From 8dad49156d202e45477285db3e3dc2658807c005 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Wed, 16 Mar 2011 15:21:59 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5792
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/ASPHERE/atom_vec_ellipsoid.cpp | 29 +--
src/COLLOID/atom_vec_colloid.cpp | 28 +--
src/DIPOLE/atom_vec_dipole.cpp | 32 +--
src/GRANULAR/atom_vec_granular.cpp | 37 ++-
src/MOLECULE/atom_vec_angle.cpp | 72 +++---
src/MOLECULE/atom_vec_bond.cpp | 49 ++--
src/MOLECULE/atom_vec_full.cpp | 144 +++++-------
src/MOLECULE/atom_vec_molecular.cpp | 141 +++++-------
src/PERI/atom_vec_peri.cpp | 34 ++-
src/USER-EFF/atom_vec_electron.cpp | 38 ++--
src/atom.cpp | 167 +++++++-------
src/atom_vec_atomic.cpp | 18 +-
src/atom_vec_charge.cpp | 23 +-
src/comm.cpp | 112 ++++-----
src/memory.cpp | 46 +++-
src/memory.h | 342 ++++++++++++++++++++++++++++
src/neigh_bond.cpp | 28 +--
src/neigh_list.cpp | 49 ++--
src/neigh_request.cpp | 2 +-
src/neigh_stencil.cpp | 1 -
src/neighbor.cpp | 90 ++++----
21 files changed, 849 insertions(+), 633 deletions(-)
diff --git a/src/ASPHERE/atom_vec_ellipsoid.cpp b/src/ASPHERE/atom_vec_ellipsoid.cpp
index b6aebdee28..11e90e74d0 100755
--- a/src/ASPHERE/atom_vec_ellipsoid.cpp
+++ b/src/ASPHERE/atom_vec_ellipsoid.cpp
@@ -66,24 +66,17 @@ void AtomVecEllipsoid::grow(int n)
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
- tag = atom->tag = (int *)
- memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
- type = atom->type = (int *)
- memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
- mask = atom->mask = (int *)
- memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
- image = atom->image = (int *)
- memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
- x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
- v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
- f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
-
- quat = atom->quat =
- memory->grow_2d_double_array(atom->quat,nmax,4,"atom:quat");
- angmom = atom->angmom =
- memory->grow_2d_double_array(atom->angmom,nmax,3,"atom:angmom");
- torque = atom->torque =
- memory->grow_2d_double_array(atom->torque,nmax,3,"atom:torque");
+ tag = memory->grow(atom->tag,nmax,"atom:tag");
+ type = memory->grow(atom->type,nmax,"atom:type");
+ mask = memory->grow(atom->mask,nmax,"atom:mask");
+ image = memory->grow(atom->image,nmax,"atom:image");
+ x = memory->grow(atom->x,nmax,3,"atom:x");
+ v = memory->grow(atom->v,nmax,3,"atom:v");
+ f = memory->grow(atom->f,nmax,3,"atom:f");
+
+ quat = memory->grow(atom->quat,nmax,4,"atom:quat");
+ angmom = memory->grow(atom->angmom,nmax,3,"atom:angmom");
+ torque = memory->grow(atom->torque,nmax,3,"atom:torque");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
diff --git a/src/COLLOID/atom_vec_colloid.cpp b/src/COLLOID/atom_vec_colloid.cpp
index 19219376b4..601692ac72 100644
--- a/src/COLLOID/atom_vec_colloid.cpp
+++ b/src/COLLOID/atom_vec_colloid.cpp
@@ -62,23 +62,17 @@ void AtomVecColloid::grow(int n)
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
- tag = atom->tag = (int *)
- memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
- type = atom->type = (int *)
- memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
- mask = atom->mask = (int *)
- memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
- image = atom->image = (int *)
- memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
- x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
- v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
- f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
-
- omega = atom->omega =
- memory->grow_2d_double_array(atom->omega,nmax,3,"atom:omega");
- torque = atom->torque =
- memory->grow_2d_double_array(atom->torque,nmax,3,"atom:torque");
-
+ tag = memory->grow(atom->tag,nmax,"atom:tag");
+ type = memory->grow(atom->type,nmax,"atom:type");
+ mask = memory->grow(atom->mask,nmax,"atom:mask");
+ image = memory->grow(atom->image,nmax,"atom:image");
+ x = memory->grow(atom->x,nmax,3,"atom:x");
+ v = memory->grow(atom->v,nmax,3,"atom:v");
+ f = memory->grow(atom->f,nmax,3,"atom:f");
+
+ omega = memory->grow(atom->omega,nmax,3,"atom:omega");
+ torque = memory->grow(atom->torque,nmax,3,"atom:torque");
+
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp
index 97b3980a4c..4facc8c3a7 100644
--- a/src/DIPOLE/atom_vec_dipole.cpp
+++ b/src/DIPOLE/atom_vec_dipole.cpp
@@ -61,26 +61,18 @@ void AtomVecDipole::grow(int n)
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
- tag = atom->tag = (int *)
- memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
- type = atom->type = (int *)
- memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
- mask = atom->mask = (int *)
- memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
