;
- atom->f = update->f_pair;
- }
-
for (m = 0; m < nstyles; m++) {
- if (styles[m] == NULL) continue;
- if (styles[m]->neigh_half_every) {
- neighbor->firstneigh = firstneigh[m];
- neighbor->numneigh = numneigh[m];
- }
- if (styles[m]->neigh_full_every) {
- neighbor->firstneigh_full = firstneigh_full[m];
- neighbor->numneigh_full = numneigh_full[m];
- }
styles[m]->compute(eflag,vflag % 2);
if (eflag) {
eng_vdwl += styles[m]->eng_vdwl;
@@ -325,17 +84,7 @@ void PairHybrid::compute(int eflag, int vflag)
if (vflag == 1) for (n = 0; n < 6; n++) virial[n] += styles[m]->virial[n];
}
- if (vflag == 2) {
- atom->f = f_original;
- virial_compute();
- }
-
- // restore ptrs to original neighbor lists
-
- neighbor->firstneigh = firstneigh_original;
- neighbor->numneigh = numneigh_original;
- neighbor->firstneigh_full = firstneigh_full_original;
- neighbor->numneigh_full = numneigh_full_original;
+ if (vflag == 2) virial_compute();
}
/* ----------------------------------------------------------------------
@@ -347,11 +96,6 @@ void PairHybrid::allocate()
allocated = 1;
int n = atom->ntypes;
- map = memory->create_2d_int_array(n+1,n+1,"pair:map");
- for (int i = 1; i <= n; i++)
- for (int j = i; j <= n; j++)
- map[i][j] = -1;
-
setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
@@ -359,27 +103,11 @@ void PairHybrid::allocate()
cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
- nnlist = new int[nstyles];
- maxneigh = new int[nstyles];
- nlist = new int*[nstyles];
- for (int m = 0; m < nstyles; m++) maxneigh[m] = 0;
- for (int m = 0; m < nstyles; m++) nlist[m] = NULL;
-
- nnlist_full = new int[nstyles];
- maxneigh_full = new int[nstyles];
- nlist_full = new int*[nstyles];
- for (int m = 0; m < nstyles; m++) maxneigh_full[m] = 0;
- for (int m = 0; m < nstyles; m++) nlist_full[m] = NULL;
-
- maxlocal = 0;
- firstneigh = new int**[nstyles];
- numneigh = new int*[nstyles];
- for (int m = 0; m < nstyles; m++) firstneigh[m] = NULL;
- for (int m = 0; m < nstyles; m++) numneigh[m] = NULL;
- firstneigh_full = new int**[nstyles];
- numneigh_full = new int*[nstyles];
- for (int m = 0; m < nstyles; m++) firstneigh_full[m] = NULL;
- for (int m = 0; m < nstyles; m++) numneigh_full[m] = NULL;
+ nmap = memory->create_2d_int_array(n+1,n+1,"pair:nmap");
+ map = memory->create_3d_int_array(n+1,n+1,nstyles,"pair:map");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ nmap[i][j] = 0;
}
/* ----------------------------------------------------------------------
@@ -403,15 +131,17 @@ void PairHybrid::settings(int narg, char **arg)
if (allocated) {
memory->destroy_2d_int_array(setflag);
- memory->destroy_2d_int_array(map);
memory->destroy_2d_double_array(cutsq);
+ memory->destroy_2d_int_array(nmap);
+ memory->destroy_3d_int_array(map);
}
allocated = 0;
// count sub-styles by skipping numeric args
// one exception is 1st arg of style "table", which is non-numeric word
- nstyles = i = 0;
+ nstyles = 0;
+ i = 0;
while (i < narg) {
if (strcmp(arg[i],"table") == 0) i++;
i++;
@@ -425,16 +155,19 @@ void PairHybrid::settings(int narg, char **arg)
keywords = new char*[nstyles];
// allocate each sub-style and call its settings() with subset of args
- // define subset of sub-styles by skipping numeric args
+ // define subset of args for a sub-style by skipping numeric args
// one exception is 1st arg of style "table", which is non-numeric word
- nstyles = i = 0;
+ nstyles = 0;
+ i = 0;
while (i < narg) {
for (m = 0; m < nstyles; m++)
if (strcmp(arg[i],keywords[m]) == 0)
error->all("Pair style hybrid cannot use same pair style twice");
if (strcmp(arg[i],"hybrid") == 0)
error->all("Pair style hybrid cannot have hybrid as an argument");
+ if (strcmp(arg[i],"none") == 0)
+ error->all("Pair style hybrid cannot have none as an argument");
styles[nstyles] = force->new_pair(arg[i]);
keywords[nstyles] = new char[strlen(arg[i])+1];
strcpy(keywords[nstyles],arg[i]);
@@ -442,7 +175,7 @@ void PairHybrid::settings(int narg, char **arg)
if (strcmp(arg[i],"table") == 0) i++;
i++;
while (i < narg && !isalpha(arg[i][0])) i++;
- if (styles[nstyles]) styles[nstyles]->settings(i-istyle-1,&arg[istyle+1]);
+ styles[nstyles]->settings(i-istyle-1,&arg[istyle+1]);
nstyles++;
}
@@ -453,14 +186,6 @@ void PairHybrid::settings(int narg, char **arg)
if (styles[m]) comm_reverse = MAX(comm_reverse,styles[m]->comm_reverse);
}
- // neigh_every = 1 if any sub-style = 1
-
- neigh_half_every = neigh_full_every = 0;
- for (m = 0; m < nstyles; m++) {
- if (styles[m] && styles[m]->neigh_half_every) neigh_half_every = 1;
- if (styles[m] && styles[m]->neigh_full_every) neigh_full_every = 1;
- }
-
// single_enable = 0 if any sub-style = 0
for (m = 0; m < nstyles; m++)
@@ -480,12 +205,18 @@ void PairHybrid::coeff(int narg, char **arg)
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
- // 3rd arg = pair style name
+ // 3rd arg = pair sub-style name
+ // allow for "none" as valid sub-style name
int m;
for (m = 0; m < nstyles; m++)
if (strcmp(arg[2],keywords[m]) == 0) break;
- if (m == nstyles) error->all("Pair coeff for hybrid has invalid style");
+
+ int none = 0;
+ if (m == nstyles) {
+ if (strcmp(arg[2],"none") == 0) none = 1;
+ else error->all("Pair coeff for hybrid has invalid style");
+ }
// move 1st/2nd args to 2nd/3rd args
@@ -494,29 +225,36 @@ void PairHybrid::coeff(int narg, char **arg)
// invoke sub-style coeff() starting with 1st arg
- if (styles[m]) styles[m]->coeff(narg-1,&arg[1]);
+ if (!none) styles[m]->coeff(narg-1,&arg[1]);
- // if pair style only allows one pair coeff call (with * * and type mapping)
- // then unset any old setflag/map assigned to that style first
+ // if sub-style only allows one pair coeff call (with * * and type mapping)
+ // then unset setflag/map assigned to that style before setting it below
// in case pair coeff for this sub-style is being called for 2nd time
- if (styles[m] && styles[m]->one_coeff)
+ if (!none && styles[m]->one_coeff)
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
- if (map[i][j] == m) {
- map[i][j] = -1;
+ if (nmap[i][j] && map[i][j][0] == m) {
setflag[i][j] = 0;
+ nmap[i][j] = 0;
}
- // set hybrid map & setflag only if substyle set its setflag
- // if sub-style is NULL for "none", still set setflag
+ // set setflag and which type pairs map to which sub-style
+ // if sub-style is none: set hybrid subflag, wipe out map
+ // else: set hybrid setflag & map only if substyle setflag is set
+ // previous mappings are wiped out
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
- if (styles[m] == NULL || styles[m]->setflag[i][j]) {
- map[i][j] = m;
+ if (none) {
setflag[i][j] = 1;
+ nmap[i][j] = 0;
+ count++;
+ } else if (styles[m]->setflag[i][j]) {
+ setflag[i][j] = 1;
+ nmap[i][j] = 1;
+ map[i][j][0] = m;
count++;
}
}
@@ -526,54 +264,169 @@ void PairHybrid::coeff(int narg, char **arg)
}
/* ----------------------------------------------------------------------
- init for one type pair i,j and corresponding j,i
+ init specific to this pair style
------------------------------------------------------------------------- */
-double PairHybrid::init_one(int i, int j)
+void PairHybrid::init_style()
{
- // if i,j is set explicity, call its sub-style
- // if i,j is not set and i,i sub-style = j,j sub-style
- // then set map[i][j] to this sub-style and call sub-style for init/mixing
- // else i,j has not been set by user
- // check for special case = style none
-
- double cut = 0.0;
- if (setflag[i][j]) {
- if (styles[map[i][j]]) {
- cut = styles[map[i][j]]->init_one(i,j);