- image = atom->image = (int *)
- memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
- x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
- v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
- f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
-
- q = atom->q = (double *)
- memory->srealloc(atom->q,nmax*sizeof(double),"atom:q");
- mu = atom->mu =
- memory->grow_2d_double_array(atom->mu,nmax,3,"atom:mu");
- omega = atom->omega =
- memory->grow_2d_double_array(atom->omega,nmax,3,"atom:omega");
- torque = atom->torque =
- memory->grow_2d_double_array(atom->torque,nmax,3,"atom:torque");
+ tag = memory->grow(atom->tag,nmax,"atom:tag");
+ type = memory->grow(atom->type,nmax,"atom:type");
+ mask = memory->grow(atom->mask,nmax,"atom:mask");
+ image = memory->grow(atom->image,nmax,"atom:image");
+ x = memory->grow(atom->x,nmax,3,"atom:x");
+ v = memory->grow(atom->v,nmax,3,"atom:v");
+ f = memory->grow(atom->f,nmax,3,"atom:f");
+
+ q = memory->grow(atom->q,nmax,"atom:q");
+ mu = memory->grow(atom->mu,nmax,3,"atom:mu");
+ omega = memory->grow(atom->omega,nmax,3,"atom:omega");
+ torque = memory->grow(atom->torque,nmax,3,"atom:torque");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
diff --git a/src/GRANULAR/atom_vec_granular.cpp b/src/GRANULAR/atom_vec_granular.cpp
index d6cca5043a..960d70b078 100644
--- a/src/GRANULAR/atom_vec_granular.cpp
+++ b/src/GRANULAR/atom_vec_granular.cpp
@@ -85,29 +85,20 @@ void AtomVecGranular::grow(int n)
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
- tag = atom->tag = (int *)
- memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
- type = atom->type = (int *)
- memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
- mask = atom->mask = (int *)
- memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
- image = atom->image = (int *)
- memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
- x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
- v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
- f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
-
- radius = atom->radius = (double *)
- memory->srealloc(atom->radius,nmax*sizeof(double),"atom:radius");
- density = atom->density = (double *)
- memory->srealloc(atom->density,nmax*sizeof(double),"atom:density");
- rmass = atom->rmass = (double *)
- memory->srealloc(atom->rmass,nmax*sizeof(double),"atom:rmass");
-
- omega = atom->omega =
- memory->grow_2d_double_array(atom->omega,nmax,3,"atom:omega");
- torque = atom->torque =
- memory->grow_2d_double_array(atom->torque,nmax,3,"atom:torque");
+ tag = memory->grow(atom->tag,nmax,"atom:tag");
+ type = memory->grow(atom->type,nmax,"atom:type");
+ mask = memory->grow(atom->mask,nmax,"atom:mask");
+ image = memory->grow(atom->image,nmax,"atom:image");
+ x = memory->grow(atom->x,nmax,3,"atom:x");
+ v = memory->grow(atom->v,nmax,3,"atom:v");
+ f = memory->grow(atom->f,nmax,3,"atom:f");
+
+ radius = memory->grow(atom->radius,nmax,"atom:radius");
+ density = memory->grow(atom->density,nmax,"atom:density");
+ rmass = memory->grow(atom->rmass,nmax,"atom:rmass");
+
+ omega = memory->grow(atom->omega,nmax,3,"atom:omega");
+ torque = memory->grow(atom->torque,nmax,3,"atom:torque");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp
index bd802cbfd4..766dab3a60 100644
--- a/src/MOLECULE/atom_vec_angle.cpp
+++ b/src/MOLECULE/atom_vec_angle.cpp
@@ -63,50 +63,34 @@ void AtomVecAngle::grow(int n)
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
- tag = atom->tag = (int *)
- memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
- type = atom->type = (int *)
- memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
- mask = atom->mask = (int *)
- memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
- image = atom->image = (int *)
- memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
- x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
- v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
- f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
-
- molecule = atom->molecule = (int *)
- memory->srealloc(atom->molecule,nmax*sizeof(int),"atom:molecule");
-
- nspecial = atom->nspecial =
- memory->grow_2d_int_array(atom->nspecial,nmax,3,"atom:nspecial");
- special = atom->special =
- memory->grow_2d_int_array(atom->special,nmax,atom->maxspecial,
- "atom:special");
-
- num_bond = atom->num_bond = (int *)
- memory->srealloc(atom->num_bond,nmax*sizeof(int),"atom:num_bond");
- bond_type = atom->bond_type =
- memory->grow_2d_int_array(atom->bond_type,nmax,atom->bond_per_atom,
- "atom:bond_type");
- bond_atom = atom->bond_atom =
- memory->grow_2d_int_array(atom->bond_atom,nmax,atom->bond_per_atom,
- "atom:bond_atom");
-
- num_angle = atom->num_angle = (int *)