- styles[map[i][j]]->cutsq[i][j] =
- styles[map[i][j]]->cutsq[j][i] = cut*cut;
- if (tail_flag) {
- etail_ij = styles[map[i][j]]->etail_ij;
- ptail_ij = styles[map[i][j]]->ptail_ij;
+ int i,m,itype,jtype,used,istyle,skip;
+
+ // error if a sub-style is not used
+
+ int ntypes = atom->ntypes;
+
+ for (istyle = 0; istyle < nstyles; istyle++) {
+ used = 0;
+ for (itype = 1; itype <= ntypes; itype++)
+ for (jtype = itype; jtype <= ntypes; jtype++)
+ for (m = 0; m < nmap[itype][jtype]; m++)
+ if (map[itype][jtype][m] == istyle) used = 1;
+ if (used == 0) error->all("Pair hybrid sub-style is not used");
+ }
+
+ // each sub-style makes its neighbor list request(s)
+
+ for (istyle = 0; istyle < nstyles; istyle++) styles[istyle]->init_style();
+
+ // create skip lists for each neigh request
+
+ for (i = 0; i < neighbor->nrequest; i++) {
+
+ // only relevant for half, full, gran, respaouter lists
+
+ if (neighbor->requests[i]->granhistory) continue;
+ if (neighbor->requests[i]->respamiddle) continue;
+ if (neighbor->requests[i]->respainner) continue;
+ if (neighbor->requests[i]->half_from_full) continue;
+
+ // find associated sub-style
+
+ for (istyle = 0; istyle < nstyles; istyle++)
+ if (styles[istyle] == neighbor->requests[i]->requestor) break;
+
+ // allocate iskip and ijskip
+ // initialize so as to skip all pair types
+ // set ijskip = 0 if type pair matches any entry in sub-style map
+ // set ijskip = 0 if mixing will assign type pair to this sub-style
+ // will occur if both I,I and J,J are assigned to single sub-style
+ // and sub-style for both I,I and J,J match istyle
+ // set iskip = 1 only if all ijskip for itype are 1
+
+ int *iskip = new int[ntypes+1];
+ int **ijskip = memory->create_2d_int_array(ntypes+1,ntypes+1,
+ "pair_hybrid:ijskip");
+
+ for (itype = 1; itype <= ntypes; itype++)
+ for (jtype = 1; jtype <= ntypes; jtype++)
+ ijskip[itype][jtype] = 1;
+
+ for (itype = 1; itype <= ntypes; itype++)
+ for (jtype = itype; jtype <= ntypes; jtype++) {
+ for (m = 0; m < nmap[itype][jtype]; m++)
+ if (map[itype][jtype][m] == istyle)
+ ijskip[itype][jtype] = ijskip[jtype][itype] = 0;
+ if (nmap[itype][itype] == 1 && map[itype][itype][0] == istyle &&
+ nmap[jtype][jtype] == 1 && map[jtype][jtype][0] == istyle)
+ ijskip[itype][jtype] = ijskip[jtype][itype] = 0;
}
+
+ for (itype = 1; itype <= ntypes; itype++) {
+ iskip[itype] = 1;
+ for (jtype = 1; jtype <= ntypes; jtype++)
+ if (ijskip[itype][jtype] == 0) iskip[itype] = 0;
}
- } else if (map[i][i] == map[j][j]) {
- map[i][j] = map[i][i];
- if (styles[map[i][j]]) {
- cut = styles[map[i][j]]->init_one(i,j);
- styles[map[i][j]]->cutsq[i][j] =
- styles[map[i][j]]->cutsq[j][i] = cut*cut;
- if (tail_flag) {
- etail_ij = styles[map[i][j]]->etail_ij;
- ptail_ij = styles[map[i][j]]->ptail_ij;
- }
+
+ // if any skipping occurs
+ // set request->skip and copy iskip and ijskip into request
+ // else delete iskip and ijskip
+
+ skip = 0;
+ for (itype = 1; itype <= ntypes; itype++)
+ for (jtype = 1; jtype <= ntypes; jtype++)
+ if (ijskip[itype][jtype] == 1) skip = 1;
+
+ if (skip) {
+ neighbor->requests[i]->skip = 1;
+ neighbor->requests[i]->iskip = iskip;
+ neighbor->requests[i]->ijskip = ijskip;
+ } else {
+ delete [] iskip;
+ memory->destroy_2d_int_array(ijskip);
}
- } else error->all("All pair coeffs are not set");
+ }
- map[j][i] = map[i][j];
+ // combine sub-style neigh list requests and create new ones if needed
- return cut;
+ modify_requests();
}
/* ----------------------------------------------------------------------
- init specific to this pair style
+ init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-void PairHybrid::init_style()
+double PairHybrid::init_one(int i, int j)
{
- for (int m = 0; m < nstyles; m++)
- if (styles[m]) styles[m]->init_style();
+ // if I,J is not set explicitly:
+ // perform mixing only if I,I sub-style = J,J sub-style
+ // also require I,I and J,J both are assigned to single sub-style
+
+ if (setflag[i][j] == 0) {
+ if (nmap[i][i] != 1 || nmap[j][j] != 1 || map[i][i][0] != map[j][j][0])
+ error->one("All pair coeffs are not set");
+ nmap[i][j] = 1;
+ map[i][j][0] = map[i][i][0];
+ }
+
+ // call init/mixing for all sub-styles of I,J
+ // set cutsq in sub-style just as pair::init_one() does
+ // sum tail corrections for I,J
+ // compute max cutoff
+ // if sub-style = none, cutmax of 0.0 will be returned
+
+ double cutmax = 0.0;
+ if (tail_flag) etail_ij = ptail_ij = 0.0;
+
+ for (int k = 0; k < nmap[i][j]; k++) {
+ map[j][i][k] = map[i][j][k];
+ double cut = styles[map[i][j][k]]->init_one(i,j);
+ styles[map[i][j][k]]->cutsq[i][j] =
+ styles[map[i][j][k]]->cutsq[j][i] = cut*cut;
+ if (tail_flag) {
+ etail_ij += styles[map[i][j][k]]->etail_ij;
+ ptail_ij += styles[map[i][j][k]]->ptail_ij;
+ }
+ cutmax = MAX(cutmax,cut);
+ }
+
+ return cutmax;
+}
+
+/* ----------------------------------------------------------------------
+ combine sub-style neigh list requests and create new ones if needed
+------------------------------------------------------------------------- */
+
+void PairHybrid::modify_requests()
+{
+ int i,j;
+
+ // if list is skip list, look for non-skip list of same kind
+ // if one exists, point at that one
+ // else make new non-skip request of same kind and point at that one
+
+ for (i = 0; i < neighbor->nrequest; i++) {
+ if (neighbor->requests[i]->skip == 0) continue;
+
+ for (j = 0; j < neighbor->nrequest; j++)
+ if (neighbor->requests[i]->same_kind(neighbor->requests[j]) &&
+ neighbor->requests[j]->skip == 0) break;
+
+ if (j < neighbor->nrequest) neighbor->requests[i]->otherlist = j;
+ else {
+ int irequest = neighbor->request(this);
+ neighbor->requests[irequest]->copy_kind(neighbor->requests[i]);
+ neighbor->requests[i]->otherlist = irequest;
+ }
+ }
}
/* ----------------------------------------------------------------------
@@ -584,14 +437,14 @@ void PairHybrid::write_restart(FILE *fp)
{
fwrite(&nstyles,sizeof(int),1,fp);
- // each sub-style writes its settings
+ // each sub-style writes its settings, but no coeff info
int n;
for (int m = 0; m < nstyles; m++) {
n = strlen(keywords[m]) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(keywords[m],sizeof(char),n,fp);
- if (styles[m]) styles[m]->write_restart_settings(fp);
+ styles[m]->write_restart_settings(fp);
}
}
@@ -601,8 +454,6 @@ void PairHybrid::write_restart(FILE *fp)
void PairHybrid::read_restart(FILE *fp)
{
- allocate();
-
int me = comm->me;
if (me == 0) fread(&nstyles,sizeof(int),1,fp);
MPI_Bcast(&nstyles,1,MPI_INT,0,world);
@@ -610,7 +461,8 @@ void PairHybrid::read_restart(FILE *fp)
styles = new Pair*[nstyles];
keywords = new char*[nstyles];
- // each sub-style is created via new_pair() and reads its settings
+ // each sub-style is created via new_pair()
+ // each reads its settings, but no coeff info
int n;
for (int m = 0; m < nstyles; m++) {
@@ -620,31 +472,56 @@ void PairHybrid::read_restart(FILE *fp)
if (me == 0) fread(keywords[m],sizeof(char),n,fp);
MPI_Bcast(keywords[m],n,MPI_CHAR,0,world);
styles[m] = force->new_pair(keywords[m]);
- if (styles[m]) styles[m]->read_restart_settings(fp);
+ styles[m]->read_restart_settings(fp);
}
}
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+ call sub-style to compute single interaction
+ since overlay could have multiple sub-styles, sum results explicitly
+------------------------------------------------------------------------- */
void PairHybrid::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
int eflag, One &one)