- memory->srealloc(atom->num_angle,nmax*sizeof(int),"atom:num_angle");
- angle_type = atom->angle_type =
- memory->grow_2d_int_array(atom->angle_type,nmax,atom->angle_per_atom,
- "atom:angle_type");
- angle_atom1 = atom->angle_atom1 =
- memory->grow_2d_int_array(atom->angle_atom1,nmax,atom->angle_per_atom,
- "atom:angle_atom1");
- angle_atom2 = atom->angle_atom2 =
- memory->grow_2d_int_array(atom->angle_atom2,nmax,atom->angle_per_atom,
- "atom:angle_atom2");
- angle_atom3 = atom->angle_atom3 =
- memory->grow_2d_int_array(atom->angle_atom3,nmax,atom->angle_per_atom,
- "atom:angle_atom3");
+ tag = memory->grow(atom->tag,nmax,"atom:tag");
+ type = memory->grow(atom->type,nmax,"atom:type");
+ mask = memory->grow(atom->mask,nmax,"atom:mask");
+ image = memory->grow(atom->image,nmax,"atom:image");
+ x = memory->grow(atom->x,nmax,3,"atom:x");
+ v = memory->grow(atom->v,nmax,3,"atom:v");
+ f = memory->grow(atom->f,nmax,3,"atom:f");
+
+ molecule = memory->grow(atom->molecule,nmax,"atom:molecule");
+
+ nspecial = memory->grow(atom->nspecial,nmax,3,"atom:nspecial");
+ special = memory->grow(atom->special,nmax,atom->maxspecial,"atom:special");
+
+ num_bond = memory->grow(atom->num_bond,nmax,"atom:num_bond");
+ bond_type = memory->grow(atom->bond_type,nmax,atom->bond_per_atom,
+ "atom:bond_type");
+ bond_atom = memory->grow(atom->bond_atom,nmax,atom->bond_per_atom,
+ "atom:bond_atom");
+
+ num_angle = memory->grow(atom->num_angle,nmax,"atom:num_angle");
+ angle_type = memory->grow(atom->angle_type,nmax,atom->angle_per_atom,
+ "atom:angle_type");
+ angle_atom1 = memory->grow(atom->angle_atom1,nmax,atom->angle_per_atom,
+ "atom:angle_atom1");
+ angle_atom2 = memory->grow(atom->angle_atom2,nmax,atom->angle_per_atom,
+ "atom:angle_atom2");
+ angle_atom3 = memory->grow(atom->angle_atom3,nmax,atom->angle_per_atom,
+ "atom:angle_atom3");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp
index 8493b31ae0..9d0ba86251 100644
--- a/src/MOLECULE/atom_vec_bond.cpp
+++ b/src/MOLECULE/atom_vec_bond.cpp
@@ -63,36 +63,25 @@ void AtomVecBond::grow(int n)
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
- tag = atom->tag = (int *)
- memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
- type = atom->type = (int *)
- memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
- mask = atom->mask = (int *)
- memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
- image = atom->image = (int *)
- memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
- x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
- v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
- f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
-
- molecule = atom->molecule = (int *)
- memory->srealloc(atom->molecule,nmax*sizeof(int),"atom:molecule");
-
- nspecial = atom->nspecial =
- memory->grow_2d_int_array(atom->nspecial,nmax,3,"atom:nspecial");
- special = atom->special =
- memory->grow_2d_int_array(atom->special,nmax,atom->maxspecial,
- "atom:special");
-
- num_bond = atom->num_bond = (int *)
- memory->srealloc(atom->num_bond,nmax*sizeof(int),"atom:num_bond");
- bond_type = atom->bond_type =
- memory->grow_2d_int_array(atom->bond_type,nmax,atom->bond_per_atom,
- "atom:bond_type");
- bond_atom = atom->bond_atom =
- memory->grow_2d_int_array(atom->bond_atom,nmax,atom->bond_per_atom,
- "atom:bond_atom");
-
+ tag = memory->grow(atom->tag,nmax,"atom:tag");
+ type = memory->grow(atom->type,nmax,"atom:type");
+ mask = memory->grow(atom->mask,nmax,"atom:mask");
+ image = memory->grow(atom->image,nmax,"atom:image");
+ x = memory->grow(atom->x,nmax,3,"atom:x");
+ v = memory->grow(atom->v,nmax,3,"atom:v");
+ f = memory->grow(atom->f,nmax,3,"atom:f");
+
+ molecule = memory->grow(atom->molecule,nmax,"atom:molecule");
+
+ nspecial = memory->grow(atom->nspecial,nmax,3,"atom:nspecial");
+ special = memory->grow(atom->special,nmax,atom->maxspecial,"atom:special");
+
+ num_bond = memory->grow(atom->num_bond,nmax,"atom:num_bond");
+ bond_type = memory->grow(atom->bond_type,nmax,atom->bond_per_atom,
+ "atom:bond_type");
+ bond_atom = memory->grow(atom->bond_atom,nmax,atom->bond_per_atom,
+ "atom:bond_atom");
+
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp
index 8f9eb97d3d..af09a8edba 100644
--- a/src/MOLECULE/atom_vec_full.cpp
+++ b/src/MOLECULE/atom_vec_full.cpp
@@ -63,88 +63,68 @@ void AtomVecFull::grow(int n)
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
- tag = atom->tag = (int *)
- memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
- type = atom->type = (int *)
- memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
- mask = atom->mask = (int *)
- memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
- image = atom->image = (int *)
- memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