{
- if (map[itype][jtype] == -1)
+ if (nmap[itype][jtype] == 0)
error->one("Invoked pair single on pair style none");
- styles[map[itype][jtype]]->
- single(i,j,itype,jtype,rsq,factor_coul,factor_lj,eflag,one);
+ double fforce = 0.0;
+ double eng_vdwl = 0.0;
+ double eng_coul = 0.0;
+
+ for (int m = 0; m < nmap[itype][jtype]; m++) {
+ styles[map[itype][jtype][m]]->
+ single(i,j,itype,jtype,rsq,factor_coul,factor_lj,eflag,one);
+ fforce += one.fforce;
+ eng_vdwl += one.eng_vdwl;
+ eng_coul += one.eng_coul;
+ }
+
+ one.fforce = fforce;
+ one.eng_vdwl = eng_vdwl;
+ one.eng_coul = eng_coul;
}
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+ call sub-style to compute single embedding interaction
+ since overlay could have multiple sub-styles, sum results explicitly
+------------------------------------------------------------------------- */
void PairHybrid::single_embed(int i, int itype, double &phi)
{
- if (map[itype][itype] == -1)
+ if (nmap[itype][itype] == 0)
error->one("Invoked pair single on pair style none");
- styles[map[itype][itype]]->single_embed(i,itype,phi);
+ phi = 0.0;
+ double phi_single;
+
+ for (int m = 0; m < nmap[itype][itype]; m++) {
+ styles[map[itype][itype][m]]->single_embed(i,itype,phi_single);
+ phi += phi_single;
+ }
}
/* ----------------------------------------------------------------------
@@ -656,20 +533,16 @@ void PairHybrid::single_embed(int i, int itype, double &phi)
void PairHybrid::modify_params(int narg, char **arg)
{
Pair::modify_params(narg,arg);
- for (int m = 0; m < nstyles; m++)
- if (styles[m]) styles[m]->modify_params(narg,arg);
+ for (int m = 0; m < nstyles; m++) styles[m]->modify_params(narg,arg);
}
/* ----------------------------------------------------------------------
- memory usage of sub-style firstneigh, numneigh, neighbor list
- add in memory usage of each sub-style itself
+ memory usage of each sub-style
------------------------------------------------------------------------- */
int PairHybrid::memory_usage()
{
- int bytes = nstyles*maxlocal * (sizeof(int *) + sizeof(int));
- for (int m = 0; m < nstyles; m++) bytes += maxneigh[m] * sizeof(int);
- for (int m = 0; m < nstyles; m++)
- if (styles[m]) bytes += styles[m]->memory_usage();
+ int bytes = 0;
+ for (int m = 0; m < nstyles; m++) bytes += styles[m]->memory_usage();
return bytes;
}
diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h
index 2686e007300d1112820d3b5de24fdd9347663d2d..ab828a1d72b651a52428ac229fc791b7b2695d26 100644
--- a/src/pair_hybrid.h
+++ b/src/pair_hybrid.h
@@ -21,17 +21,17 @@ namespace LAMMPS_NS {
class PairHybrid : public Pair {
public:
- int nstyles; // # of different pair styles
- Pair **styles; // class list for each Pair style
- char **keywords; // sub-style name for each Pair style
+ int nstyles; // # of different sub-styles
+ Pair **styles; // list of Pair style classes
+ char **keywords; // style name of each Pair style
PairHybrid(class LAMMPS *);
~PairHybrid();
void compute(int, int);
void settings(int, char **);
- void coeff(int, char **);
- double init_one(int, int);
+ virtual void coeff(int, char **);
void init_style();
+ double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void single(int, int, int, int, double, double, double, int, One &);
@@ -39,24 +39,12 @@ class PairHybrid : public Pair {
void modify_params(int narg, char **arg);
int memory_usage();
- private:
- int **map; // which style each itype,jtype points to
-
- int *nnlist; // # of half neighs in sub-style neigh lists
- int *maxneigh; // max # of neighs sub-style lists can store
- int **nlist; // half neigh list for each sub-style
-
- int *nnlist_full; // # of full neighs in sub-style neigh lists
- int *maxneigh_full; // max # of neighs sub-style lists can store
- int **nlist_full; // full neigh list for each sub-style
-
- int ***firstneigh; // each sub-style's per-atom firstneigh
- int **numneigh; // each sub-style's per-atom numneigh
- int ***firstneigh_full; // each sub-style's per-atom firstneigh_full
- int **numneigh_full; // each sub-style's per-atom numneigh_full
- int maxlocal; // max length of each ss's firstneigh,numneigh
+ protected:
+ int **nmap; // # of sub-styles itype,jtype points to
+ int ***map; // list of sub-styles itype,jtype points to
void allocate();
+ virtual void modify_requests();
};
}
diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp
index dc342a13b70c9e7d7aaa83d8262cfbab85565ed1..af2743af5c1d7890462748509122b5d91e64f14b 100644
--- a/src/pair_lj_cut.cpp
+++ b/src/pair_lj_cut.cpp
@@ -24,6 +24,8 @@
#include "comm.h"
#include "force.h"
#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
@@ -65,36 +67,40 @@ PairLJCut::~PairLJCut()
void PairLJCut::compute(int eflag, int vflag)
{
- int i,j,k,numneigh,itype,jtype;
+ int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcelj,fforce,factor_lj,philj;
- int *neighs;
- double **f;
+ int *ilist,*jlist,*numneigh,**firstneigh;
eng_vdwl = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
- if (vflag == 2) f = update->f_pair;
- else f = atom->f;
double **x = atom->x;
+ double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
// loop over neighbors of my atoms
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
- neighs = neighbor->firstneigh[i];
- numneigh = neighbor->numneigh[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
@@ -149,21 +155,24 @@ void PairLJCut::compute(int eflag, int vflag)
void PairLJCut::compute_inner()
{
- int i,j,k,numneigh,itype,jtype;
+ int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
- double rsq,r2inv,r6inv,forcelj,fforce,factor_lj;
- double rsw;
- int *neighs;
- double **f;
+ double rsq,r2inv,r6inv,forcelj,fforce,factor_lj,rsw;
+ int *ilist,*jlist,*numneigh,**firstneigh;
- f = atom->f;
double **x = atom->x;
+ double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
+ inum = listinner->inum;
+ ilist = listinner->ilist;
+ numneigh = listinner->numneigh;
+ firstneigh = listinner->firstneigh;
+
double cut_out_on = cut_respa[0];
double cut_out_off = cut_respa[1];
@@ -173,16 +182,17 @@ void PairLJCut::compute_inner()
// loop over neighbors of my atoms
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
- neighs = neighbor->firstneigh_inner[i];
- numneigh = neighbor->numneigh_inner[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
@@ -223,21 +233,24 @@ void PairLJCut::compute_inner()
void PairLJCut::compute_middle()
{
- int i,j,k,numneigh,itype,jtype;
+ int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
- double rsq,r2inv,r6inv,forcelj,fforce,factor_lj;
- double rsw;
- int *neighs;
- double **f;
+ double rsq,r2inv,r6inv,forcelj,fforce,factor_lj,rsw;
+ int *ilist,*jlist,*numneigh,**firstneigh;
- f = atom->f;
double **x = atom->x;
+ double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
+ inum = listmiddle->inum;
+ ilist = listmiddle->ilist;
+ numneigh = listmiddle->numneigh;
+ firstneigh = listmiddle->firstneigh;
+
double cut_in_off = cut_respa[0];
double cut_in_on = cut_respa[1];
double cut_out_on = cut_respa[2];
@@ -252,16 +265,17 @@ void PairLJCut::compute_middle()
// loop over neighbors of my atoms
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
- neighs = neighbor->firstneigh_middle[i];
- numneigh = neighbor->numneigh_middle[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
@@ -306,24 +320,27 @@ void PairLJCut::compute_middle()
void PairLJCut::compute_outer(int eflag, int vflag)
{
- int i,j,k,numneigh,itype,jtype;
+ int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
- double rsq,r2inv,r6inv,forcelj,fforce,factor_lj,philj;
- double rsw;
- int *neighs;
- double **f;
+ double rsq,r2inv,r6inv,forcelj,fforce,factor_lj,philj,rsw;
+ int *ilist,*jlist,*numneigh,**firstneigh;
eng_vdwl = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
- f = atom->f;
double **x = atom->x;
+ double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
+ inum = listouter->inum;
+ ilist = listouter->ilist;
+ numneigh = listouter->numneigh;
+ firstneigh = listouter->firstneigh;
+
double cut_in_off = cut_respa[2];
double cut_in_on = cut_respa[3];
@@ -333,16 +350,17 @@ void PairLJCut::compute_outer(int eflag, int vflag)
// loop over neighbors of my atoms
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
- neighs = neighbor->firstneigh[i];
- numneigh = neighbor->numneigh[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
@@ -487,6 +505,62 @@ void PairLJCut::coeff(int narg, char **arg)
if (count == 0) error->all("Incorrect args for pair coefficients");
}
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairLJCut::init_style()
+{
+ // request regular or rRESPA neighbor lists
+
+ int irequest;
+
+ if (update->whichflag == 0 && strcmp(update->integrate_style,"respa") == 0) {
+ int respa = 0;
+ if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
+ if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
+
+ if (respa == 0) irequest = neighbor->request(this);
+ else if (respa == 1) {
+ irequest = neighbor->request(this);
+ neighbor->requests[irequest]->id = 1;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->respainner = 1;
+ irequest = neighbor->request(this);
+ neighbor->requests[irequest]->id = 3;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->respaouter = 1;
+ } else {
+ irequest = neighbor->request(this);
+ neighbor->requests[irequest]->id = 1;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->respainner = 1;
+ irequest = neighbor->request(this);
+ neighbor->requests[irequest]->id = 2;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->respamiddle = 1;
+ irequest = neighbor->request(this);
+ neighbor->requests[irequest]->id = 3;
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->respaouter = 1;
+ }
+
+ } else irequest = neighbor->request(this);
+}
+
+/* ----------------------------------------------------------------------
+ neighbor callback to inform pair style of neighbor list to use
+ regular or rRESPA
+------------------------------------------------------------------------- */
+
+void PairLJCut::init_list(int id, NeighList *ptr)
+{
+ if (id == 0) list = ptr;
+ else if (id == 1) listinner = ptr;
+ else if (id == 2) listmiddle = ptr;
+ else if (id == 3) listouter = ptr;
+}
+
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
diff --git a/src/pair_lj_cut.h b/src/pair_lj_cut.h
index e89a4d0bddd6951362c89a69c29c101fa3071cf7..a91dec05ab956e0383f4ddae39a8c521a66774e2 100644
--- a/src/pair_lj_cut.h
+++ b/src/pair_lj_cut.h
@@ -25,6 +25,8 @@ class PairLJCut : public Pair {
void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
+ void init_style();
+ void init_list(int, class NeighList *);
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp
index 9993f0edd7754cb9f0be99476bedef4147cbdf51..5c0d08a4dba0de28549c86c73046bb3402ad2ca4 100644
--- a/src/pair_lj_cut_coul_cut.cpp
+++ b/src/pair_lj_cut_coul_cut.cpp
@@ -19,9 +19,9 @@
#include "atom.h"
#include "comm.h"
#include "force.h"
-#include "update.h"
-#include "memory.h"
#include "neighbor.h"
+#include "neigh_list.h"
+#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -59,19 +59,17 @@ PairLJCutCoulCut::~PairLJCutCoulCut()
void PairLJCutCoulCut::compute(int eflag, int vflag)
{
- int i,j,k,numneigh,itype,jtype;
+ int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcecoul,forcelj,fforce,factor_coul,factor_lj;
double factor,phicoul,philj;
- int *neighs;
- double **f;
+ int *ilist,*jlist,*numneigh,**firstneigh;
eng_vdwl = eng_coul = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
- if (vflag == 2) f = update->f_pair;
- else f = atom->f;
double **x = atom->x;
+ double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
@@ -81,19 +79,25 @@ void PairLJCutCoulCut::compute(int eflag, int vflag)
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
// loop over neighbors of my atoms
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
- neighs = neighbor->firstneigh[i];
- numneigh = neighbor->numneigh[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
@@ -250,6 +254,18 @@ void PairLJCutCoulCut::coeff(int narg, char **arg)
if (count == 0) error->all("Incorrect args for pair coefficients");
}
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairLJCutCoulCut::init_style()
+{
+ if (!atom->q_flag)
+ error->all("Pair style lj/cut/coul/cut requires atom attribute q");
+
+ int irequest = neighbor->request(this);
+}
+
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
@@ -316,16 +332,6 @@ double PairLJCutCoulCut::init_one(int i, int j)
return cut;
}
-/* ----------------------------------------------------------------------
- init specific to this pair style
-------------------------------------------------------------------------- */
-
-void PairLJCutCoulCut::init_style()
-{
- if (!atom->q_flag)
- error->all("Pair style lj/cut/coul/cut requires atom attribute q");
-}
-
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
diff --git a/src/pair_lj_cut_coul_cut.h b/src/pair_lj_cut_coul_cut.h
index 8e027e5ac9ac04091c176a3f25f8a9b0bb12080e..8af68331cbdc927aa738a47ba749bbb5d1458097 100644
--- a/src/pair_lj_cut_coul_cut.h
+++ b/src/pair_lj_cut_coul_cut.h
@@ -25,8 +25,8 @@ class PairLJCutCoulCut : public Pair {
virtual void compute(int, int);
virtual void settings(int, char **);
void coeff(int, char **);
- double init_one(int, int);
void init_style();
+ double init_one(int, int);
virtual void write_restart(FILE *);
virtual void read_restart(FILE *);
virtual void write_restart_settings(FILE *);
diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/pair_lj_cut_coul_debye.cpp
index 4331a11e612c9e94625eb60445a523b9c712c35c..f4c28e6dba23dff225c06feb7b01a5331d038eb1 100644
--- a/src/pair_lj_cut_coul_debye.cpp
+++ b/src/pair_lj_cut_coul_debye.cpp
@@ -15,10 +15,9 @@
#include "stdlib.h"
#include "pair_lj_cut_coul_debye.h"
#include "atom.h"
-#include "neighbor.h"
+#include "neigh_list.h"
#include "force.h"
#include "comm.h"
-#include "update.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -31,20 +30,18 @@ PairLJCutCoulDebye::PairLJCutCoulDebye(LAMMPS *lmp) : PairLJCutCoulCut(lmp) {}
void PairLJCutCoulDebye::compute(int eflag, int vflag)
{
- int i,j,k,numneigh,itype,jtype;
+ int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcecoul,forcelj,fforce,factor_coul,factor_lj;
double factor,phicoul,philj;
double r,rinv,screening;
- int *neighs;
- double **f;
+ int *ilist,*jlist,*numneigh,**firstneigh;
eng_vdwl = eng_coul = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
- if (vflag == 2) f = update->f_pair;
- else f = atom->f;
double **x = atom->x;
+ double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
@@ -54,19 +51,25 @@ void PairLJCutCoulDebye::compute(int eflag, int vflag)
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
// loop over neighbors of my atoms
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
- neighs = neighbor->firstneigh[i];
- numneigh = neighbor->numneigh[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp
index 3050307ead8ecb9629c054b9dd698bb826b6b63d..f43d8d62bfcd9ef99084e8c78289944c933ec257 100644
--- a/src/pair_lj_expand.cpp