- x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
- v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
- f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
-
- q = atom->q = (double *)
- memory->srealloc(atom->q,nmax*sizeof(double),"atom:q");
- molecule = atom->molecule = (int *)
- memory->srealloc(atom->molecule,nmax*sizeof(int),"atom:molecule");
-
- nspecial = atom->nspecial =
- memory->grow_2d_int_array(atom->nspecial,nmax,3,"atom:nspecial");
- special = atom->special =
- memory->grow_2d_int_array(atom->special,nmax,atom->maxspecial,
- "atom:special");
-
- num_bond = atom->num_bond = (int *)
- memory->srealloc(atom->num_bond,nmax*sizeof(int),"atom:num_bond");
- bond_type = atom->bond_type =
- memory->grow_2d_int_array(atom->bond_type,nmax,atom->bond_per_atom,
- "atom:bond_type");
- bond_atom = atom->bond_atom =
- memory->grow_2d_int_array(atom->bond_atom,nmax,atom->bond_per_atom,
- "atom:bond_atom");
-
- num_angle = atom->num_angle = (int *)
- memory->srealloc(atom->num_angle,nmax*sizeof(int),"atom:num_angle");
- angle_type = atom->angle_type =
- memory->grow_2d_int_array(atom->angle_type,nmax,atom->angle_per_atom,
- "atom:angle_type");
- angle_atom1 = atom->angle_atom1 =
- memory->grow_2d_int_array(atom->angle_atom1,nmax,atom->angle_per_atom,
- "atom:angle_atom1");
- angle_atom2 = atom->angle_atom2 =
- memory->grow_2d_int_array(atom->angle_atom2,nmax,atom->angle_per_atom,
- "atom:angle_atom2");
- angle_atom3 = atom->angle_atom3 =
- memory->grow_2d_int_array(atom->angle_atom3,nmax,atom->angle_per_atom,
- "atom:angle_atom3");
-
- num_dihedral = atom->num_dihedral = (int *)
- memory->srealloc(atom->num_dihedral,nmax*sizeof(int),"atom:num_dihedral");
- dihedral_type = atom->dihedral_type =
- memory->grow_2d_int_array(atom->dihedral_type,nmax,atom->dihedral_per_atom,
- "atom:dihedral_type");
- dihedral_atom1 = atom->dihedral_atom1 =
- memory->grow_2d_int_array(atom->dihedral_atom1,nmax,
- atom->dihedral_per_atom,"atom:dihedral_atom1");
- dihedral_atom2 = atom->dihedral_atom2 =
- memory->grow_2d_int_array(atom->dihedral_atom2,nmax,
- atom->dihedral_per_atom,"atom:dihedral_atom2");
- dihedral_atom3 = atom->dihedral_atom3 =
- memory->grow_2d_int_array(atom->dihedral_atom3,nmax,
- atom->dihedral_per_atom,"atom:dihedral_atom3");
- dihedral_atom4 = atom->dihedral_atom4 =
- memory->grow_2d_int_array(atom->dihedral_atom4,nmax,
- atom->dihedral_per_atom,"atom:dihedral_atom4");
-
- num_improper = atom->num_improper = (int *)
- memory->srealloc(atom->num_improper,nmax*sizeof(int),"atom:num_improper");
- improper_type = atom->improper_type =
- memory->grow_2d_int_array(atom->improper_type,nmax,atom->improper_per_atom,
- "atom:improper_type");
- improper_atom1 = atom->improper_atom1 =
- memory->grow_2d_int_array(atom->improper_atom1,nmax,
- atom->improper_per_atom,"atom:improper_atom1");
- improper_atom2 = atom->improper_atom2 =
- memory->grow_2d_int_array(atom->improper_atom2,nmax,
- atom->improper_per_atom,"atom:improper_atom2");
- improper_atom3 = atom->improper_atom3 =
- memory->grow_2d_int_array(atom->improper_atom3,nmax,
- atom->improper_per_atom,"atom:improper_atom3");
- improper_atom4 = atom->improper_atom4 =
- memory->grow_2d_int_array(atom->improper_atom4,nmax,
- atom->improper_per_atom,"atom:improper_atom4");
+ tag = memory->grow(atom->tag,nmax,"atom:tag");
+ type = memory->grow(atom->type,nmax,"atom:type");
+ mask = memory->grow(atom->mask,nmax,"atom:mask");
+ image = memory->grow(atom->image,nmax,"atom:image");
+ x = memory->grow(atom->x,nmax,3,"atom:x");
+ v = memory->grow(atom->v,nmax,3,"atom:v");
+ f = memory->grow(atom->f,nmax,3,"atom:f");
+
+ q = memory->grow(atom->q,nmax,"atom:q");
+ molecule = memory->grow(atom->molecule,nmax,"atom:molecule");
+
+ nspecial = memory->grow(atom->nspecial,nmax,3,"atom:nspecial");
+ special = memory->grow(atom->special,nmax,atom->maxspecial,"atom:special");
+
+ num_bond = memory->grow(atom->num_bond,nmax,"atom:num_bond");
+ bond_type = memory->grow(atom->bond_type,nmax,atom->bond_per_atom,
+ "atom:bond_type");
+ bond_atom = memory->grow(atom->bond_atom,nmax,atom->bond_per_atom,
+ "atom:bond_atom");
+
+ num_angle = memory->grow(atom->num_angle,nmax,"atom:num_angle");
+ angle_type = memory->grow(atom->angle_type,nmax,atom->angle_per_atom,
+ "atom:angle_type");
+ angle_atom1 = memory->grow(atom->angle_atom1,nmax,atom->angle_per_atom,
+ "atom:angle_atom1");
+ angle_atom2 = memory->grow(atom->angle_atom2,nmax,atom->angle_per_atom,
+ "atom:angle_atom2");
+ angle_atom3 = memory->grow(atom->angle_atom3,nmax,atom->angle_per_atom,
+ "atom:angle_atom3");
+
+ num_dihedral = memory->grow(atom->num_dihedral,nmax,"atom:num_dihedral");
+ dihedral_type = memory->grow(atom->dihedral_type,nmax,
+ atom->dihedral_per_atom,"atom:dihedral_type");