+++ b/src/pair_lj_expand.cpp
@@ -18,9 +18,8 @@
#include "atom.h"
#include "comm.h"
#include "force.h"
-#include "update.h"
+#include "neigh_list.h"
#include "memory.h"
-#include "neighbor.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -56,37 +55,41 @@ PairLJExpand::~PairLJExpand()
void PairLJExpand::compute(int eflag, int vflag)
{
- int i,j,k,numneigh,itype,jtype;
+ int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,forcelj,fforce,factor_lj,philj;
double r,rshift,rshiftsq;
- int *neighs;
- double **f;
+ int *ilist,*jlist,*numneigh,**firstneigh;
eng_vdwl = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
- if (vflag == 2) f = update->f_pair;
- else f = atom->f;
double **x = atom->x;
+ double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
// loop over neighbors of my atoms
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
- neighs = neighbor->firstneigh[i];
- numneigh = neighbor->numneigh[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp
index 0ee2c06649f6bb881d36f5722a6300a576d1a07e..5a70395d24a0948e64c244c9024b9a04af42e277 100644
--- a/src/pair_lj_smooth.cpp
+++ b/src/pair_lj_smooth.cpp
@@ -22,8 +22,7 @@
#include "atom.h"
#include "comm.h"
#include "force.h"
-#include "neighbor.h"
-#include "update.h"
+#include "neigh_list.h"
#include "memory.h"
#include "error.h"
@@ -66,38 +65,42 @@ PairLJSmooth::~PairLJSmooth()
void PairLJSmooth::compute(int eflag, int vflag)
{
- int i,j,k,numneigh,itype,jtype;
+ int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r6inv,r,forcelj,fforce,factor_lj,philj;
double t,tsq,fskin;
- int *neighs;
- double **f;
+ int *ilist,*jlist,*numneigh,**firstneigh;
eng_vdwl = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
- if (vflag == 2) f = update->f_pair;
- else f = atom->f;
double **x = atom->x;
+ double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
- // loop over neighbors of my atoms
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
- for (i = 0; i < nlocal; i++) {
+ // loop over neighbors of my atoms
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
- neighs = neighbor->firstneigh[i];
- numneigh = neighbor->numneigh[i];
-
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
-
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp
index f09d29c509554e886af2f9134752c774fc191c14..66cc36ec0175b1d76f7675af465ea43ebbaf9f63 100644
--- a/src/pair_morse.cpp
+++ b/src/pair_morse.cpp
@@ -18,9 +18,8 @@
#include "atom.h"
#include "comm.h"
#include "force.h"
-#include "update.h"
+#include "neigh_list.h"
#include "memory.h"
-#include "neighbor.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -53,36 +52,40 @@ PairMorse::~PairMorse()
void PairMorse::compute(int eflag, int vflag)
{
- int i,j,k,numneigh,itype,jtype;
+ int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r,dr,dexp,fforce,factor_lj,phi;
- int *neighs;
- double **f;
+ int *ilist,*jlist,*numneigh,**firstneigh;
eng_vdwl = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
- if (vflag == 2) f = update->f_pair;
- else f = atom->f;
double **x = atom->x;
+ double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
// loop over neighbors of my atoms
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
- neighs = neighbor->firstneigh[i];
- numneigh = neighbor->numneigh[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp
index 744c77795299dcdff3e95953791127c436f24b83..afd46c6dfdfaa09d17e4320f72a8759dca0095f6 100644
--- a/src/pair_soft.cpp
+++ b/src/pair_soft.cpp
@@ -19,8 +19,8 @@
#include "comm.h"
#include "force.h"
#include "update.h"
+#include "neigh_list.h"
#include "memory.h"
-#include "neighbor.h"
#include "error.h"
using namespace LAMMPS_NS;
@@ -54,11 +54,10 @@ PairSoft::~PairSoft()
void PairSoft::compute(int eflag, int vflag)
{
- int i,j,k,numneigh,itype,jtype;
+ int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double r,rsq,arg,fforce,factor_lj,philj;
- int *neighs;
- double **f;
+ int *ilist,*jlist,*numneigh,**firstneigh;
// set current prefactor
// for minimization, set to prestop
@@ -78,27 +77,32 @@ void PairSoft::compute(int eflag, int vflag)
eng_vdwl = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
- if (vflag == 2) f = update->f_pair;
- else f = atom->f;
double **x = atom->x;
+ double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
// loop over neighbors of my atoms
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
- neighs = neighbor->firstneigh[i];
- numneigh = neighbor->numneigh[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
diff --git a/src/pair_table.cpp b/src/pair_table.cpp
index 7972d42db53e4d7fb3584309533e864b9565bfa2..f59a20d1ea5b09afb87d31a370045997dd5c1bf0 100644
--- a/src/pair_table.cpp
+++ b/src/pair_table.cpp
@@ -22,9 +22,8 @@
#include "pair_table.h"
#include "atom.h"
#include "force.h"
-#include "update.h"
#include "comm.h"
-#include "neighbor.h"
+#include "neigh_list.h"
#include "memory.h"
#include "error.h"
@@ -70,11 +69,10 @@ PairTable::~PairTable()
void PairTable::compute(int eflag, int vflag)
{
- int i,j,k,numneigh,itype,jtype,itable;
+ int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double fforce,factor_lj,phi,fraction,value,a,b;
- int *neighs;
- double **f;
+ int *ilist,*jlist,*numneigh,**firstneigh;
Table *tb;
float rsq_single;
int *int_rsq = (int *) &rsq_single;
@@ -82,27 +80,32 @@ void PairTable::compute(int eflag, int vflag)
eng_vdwl = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
- if (vflag == 2) f = update->f_pair;
- else f = atom->f;
double **x = atom->x;
+ double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
// loop over neighbors of my atoms
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
- neighs = neighbor->firstneigh[i];
- numneigh = neighbor->numneigh[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp
index b6db7c04e297e1b2b4e4910ac9dddfdbfd7bcc04..f709917477362a9b60af6f8dd7f5da358847b4f4 100644
--- a/src/pair_yukawa.cpp
+++ b/src/pair_yukawa.cpp
@@ -15,10 +15,9 @@
#include "stdlib.h"
#include "pair_yukawa.h"
#include "atom.h"
-#include "neighbor.h"
#include "force.h"
#include "comm.h"
-#include "update.h"
+#include "neigh_list.h"
#include "memory.h"
#include "error.h"
@@ -50,36 +49,40 @@ PairYukawa::~PairYukawa()
void PairYukawa::compute(int eflag, int vflag)
{
- int i,j,k,numneigh,itype,jtype;
+ int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,r2inv,r,rinv,screening,forceyukawa,fforce,factor_coul,phi;
- int *neighs;
- double **f;
+ int *ilist,*jlist,*numneigh,**firstneigh;
eng_coul = 0.0;
if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
- if (vflag == 2) f = update->f_pair;
- else f = atom->f;
double **x = atom->x;
+ double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
// loop over neighbors of my atoms
- for (i = 0; i < nlocal; i++) {
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
- neighs = neighbor->firstneigh[i];
- numneigh = neighbor->numneigh[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
- for (k = 0; k < numneigh; k++) {
- j = neighs[k];
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
if (j < nall) factor_coul = 1.0;
else {
diff --git a/src/respa.cpp b/src/respa.cpp
index 39a66cb9411440e7aac03ad9795a8c5fc37036e5..3ba4a4f6defe691fdc3f1551eb1fc732442454c7 100644
--- a/src/respa.cpp
+++ b/src/respa.cpp
@@ -255,9 +255,9 @@ void Respa::init()
// will delete it at end of run
char **fixarg = new char*[4];
- fixarg[0] = "RESPA";
- fixarg[1] = "all";
- fixarg[2] = "RESPA";
+ fixarg[0] = (char *) "RESPA";
+ fixarg[1] = (char *) "all";
+ fixarg[2] = (char *) "RESPA";