+ dihedral_atom1 =
+ memory->grow(atom->dihedral_atom1,nmax,atom->dihedral_per_atom,
+ "atom:dihedral_atom1");
+ dihedral_atom2 =
+ memory->grow(atom->dihedral_atom2,nmax,atom->dihedral_per_atom,
+ "atom:dihedral_atom2");
+ dihedral_atom3 =
+ memory->grow(atom->dihedral_atom3,nmax,atom->dihedral_per_atom,
+ "atom:dihedral_atom3");
+ dihedral_atom4 =
+ memory->grow(atom->dihedral_atom4,nmax,atom->dihedral_per_atom,
+ "atom:dihedral_atom4");
+
+ num_improper = memory->grow(atom->num_improper,nmax,"atom:num_improper");
+ improper_type =
+ memory->grow(atom->improper_type,nmax,atom->improper_per_atom,
+ "atom:improper_type");
+ improper_atom1 =
+ memory->grow(atom->improper_atom1,nmax,atom->improper_per_atom,
+ "atom:improper_atom1");
+ improper_atom2 =
+ memory->grow(atom->improper_atom2,nmax,atom->improper_per_atom,
+ "atom:improper_atom2");
+ improper_atom3 =
+ memory->grow(atom->improper_atom3,nmax,atom->improper_per_atom,
+ "atom:improper_atom3");
+ improper_atom4 =
+ memory->grow(atom->improper_atom4,nmax,atom->improper_per_atom,
+ "atom:improper_atom4");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp
index 555e1ed65d..3e809184fa 100644
--- a/src/MOLECULE/atom_vec_molecular.cpp
+++ b/src/MOLECULE/atom_vec_molecular.cpp
@@ -63,86 +63,67 @@ void AtomVecMolecular::grow(int n)
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
- tag = atom->tag = (int *)
- memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
- type = atom->type = (int *)
- memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
- mask = atom->mask = (int *)
- memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
- image = atom->image = (int *)
- memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
- x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
- v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
- f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
-
- molecule = atom->molecule = (int *)
- memory->srealloc(atom->molecule,nmax*sizeof(int),"atom:molecule");
-
- nspecial = atom->nspecial =
- memory->grow_2d_int_array(atom->nspecial,nmax,3,"atom:nspecial");
- special = atom->special =
- memory->grow_2d_int_array(atom->special,nmax,atom->maxspecial,
- "atom:special");
-
- num_bond = atom->num_bond = (int *)
- memory->srealloc(atom->num_bond,nmax*sizeof(int),"atom:num_bond");
- bond_type = atom->bond_type =
- memory->grow_2d_int_array(atom->bond_type,nmax,atom->bond_per_atom,
- "atom:bond_type");
- bond_atom = atom->bond_atom =
- memory->grow_2d_int_array(atom->bond_atom,nmax,atom->bond_per_atom,
- "atom:bond_atom");
-
- num_angle = atom->num_angle = (int *)
- memory->srealloc(atom->num_angle,nmax*sizeof(int),"atom:num_angle");
- angle_type = atom->angle_type =
- memory->grow_2d_int_array(atom->angle_type,nmax,atom->angle_per_atom,
- "atom:angle_type");
- angle_atom1 = atom->angle_atom1 =
- memory->grow_2d_int_array(atom->angle_atom1,nmax,atom->angle_per_atom,
- "atom:angle_atom1");
- angle_atom2 = atom->angle_atom2 =
- memory->grow_2d_int_array(atom->angle_atom2,nmax,atom->angle_per_atom,
- "atom:angle_atom2");
- angle_atom3 = atom->angle_atom3 =
- memory->grow_2d_int_array(atom->angle_atom3,nmax,atom->angle_per_atom,
- "atom:angle_atom3");
-
- num_dihedral = atom->num_dihedral = (int *)
- memory->srealloc(atom->num_dihedral,nmax*sizeof(int),"atom:num_dihedral");
- dihedral_type = atom->dihedral_type =
- memory->grow_2d_int_array(atom->dihedral_type,nmax,atom->dihedral_per_atom,
- "atom:dihedral_type");
- dihedral_atom1 = atom->dihedral_atom1 =
- memory->grow_2d_int_array(atom->dihedral_atom1,nmax,
- atom->dihedral_per_atom,"atom:dihedral_atom1");
- dihedral_atom2 = atom->dihedral_atom2 =
- memory->grow_2d_int_array(atom->dihedral_atom2,nmax,
- atom->dihedral_per_atom,"atom:dihedral_atom2");
- dihedral_atom3 = atom->dihedral_atom3 =
- memory->grow_2d_int_array(atom->dihedral_atom3,nmax,
- atom->dihedral_per_atom,"atom:dihedral_atom3");
- dihedral_atom4 = atom->dihedral_atom4 =
- memory->grow_2d_int_array(atom->dihedral_atom4,nmax,
- atom->dihedral_per_atom,"atom:dihedral_atom4");
-
- num_improper = atom->num_improper = (int *)
- memory->srealloc(atom->num_improper,nmax*sizeof(int),"atom:num_improper");
- improper_type = atom->improper_type =
- memory->grow_2d_int_array(atom->improper_type,nmax,atom->improper_per_atom,
- "atom:improper_type");
- improper_atom1 = atom->improper_atom1 =
- memory->grow_2d_int_array(atom->improper_atom1,nmax,
- atom->improper_per_atom,"atom:improper_atom1");
- improper_atom2 = atom->improper_atom2 =
- memory->grow_2d_int_array(atom->improper_atom2,nmax,
- atom->improper_per_atom,"atom:improper_atom2");
- improper_atom3 = atom->improper_atom3 =
- memory->grow_2d_int_array(atom->improper_atom3,nmax,
- atom->improper_per_atom,"atom:improper_atom3");
- improper_atom4 = atom->improper_atom4 =
- memory->grow_2d_int_array(atom->improper_atom4,nmax,
- atom->improper_per_atom,"atom:improper_atom4");
+ tag = memory->grow(atom->tag,nmax,"atom:tag");
+ type = memory->grow(atom->type,nmax,"atom:type");
+ mask = memory->grow(atom->mask,nmax,"atom:mask");
+ image = memory->grow(atom->image,nmax,"atom:image");
+ x = memory->grow(atom->x,nmax,3,"atom:x");
+ v = memory->grow(atom->v,nmax,3,"atom:v");
+ f = memory->grow(atom->f,nmax,3,"atom:f");
+
+ molecule = memory->grow(atom->molecule,nmax,"atom:molecule");
+
+ nspecial = memory->grow(atom->nspecial,nmax,3,"atom:nspecial");
+ special = memory->grow(atom->special,nmax,atom->maxspecial,"atom:special");
+
+ num_bond = memory->grow(atom->num_bond,nmax,"atom:num_bond");
+ bond_type = memory->grow(atom->bond_type,nmax,atom->bond_per_atom,
+ "atom:bond_type");
+ bond_atom = memory->grow(atom->bond_atom,nmax,atom->bond_per_atom,
+ "atom:bond_atom");
+
+ num_angle = memory->grow(atom->num_angle,nmax,"atom:num_angle");
+ angle_type = memory->grow(atom->angle_type,nmax,atom->angle_per_atom,
+ "atom:angle_type");
+ angle_atom1 = memory->grow(atom->angle_atom1,nmax,atom->angle_per_atom,
+ "atom:angle_atom1");
+ angle_atom2 = memory->grow(atom->angle_atom2,nmax,atom->angle_per_atom,
+ "atom:angle_atom2");
+ angle_atom3 = memory->grow(atom->angle_atom3,nmax,atom->angle_per_atom,
+ "atom:angle_atom3");
+
+ num_dihedral = memory->grow(atom->num_dihedral,nmax,"atom:num_dihedral");
+ dihedral_type = memory->grow(atom->dihedral_type,nmax,
+ atom->dihedral_per_atom,"atom:dihedral_type");
+ dihedral_atom1 =
+ memory->grow(atom->dihedral_atom1,nmax,atom->dihedral_per_atom,
+ "atom:dihedral_atom1");
+ dihedral_atom2 =
+ memory->grow(atom->dihedral_atom2,nmax,atom->dihedral_per_atom,
+ "atom:dihedral_atom2");
+ dihedral_atom3 =
+ memory->grow(atom->dihedral_atom3,nmax,atom->dihedral_per_atom,
+ "atom:dihedral_atom3");
+ dihedral_atom4 =
+ memory->grow(atom->dihedral_atom4,nmax,atom->dihedral_per_atom,
+ "atom:dihedral_atom4");
+
+ num_improper = memory->grow(atom->num_improper,nmax,"atom:num_improper");
+ improper_type =
+ memory->grow(atom->improper_type,nmax,atom->improper_per_atom,
+ "atom:improper_type");
+ improper_atom1 =
+ memory->grow(atom->improper_atom1,nmax,atom->improper_per_atom,
+ "atom:improper_atom1");
+ improper_atom2 =
+ memory->grow(atom->improper_atom2,nmax,atom->improper_per_atom,
+ "atom:improper_atom2");
+ improper_atom3 =
+ memory->grow(atom->improper_atom3,nmax,atom->improper_per_atom,
+ "atom:improper_atom3");
+ improper_atom4 =
+ memory->grow(atom->improper_atom4,nmax,atom->improper_per_atom,
+ "atom:improper_atom4");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp
index ea3d896466..322fa56ca7 100644
--- a/src/PERI/atom_vec_peri.cpp
+++ b/src/PERI/atom_vec_peri.cpp
@@ -64,27 +64,19 @@ void AtomVecPeri::grow(int n)
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
- tag = atom->tag = (int *)
- memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
- type = atom->type = (int *)
- memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
- mask = atom->mask = (int *)
- memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
- image = atom->image = (int *)
- memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
- x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
- v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
- f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
-
- vfrac = atom->vfrac = (double *)
- memory->srealloc(atom->vfrac,nmax*sizeof(double),"atom:vfrac");
- density = atom->density = (double *)
- memory->srealloc(atom->density,nmax*sizeof(double),"atom:density");
- rmass = atom->rmass = (double *)
- memory->srealloc(atom->rmass,nmax*sizeof(double),"atom:rmass");
- s0 = atom->s0 = (double *)
- memory->srealloc(atom->s0,nmax*sizeof(double),"atom:s0");
- x0 = atom->x0 = memory->grow_2d_double_array(atom->x0,nmax,3,"atom:x0");
+ tag = memory->grow(atom->tag,nmax,"atom:tag");
+ type = memory->grow(atom->type,nmax,"atom:type");
+ mask = memory->grow(atom->mask,nmax,"atom:mask");
+ image = memory->grow(atom->image,nmax,"atom:image");
+ x = memory->grow(atom->x,nmax,3,"atom:x");
+ v = memory->grow(atom->v,nmax,3,"atom:v");
+ f = memory->grow(atom->f,nmax,3,"atom:f");
+
+ vfrac = memory->grow(atom->vfrac,nmax,"atom:vfrac");
+ density = memory->grow(atom->density,nmax,"atom:density");
+ rmass = memory->grow(atom->rmass,nmax,"atom:rmass");
+ s0 = memory->grow(atom->s0,nmax,"atom:s0");
+ x0 = memory->grow(atom->x0,nmax,3,"atom:x0");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp
index d761d128f5..15de2e1a84 100644
--- a/src/USER-EFF/atom_vec_electron.cpp
+++ b/src/USER-EFF/atom_vec_electron.cpp