fixarg[3] = new char[8];
sprintf(fixarg[3],"%d",nlevels);
modify->add_fix(4,fixarg);
diff --git a/src/style.h b/src/style.h
index 43f44000ca9f9bfd003f7008e76740b7e2b28185..9cdf05bac74416600a08332dd3409f4365578a64 100644
--- a/src/style.h
+++ b/src/style.h
@@ -76,16 +76,17 @@ CommandStyle(write_restart,WriteRestart)
#endif
#ifdef ComputeInclude
+#include "compute_attribute_atom.h"
#include "compute_centro_atom.h"
#include "compute_coord_atom.h"
#include "compute_ebond_atom.h"
#include "compute_epair_atom.h"
-#include "compute_etotal_atom.h"
#include "compute_ke_atom.h"
#include "compute_pressure.h"
#include "compute_rotate_dipole.h"
#include "compute_rotate_gran.h"
#include "compute_stress_atom.h"
+#include "compute_sum_atom.h"
#include "compute_temp.h"
#include "compute_temp_deform.h"
#include "compute_temp_partial.h"
@@ -96,16 +97,17 @@ CommandStyle(write_restart,WriteRestart)
#endif
#ifdef ComputeClass
+ComputeStyle(attribute/atom,ComputeAttributeAtom)
ComputeStyle(centro/atom,ComputeCentroAtom)
ComputeStyle(coord/atom,ComputeCoordAtom)
ComputeStyle(ebond/atom,ComputeEbondAtom)
ComputeStyle(epair/atom,ComputeEpairAtom)
-ComputeStyle(etotal/atom,ComputeEtotalAtom)
ComputeStyle(ke/atom,ComputeKEAtom)
ComputeStyle(pressure,ComputePressure)
ComputeStyle(rotate/dipole,ComputeRotateDipole)
ComputeStyle(rotate/gran,ComputeRotateGran)
ComputeStyle(stress/atom,ComputeStressAtom)
+ComputeStyle(sum/atom,ComputeSumAtom)
ComputeStyle(temp,ComputeTemp)
ComputeStyle(temp/deform,ComputeTempDeform)
ComputeStyle(temp/partial,ComputeTempPartial)
@@ -137,6 +139,7 @@ DumpStyle(xyz,DumpXYZ)
#ifdef FixInclude
#include "fix_add_force.h"
+#include "fix_ave_atom.h"
#include "fix_ave_force.h"
#include "fix_ave_spatial.h"
#include "fix_ave_time.h"
@@ -186,6 +189,7 @@ DumpStyle(xyz,DumpXYZ)
#ifdef FixClass
FixStyle(addforce,FixAddForce)
+FixStyle(ave/atom,FixAveAtom)
FixStyle(aveforce,FixAveForce)
FixStyle(ave/spatial,FixAveSpatial)
FixStyle(ave/time,FixAveTime)
@@ -270,7 +274,9 @@ MinimizeStyle(sd,MinSD)
#ifdef PairInclude
#include "pair_buck.h"
#include "pair_buck_coul_cut.h"
+#include "pair_coul_cut.h"
#include "pair_hybrid.h"
+#include "pair_hybrid_overlay.h"
#include "pair_lj_cut.h"
#include "pair_lj_cut_coul_cut.h"
#include "pair_lj_cut_coul_debye.h"
@@ -285,7 +291,9 @@ MinimizeStyle(sd,MinSD)
#ifdef PairClass
PairStyle(buck,PairBuck)
PairStyle(buck/coul/cut,PairBuckCoulCut)
+PairStyle(coul/cut,PairCoulCut)
PairStyle(hybrid,PairHybrid)
+PairStyle(hybrid/overlay,PairHybridOverlay)
PairStyle(lj/cut,PairLJCut)
PairStyle(lj/cut/coul/cut,PairLJCutCoulCut)
PairStyle(lj/cut/coul/debye,PairLJCutCoulDebye)
@@ -315,7 +323,7 @@ RegionStyle(sphere,RegSphere)
RegionStyle(union,RegUnion)
#endif
-// style files for optional packages
+// style files for standard packages
#include "style_asphere.h"
#include "style_class2.h"
@@ -331,8 +339,7 @@ RegionStyle(union,RegUnion)
#include "style_poems.h"
#include "style_xtc.h"
-//#include "style_extra.h"
-
-// user add-ons
+// user add-ons: individual classes and packages
#include "style_user.h"
+#include "style_user_packages.h"
diff --git a/src/style_kspace.h b/src/style_kspace.h
index 52cae87bdb42ae3534b1c694b7fb9bbf1feb0d5c..8c7244afb9d3684fbbe0e51a1e6dd3cfe7f55bdb 100644
--- a/src/style_kspace.h
+++ b/src/style_kspace.h
@@ -25,6 +25,7 @@ KSpaceStyle(pppm/tip4p,PPPMTIP4P)
#ifdef PairInclude
#include "pair_buck_coul_long.h"
+#include "pair_coul_long.h"
#include "pair_lj_cut_coul_long.h"
#include "pair_lj_cut_coul_long_tip4p.h"
#include "pair_lj_charmm_coul_long.h"
@@ -32,6 +33,7 @@ KSpaceStyle(pppm/tip4p,PPPMTIP4P)
#ifdef PairClass
PairStyle(buck/coul/long,PairBuckCoulLong)
+PairStyle(coul/long,PairCoulLong)
PairStyle(lj/cut/coul/long,PairLJCutCoulLong)
PairStyle(lj/cut/coul/long/tip4p,PairLJCutCoulLongTIP4P)
PairStyle(lj/charmm/coul/long,PairLJCharmmCoulLong)
diff --git a/src/style_user.h b/src/style_user.h
index b4eeb828b4e385b477ed32b588cfd3e34f2742cf..cb024f6ee921119148ee9e731f4e2556b58a8912 100644
--- a/src/style_user.h
+++ b/src/style_user.h
@@ -11,6 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
+// add a style class to LAMMPS by adding 2 lines to this file
// add new include files in appropriate Include ifdef
// add new style keywords and class names in appropriate Class ifdef
// see style.h for examples
@@ -73,7 +74,7 @@
#endif
#ifdef IntegrateClass
-#endif
+# endif
#ifdef KSpaceInclude
#endif
@@ -85,7 +86,7 @@
#endif
#ifdef MinimizeClass
-# endif
+#endif
#ifdef PairInclude
#endif
diff --git a/src/thermo.cpp b/src/thermo.cpp
index 9898059454d389e0df93d50734625edf39f5c486..33f47619bca93e1c350500b358a127dc21667cc6 100644
--- a/src/thermo.cpp
+++ b/src/thermo.cpp
@@ -120,10 +120,10 @@ Thermo::Thermo(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
index_temp = index_press = index_drot = index_grot = -1;
internal_drot = internal_grot = 0;
- id_temp = "thermo_temp";
- id_press = "thermo_pressure";
- id_drot = "thermo_rotate_dipole";
- id_grot = "thermo_rotate_gran";
+ id_temp = (char *) "thermo_temp";
+ id_press = (char *) "thermo_pressure";
+ id_drot = (char *) "thermo_rotate_dipole";
+ id_grot = (char *) "thermo_rotate_gran";
// count fields in line
// allocate per-field memory
@@ -137,22 +137,22 @@ Thermo::Thermo(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
// temperature and pressure always exist b/c Output class created them
if (index_drot >= 0) {
- create_compute(id_drot,"rotate/dipole",NULL);
+ create_compute(id_drot,(char *) "rotate/dipole",NULL);
internal_drot = 1;
}
if (index_grot >= 0) {
- create_compute(id_grot,"rotate/gran",NULL);
+ create_compute(id_grot,(char *) "rotate/gran",NULL);
internal_grot = 1;
}
// format strings
- format_multi = "---------------- Step %8d ----- "
- "CPU = %11.4f (sec) ----------------";
- format_int_one_def = "%8d";
- format_int_multi_def = "%14d";
- format_g_def = "%12.8g";
- format_f_def = "%14.4f";
+ format_multi = (char *) "---------------- Step %8d ----- "
+ "CPU = %11.4f (sec) ----------------";
+ format_int_one_def = (char *) "%8d";
+ format_int_multi_def = (char *) "%14d";
+ format_g_def = (char *) "%12.8g";
+ format_f_def = (char *) "%14.4f";
format_int_user = NULL;
format_float_user = NULL;
@@ -398,17 +398,17 @@ void Thermo::modify_params(int narg, char **arg)
if (temperature->igroup != 0 && comm->me == 0)
error->warning("Temperature for thermo pressure is not for group all");
- // reset id_pre of pressure to new temp ID
+ // reset id_pre[0] of pressure to new temp ID
// either pressure currently being used by thermo or "thermo_pressure"
if (index_press >= 0) {
icompute = modify->find_compute(id_compute[index_press]);
if (icompute < 0) error->all("Press ID for thermo does not exist");
- } else icompute = modify->find_compute("thermo_pressure");
+ } else icompute = modify->find_compute((char *) "thermo_pressure");
- delete [] modify->compute[icompute]->id_pre;
- modify->compute[icompute]->id_pre = new char[n];
- strcpy(modify->compute[icompute]->id_pre,arg[iarg+1]);
+ delete [] modify->compute[icompute]->id_pre[0];
+ modify->compute[icompute]->id_pre[0] = new char[n];
+ strcpy(modify->compute[icompute]->id_pre[0],arg[iarg+1]);
iarg += 2;
@@ -427,13 +427,13 @@ void Thermo::modify_params(int narg, char **arg)
if (pressure->pressflag == 0)
error->all("Thermo_modify press ID does not compute pressure");
- // if id_pre of new pressure is not being computed, add to compute list
- // swap it with pressure in list so id_pre will be computed first