@@ -64,30 +64,20 @@ void AtomVecElectron::grow(int n)
else nmax = n;
atom->nmax = nmax;
- tag = atom->tag = (int *)
- memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
- type = atom->type = (int *)
- memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
- mask = atom->mask = (int *)
- memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
- image = atom->image = (int *)
- memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
-
- x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
- v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
- f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
-
- q = atom->q = (double *)
- memory->srealloc(atom->q,nmax*sizeof(double),"atom:q");
- spin = atom->spin = (int *)
- memory->srealloc(atom->spin,nmax*sizeof(int),"atom:spin");
- eradius = atom->eradius = (double *)
- memory->srealloc(atom->eradius,nmax*sizeof(double),"atom:eradius");
- ervel = atom->ervel = (double *)
- memory->srealloc(atom->ervel,nmax*sizeof(double),"atom:ervel");
- erforce = atom->erforce = (double *)
- memory->srealloc(atom->erforce,nmax*sizeof(double),"atom:erforce");
-
+ tag = memory->grow(atom->tag,nmax,"atom:tag");
+ type = memory->grow(atom->type,nmax,"atom:type");
+ mask = memory->grow(atom->mask,nmax,"atom:mask");
+ image = memory->grow(atom->image,nmax,"atom:image");
+ x = memory->grow(atom->x,nmax,3,"atom:x");
+ v = memory->grow(atom->v,nmax,3,"atom:v");
+ f = memory->grow(atom->f,nmax,3,"atom:f");
+
+ q = memory->grow(atom->q,nmax,"atom:q");
+ spin = memory->grow(atom->spin,nmax,"atom:spin");
+ eradius = memory->grow(atom->eradius,nmax,"atom:eradius");
+ ervel = memory->grow(atom->ervel,nmax,"atom:ervel");
+ erforce = memory->grow(atom->erforce,nmax,"atom:erforce");
+
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
diff --git a/src/atom.cpp b/src/atom.cpp
index 118a3ce706..7db4daccd8 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -152,83 +152,83 @@ Atom::~Atom()
delete avec;
delete [] firstgroupname;
- memory->sfree(binhead);
- memory->sfree(next);
- memory->sfree(permute);
+ memory->destroy(binhead);
+ memory->destroy(next);
+ memory->destroy(permute);
// delete atom arrays
// customize by adding new array
- memory->sfree(tag);
- memory->sfree(type);
- memory->sfree(mask);
- memory->sfree(image);
- memory->destroy_2d_double_array(x);
- memory->destroy_2d_double_array(v);
- memory->destroy_2d_double_array(f);
-
- memory->sfree(q);
- memory->destroy_2d_double_array(mu);
- memory->destroy_2d_double_array(quat);
- memory->destroy_2d_double_array(omega);
- memory->destroy_2d_double_array(angmom);
- memory->destroy_2d_double_array(torque);
-
- memory->sfree(radius);
- memory->sfree(density);
- memory->sfree(rmass);
- memory->sfree(vfrac);
- memory->sfree(s0);
- memory->destroy_2d_double_array(x0);
-
- memory->sfree(spin);
- memory->sfree(eradius);
- memory->sfree(ervel);
- memory->sfree(erforce);
-
- memory->sfree(molecule);
-
- memory->destroy_2d_int_array(nspecial);
- memory->destroy_2d_int_array(special);
-
- memory->sfree(num_bond);
- memory->destroy_2d_int_array(bond_type);
- memory->destroy_2d_int_array(bond_atom);
-
- memory->sfree(num_angle);
- memory->destroy_2d_int_array(angle_type);
- memory->destroy_2d_int_array(angle_atom1);
- memory->destroy_2d_int_array(angle_atom2);
- memory->destroy_2d_int_array(angle_atom3);
-
- memory->sfree(num_dihedral);
- memory->destroy_2d_int_array(dihedral_type);
- memory->destroy_2d_int_array(dihedral_atom1);
- memory->destroy_2d_int_array(dihedral_atom2);
- memory->destroy_2d_int_array(dihedral_atom3);
- memory->destroy_2d_int_array(dihedral_atom4);
-
- memory->sfree(num_improper);
- memory->destroy_2d_int_array(improper_type);
- memory->destroy_2d_int_array(improper_atom1);
- memory->destroy_2d_int_array(improper_atom2);
- memory->destroy_2d_int_array(improper_atom3);
- memory->destroy_2d_int_array(improper_atom4);
+ memory->destroy(tag);
+ memory->destroy(type);
+ memory->destroy(mask);
+ memory->destroy(image);
+ memory->destroy(x);
+ memory->destroy(v);
+ memory->destroy(f);
+
+ memory->destroy(q);
+ memory->destroy(mu);
+ memory->destroy(quat);
+ memory->destroy(omega);
+ memory->destroy(angmom);
+ memory->destroy(torque);
+
+ memory->destroy(radius);
+ memory->destroy(density);
+ memory->destroy(rmass);
+ memory->destroy(vfrac);
+ memory->destroy(s0);
+ memory->destroy(x0);
+
+ memory->destroy(spin);
+ memory->destroy(eradius);
+ memory->destroy(ervel);
+ memory->destroy(erforce);
+
+ memory->destroy(molecule);
+
+ memory->destroy(nspecial);
+ memory->destroy(special);
+
+ memory->destroy(num_bond);
+ memory->destroy(bond_type);
+ memory->destroy(bond_atom);
+
+ memory->destroy(num_angle);
+ memory->destroy(angle_type);
+ memory->destroy(angle_atom1);
+ memory->destroy(angle_atom2);