+ // if id_pre[0] of new pressure not being computed, add to compute list
+ // swap it with pressure in list so id_pre[0] will be computed first
// OK to call add_compute with "which" acting as index
int which = compute_which[index_press];
int ncompute_current = ncompute;
- icompute = add_compute(pressure->id_pre,which);
+ icompute = add_compute(pressure->id_pre[0],which);
if (icompute == ncompute_current) {
int iswap = compute_which[index_press];
compute_which[index_press] = compute_which[icompute];
@@ -554,7 +554,6 @@ void Thermo::modify_params(int narg, char **arg)
/* ----------------------------------------------------------------------
allocate all per-field memory
- allow each c_ID to imply 2 Compute objects (if it has id_pre)
------------------------------------------------------------------------- */
void Thermo::allocate()
@@ -577,9 +576,9 @@ void Thermo::allocate()
arg_object = new int[n];
ncompute = 0;
- id_compute = new char*[2*n];
- compute_which = new int[2*n];
- computes = new Compute*[2*n];
+ id_compute = NULL;
+ compute_which = NULL;
+ computes = NULL;
nfix = 0;
id_fix = new char*[n];
@@ -611,9 +610,9 @@ void Thermo::deallocate()
delete [] arg_object;
for (int i = 0; i < ncompute; i++) delete [] id_compute[i];
- delete [] id_compute;
- delete [] compute_which;
- delete [] computes;
+ memory->sfree(id_compute);
+ memory->sfree(compute_which);
+ memory->sfree(computes);
for (int i = 0; i < nfix; i++) delete [] id_fix[i];
delete [] id_fix;
@@ -760,7 +759,7 @@ void Thermo::parse_fields(char *str)
// compute value = c_ID, fix value = f_ID, variable value = v_ID
// if no trailing [], then arg is set to 0, else arg is between []
// copy = at most 8 chars of ID to pass to addfield
- // for compute, if has pre-compute object, first add it to list
+ // if Compute has pre-computes, first add them to list
} else if ((strncmp(word,"c_",2) == 0) || (strncmp(word,"f_",2) == 0) ||
(strncmp(word,"v_",2) == 0)) {
@@ -790,8 +789,10 @@ void Thermo::parse_fields(char *str)
if (arg_object[nfield] > 0 &&
arg_object[nfield] > modify->compute[n]->size_vector)
error->all("Thermo compute ID vector is not large enough");
- if (modify->compute[n]->id_pre)
- int tmp = add_compute(modify->compute[n]->id_pre,arg_object[nfield]);
+ if (modify->compute[n]->npre)
+ for (int ic = 0; ic < modify->compute[n]->npre; ic++)
+ int tmp = add_compute(modify->compute[n]->id_pre[ic],
+ arg_object[nfield]);
field2object[nfield] = add_compute(id,arg_object[nfield]);
addfield(copy,&Thermo::compute_compute,FLOAT);
@@ -820,7 +821,7 @@ void Thermo::parse_fields(char *str)
add field to list of quantities to print
------------------------------------------------------------------------- */
-void Thermo::addfield(char *key, FnPtr func, int typeflag)
+void Thermo::addfield(const char *key, FnPtr func, int typeflag)
{
strcpy(keyword[nfield],key);
vfunc[nfield] = func;
@@ -830,13 +831,15 @@ void Thermo::addfield(char *key, FnPtr func, int typeflag)
/* ----------------------------------------------------------------------
add compute ID to list of Compute objects to call
- if already in list, do not add, just return location, else add to list
+ return index of where this Compute is in list
+ if already in list, do not add, just return index, else add to list
convert index into which param
index = 0 -> scalar, index >= 1 -> vector
which = 1 -> scalar only, which = 2 -> vector only, which = 3 -> both
+ change which param if Compute is in list with different which param
------------------------------------------------------------------------- */
-int Thermo::add_compute(char *id, int index)
+int Thermo::add_compute(const char *id, int index)
{
int icompute;
for (icompute = 0; icompute < ncompute; icompute++)
@@ -849,6 +852,16 @@ int Thermo::add_compute(char *id, int index)
}
if (icompute < ncompute) return icompute;
+ id_compute = (char **)
+ memory->srealloc(id_compute,(ncompute+1)*sizeof(char *),
+ "thermo:id_compute");
+ compute_which = (int *)
+ memory->srealloc(compute_which,(ncompute+1)*sizeof(int),
+ "thermo:compute_which");
+ computes = (Compute **)
+ memory->srealloc(computes,(ncompute+1)*sizeof(Compute *),
+ "thermo:computes");
+
int n = strlen(id) + 1;
id_compute[ncompute] = new char[n];
strcpy(id_compute[ncompute],id);
@@ -862,7 +875,7 @@ int Thermo::add_compute(char *id, int index)
add fix ID to list of Fix objects to call
------------------------------------------------------------------------- */
-int Thermo::add_fix(char *id)
+int Thermo::add_fix(const char *id)
{
int n = strlen(id) + 1;
id_fix[nfix] = new char[n];
@@ -875,7 +888,7 @@ int Thermo::add_fix(char *id)
add variable ID to list of Variables to evaluate
------------------------------------------------------------------------- */
-int Thermo::add_variable(char *id)
+int Thermo::add_variable(const char *id)
{
int n = strlen(id) + 1;
id_variable[nvariable] = new char[n];
@@ -892,7 +905,7 @@ void Thermo::create_compute(char *id, char *cstyle, char *extra)
{
char **newarg = new char*[4];
newarg[0] = id;
- newarg[1] = "all";
+ newarg[1] = (char *) "all";
newarg[2] = cstyle;
if (extra) newarg[3] = extra;
if (extra) modify->add_compute(4,newarg);
diff --git a/src/thermo.h b/src/thermo.h
index d5e00ae106d28012eb11a2b9d5bb263c0661bd59..e1bf0f22d7e1b72ef9218e42c2258ff569ef9f28 100644
--- a/src/thermo.h
+++ b/src/thermo.h
@@ -100,13 +100,13 @@ class Thermo : protected Pointers {
void deallocate();
void parse_fields(char *);
- int add_compute(char *, int);
- int add_fix(char *);
- int add_variable(char *);
+ int add_compute(const char *, int);
+ int add_fix(const char *);
+ int add_variable(const char *);
void create_compute(char *, char *, char *);
typedef void (Thermo::*FnPtr)();
- void addfield(char *, FnPtr, int);
+ void addfield(const char *, FnPtr, int);
FnPtr *vfunc; // list of ptrs to functions
void compute_compute(); // functions that compute a single value
diff --git a/src/universe.cpp b/src/universe.cpp
index baa1266ecf302d619c827751cd62b4bc4cc1a82e..6a9d9db0bbc2da6e9e1079e5ed178d10534d6525 100644
--- a/src/universe.cpp
+++ b/src/universe.cpp
@@ -26,7 +26,7 @@ using namespace LAMMPS_NS;
Universe::Universe(LAMMPS *lmp, MPI_Comm communicator) : Pointers(lmp)
{
- version = "22 Jun 2007";
+ version = (char *) "22 Jun 2007";
uworld = communicator;
MPI_Comm_rank(uworld,&me);
diff --git a/src/update.cpp b/src/update.cpp
index d24d580c66bf5d473720f033242550105558fffc..a3b7879483ea4fca55acedba3488af6dd6b2fb50 100644
--- a/src/update.cpp
+++ b/src/update.cpp
@@ -41,19 +41,16 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp)
firststep = laststep = 0;
beginstep = endstep = 0;
- maxpair = 0;
- f_pair = NULL;
-
unit_style = NULL;
set_units("lj");
- str = "verlet";
+ str = (char *) "verlet";
n = strlen(str) + 1;
integrate_style = new char[n];
strcpy(integrate_style,str);
integrate = new Verlet(lmp,0,NULL);
- str = "cg";
+ str = (char *) "cg";
n = strlen(str) + 1;
minimize_style = new char[n];
strcpy(minimize_style,str);
@@ -64,8 +61,6 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp)
Update::~Update()
{
- memory->destroy_2d_double_array(f_pair);
-
delete [] unit_style;
delete [] integrate_style;
@@ -93,7 +88,7 @@ void Update::init()
/* ---------------------------------------------------------------------- */
-void Update::set_units(char *style)
+void Update::set_units(const char *style)
{
// physical constants from:
// http://physics.nist.gov/cuu/Constants/Table/allascii.txt
@@ -190,7 +185,7 @@ void Update::create_minimize(int narg, char **arg)
int Update::memory_usage()
{
- int bytes = maxpair*3 * sizeof(double);
+ int bytes = 0;
if (whichflag == 0) bytes += integrate->memory_usage();
else if (whichflag == 1) bytes += minimize->memory_usage();
return bytes;
diff --git a/src/update.h b/src/update.h
index b28c35b279b4a36e55e81738e09724c41b9c9002..0373bf69030c9e807826a17b597bdb086e2e73df 100644
--- a/src/update.h
+++ b/src/update.h
@@ -30,9 +30,6 @@ class Update : protected Pointers {
int first_update; // 0 before initial update, 1 after
int max_eval; // max force evaluations for minimizer
- double **f_pair; // used by pair to compute force & virial
- int maxpair;
-
char *unit_style;
class Integrate *integrate;
@@ -44,7 +41,7 @@ class Update : protected Pointers {
Update(class LAMMPS *);
~Update();
void init();
- void set_units(char *);
+ void set_units(const char *);
void create_integrate(int, char **);
void create_minimize(int, char **);
int memory_usage();
diff --git a/src/variable.cpp b/src/variable.cpp
index e920ad4be18603ee0c5a21f8b16b3a853098ca85..cb7311647f4fe3325b195b3c3b38b28941ff946a 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -217,7 +217,7 @@ void Variable::set(char *name, char *value)
{
char **newarg = new char*[3];
newarg[0] = name;
- newarg[1] = "index";
+ newarg[1] = (char *) "index";
newarg[2] = value;
set(3,newarg);
delete [] newarg;
@@ -697,28 +697,32 @@ double Variable::evaluate(char *str, Tree *tree)
modify->compute[icompute]->init();
// call compute() if index = 0, else compute_vector()
- // make pre-call to Compute object's id_pre if it is defined
+ // make pre-call to Compute object's pre-compute(s) if defined
int index = atoi(arg);
if (index == 0) {
if (modify->compute[icompute]->scalar_flag == 0)
error->all("Variable compute ID does not compute scalar info");
- if (modify->compute[icompute]->id_pre) {
- int ipre = modify->find_compute(modify->compute[icompute]->id_pre);
- if (ipre < 0) error->all("Could not pre-compute in variable");
- answer = modify->compute[ipre]->compute_scalar();
- }
+ if (modify->compute[icompute]->npre)
+ for (int ic = 0; ic < modify->compute[icompute]->npre; ic++) {
+ int ipre =
+ modify->find_compute(modify->compute[icompute]->id_pre[ic]);
+ if (ipre < 0) error->all("Could not pre-compute in variable");
+ double tmp = modify->compute[ipre]->compute_scalar();
+ }
answer = modify->compute[icompute]->compute_scalar();
} else if (index > 0) {
if (modify->compute[icompute]->vector_flag == 0)
error->all("Variable compute ID does not compute scalar info");
if (index > modify->compute[icompute]->size_vector)
error->all("Variable compute ID vector is not large enough");
- if (modify->compute[icompute]->id_pre) {
- int ipre = modify->find_compute(modify->compute[icompute]->id_pre);
- if (ipre < 0) error->all("Could not pre-compute in variable");
- modify->compute[ipre]->compute_vector();
- }
+ if (modify->compute[icompute]->npre)
+ for (int ic = 0; ic < modify->compute[icompute]->npre; ic++) {
+ int ipre =
+ modify->find_compute(modify->compute[icompute]->id_pre[ic]);
+ if (ipre < 0) error->all("Could not pre-compute in variable");
+ modify->compute[ipre]->compute_vector();
+ }
modify->compute[icompute]->compute_vector();
answer = modify->compute[icompute]->vector[index-1];
} else error->all("Invalid compute ID index in variable");
diff --git a/src/velocity.cpp b/src/velocity.cpp
index 7167c10b2a71c168dc5152b2c8fea45a18eb4bad..138891fc309650f411199112a130b8210aa5a17a 100644
--- a/src/velocity.cpp
+++ b/src/velocity.cpp
@@ -131,9 +131,9 @@ void Velocity::create(int narg, char **arg)
int tflag = 0;
if (temperature == NULL) {
char **arg = new char*[3];
- arg[0] = "velocity_temp";
+ arg[0] = (char *) "velocity_temp";
arg[1] = group->names[igroup];
- arg[2] = "temp";
+ arg[2] = (char *) "temp";
temperature = new ComputeTemp(lmp,3,arg);
tflag = 1;
delete [] arg;
@@ -215,7 +215,7 @@ void Velocity::create(int narg, char **arg)
MPI_Allreduce(&idmax,&idmaxall,1,MPI_INT,MPI_MAX,world);
if (idminall != 1 || idmaxall != natoms) {
- char *str = "Cannot use velocity create loop all with non-contiguous atom IDs";
+ char *str = (char *) "Cannot use velocity create loop all with non-contiguous atom IDs";
error->all(str);
}
@@ -390,9 +390,9 @@ void Velocity::scale(int narg, char **arg)
int tflag = 0;
if (temperature == NULL) {
char **arg = new char*[3];
- arg[0] = "velocity_temp";
+ arg[0] = (char *) "velocity_temp";
arg[1] = group->names[igroup];
- arg[2] = "temp";
+ arg[2] = (char *) "temp";
temperature = new ComputeTemp(lmp,3,arg);
tflag = 1;
delete [] arg;
diff --git a/src/verlet.cpp b/src/verlet.cpp
index 5d4ff28b8731d13bb2042bf55fe175e3ab2cdd2f..fe48c8ccd865761766cc8e0003dc68e73bc2d93a 100644
--- a/src/verlet.cpp
+++ b/src/verlet.cpp
@@ -93,21 +93,13 @@ void Verlet::init()
// set flags for what arrays to clear in force_clear()
// need to clear torques if array exists
- // don't need to clear f_pair if atom_style is only granular (no virial)
torqueflag = 0;
if (atom->torque_flag) torqueflag = 1;
- pairflag = 1;
- if (strcmp(atom->atom_style,"granular") == 0) pairflag = 0;
// orthogonal vs triclinic simulation box
triclinic = domain->triclinic;
-
- // local copies of Update quantities
-
- maxpair = update->maxpair;
- f_pair = update->f_pair;
}
/* ----------------------------------------------------------------------
@@ -139,6 +131,8 @@ void Verlet::setup()
int vflag = virial_style;
force_clear(vflag);
+ if (force->pair) force->pair->compute(eflag,vflag);
+
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
@@ -146,8 +140,6 @@ void Verlet::setup()
if (force->improper) force->improper->compute(eflag,vflag);
}
- if (force->pair) force->pair->compute(eflag,vflag);
-
if (force->kspace) {
force->kspace->setup();
force->kspace->compute(eflag,vflag);
@@ -233,6 +225,12 @@ void Verlet::iterate(int n)
force_clear(vflag);
timer->stamp();
+
+ if (force->pair) {
+ force->pair->compute(eflag,vflag);
+ timer->stamp(TIME_PAIR);
+ }
+
if (atom->molecular) {
if (force->bond) force->bond->compute(eflag,vflag);
if (force->angle) force->angle->compute(eflag,vflag);
@@ -241,11 +239,6 @@ void Verlet::iterate(int n)
timer->stamp(TIME_BOND);
}
- if (force->pair) {
- force->pair->compute(eflag,vflag);
- timer->stamp(TIME_PAIR);
- }
-
if (force->kspace) {
force->kspace->compute(eflag,vflag);
timer->stamp(TIME_KSPACE);
@@ -305,23 +298,6 @@ void Verlet::force_clear(int vflag)
torque[i][2] = 0.0;
}
}
-
- // clear f_pair array if using it this timestep to compute virial
-
- if (vflag == 2 && pairflag) {
- if (atom->nmax > maxpair) {
- maxpair = atom->nmax;
- memory->destroy_2d_double_array(f_pair);
- f_pair = memory->create_2d_double_array(maxpair,3,"verlet:f_pair");
- update->maxpair = maxpair;
- update->f_pair = f_pair;
- }
- for (i = 0; i < nall; i++) {
- f_pair[i][0] = 0.0;
- f_pair[i][1] = 0.0;
- f_pair[i][2] = 0.0;
- }
- }
}
/* ----------------------------------------------------------------------
diff --git a/src/verlet.h b/src/verlet.h
index f63cf539f3388448ff03448743c99991beb55029..a0c31dbd7b66fbb4ce7436a21ffeb4726419fe5f 100644
--- a/src/verlet.h
+++ b/src/verlet.h
@@ -35,9 +35,7 @@ class Verlet : public Integrate {
int *next_fix_virial; // next timestep they need it
int triclinic; // 0 if domain is orthog, 1 if triclinic
- int pairflag,torqueflag; // arrays to zero out every step
- int maxpair; // local copies of Update quantities
- double **f_pair;
+ int torqueflag; // arrays to zero out every step
void force_clear(int);
int fix_virial(int);