+ memory->destroy(angle_atom3);
+
+ memory->destroy(num_dihedral);
+ memory->destroy(dihedral_type);
+ memory->destroy(dihedral_atom1);
+ memory->destroy(dihedral_atom2);
+ memory->destroy(dihedral_atom3);
+ memory->destroy(dihedral_atom4);
+
+ memory->destroy(num_improper);
+ memory->destroy(improper_type);
+ memory->destroy(improper_atom1);
+ memory->destroy(improper_atom2);
+ memory->destroy(improper_atom3);
+ memory->destroy(improper_atom4);
// delete per-type arrays
delete [] mass;
delete [] mass_setflag;
- memory->destroy_2d_double_array(shape);
+ memory->destroy(shape);
delete [] shape_setflag;
delete [] dipole;
delete [] dipole_setflag;
// delete extra arrays
- memory->sfree(extra_grow);
- memory->sfree(extra_restart);
- memory->destroy_2d_double_array(extra);
+ memory->destroy(extra_grow);
+ memory->destroy(extra_restart);
+ memory->destroy(extra);
// delete mapping data structures
@@ -300,7 +300,7 @@ void Atom::init()
// delete extra array since it doesn't persist past first run
if (nextra_store) {
- memory->destroy_2d_double_array(extra);
+ memory->destroy(extra);
extra = NULL;
nextra_store = 0;
}
@@ -420,8 +420,7 @@ void Atom::map_init()
MPI_Allreduce(&max,&map_tag_max,1,MPI_INT,MPI_MAX,world);
if (map_style == 1) {
- map_array = (int *)
- memory->smalloc((map_tag_max+1)*sizeof(int),"atom:map_array");
+ memory->create(map_array,map_tag_max+1,"atom:map_array");
for (int i = 0; i <= map_tag_max; i++) map_array[i] = -1;
} else {
@@ -605,7 +604,7 @@ void Atom::map_one(int global, int local)
void Atom::map_delete()
{
if (map_style == 1) {
- if (map_tag_max) memory->sfree(map_array);
+ if (map_tag_max) memory->destroy(map_array);
} else {
if (map_nhash) {
delete [] map_bucket;
@@ -696,20 +695,21 @@ int Atom::tag_consecutive()
int Atom::count_words(const char *line)
{
int n = strlen(line) + 1;
- char *copy = (char *) memory->smalloc(n*sizeof(char),"copy");
+ char *copy;
+ memory->create(copy,n,"atom:copy");
strcpy(copy,line);
char *ptr;
if (ptr = strchr(copy,'#')) *ptr = '\0';
if (strtok(copy," \t\n\r\f") == NULL) {
- memory->sfree(copy);
+ memory->destroy(copy);
return 0;
}
n = 1;
while (strtok(NULL," \t\n\r\f")) n++;
- memory->sfree(copy);
+ memory->destroy(copy);
return n;
}
@@ -1066,7 +1066,7 @@ void Atom::allocate_type_arrays()
for (int itype = 1; itype <= ntypes; itype++) mass_setflag[itype] = 0;
}
if (avec->shape_type) {
- shape = memory->create_2d_double_array(ntypes+1,3,"atom:shape");
+ memory->create(shape,ntypes+1,3,"atom:shape");
shape_setflag = new int[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) shape_setflag[itype] = 0;
}
@@ -1365,11 +1365,11 @@ void Atom::sort()
// reallocate per-atom vectors if needed
if (nlocal > maxnext) {
- memory->sfree(next);
- memory->sfree(permute);
+ memory->destroy(next);
+ memory->destroy(permute);
maxnext = atom->nmax;
- next = (int *) memory->smalloc(maxnext*sizeof(int),"atom:next");
- permute = (int *) memory->smalloc(maxnext*sizeof(int),"atom:permute");
+ memory->create(next,maxnext,"atom:next");
+ memory->create(permute,maxnext,"atom:permute");
}
// insure there is one extra atom location at end of arrays for swaps
@@ -1497,9 +1497,9 @@ void Atom::setup_sort_bins()
// reallocate per-bin memory if needed
if (nbins > maxbin) {
- memory->sfree(binhead);
+ memory->destroy(binhead);
maxbin = nbins;
- binhead = (int *) memory->smalloc(maxbin*sizeof(int),"atom:binhead");
+ memory->create(binhead,maxbin,"atom:binhead");
}
}
@@ -1528,18 +1528,14 @@ void Atom::add_callback(int flag)
if (flag == 0) {
if (nextra_grow == nextra_grow_max) {
nextra_grow_max += DELTA;
- extra_grow = (int *)
- memory->srealloc(extra_grow,nextra_grow_max*sizeof(int),
- "atom:extra_grow");
+ memory->grow(extra_grow,nextra_grow_max,"atom:extra_grow");
}
extra_grow[nextra_grow] = ifix;
nextra_grow++;
} else if (flag == 1) {
if (nextra_restart == nextra_restart_max) {
nextra_restart_max += DELTA;
- extra_restart = (int *)
- memory->srealloc(extra_restart,nextra_restart_max*sizeof(int),
- "atom:extra_restart");
+ memory->grow(extra_restart,nextra_restart_max,"atom:extra_restart");
}
extra_restart[nextra_restart] = ifix;
nextra_restart++;
@@ -1619,7 +1615,7 @@ void *Atom::extract(char *name)
double Atom::memory_usage()
{
memlength = DELTA_MEMSTR;
- memstr = (char *) memory->smalloc(memlength*sizeof(char),"atom:memstr");
+ memory->create(memstr,memlength,"atom:memstr");
memstr[0] = '\0';
double bytes = avec->memory_usage();
@@ -1630,7 +1626,7 @@ double Atom::memory_usage()
bytes += map_nhash*sizeof(HashElem);
}
- memory->sfree(memstr);
+ memory->destroy(memstr);
return bytes;
}
@@ -1654,8 +1650,7 @@ int Atom::memcheck(const char *str)
if (strlen(memstr) + n >= memlength) {
memlength += DELTA_MEMSTR;
- memstr = (char *) memory->srealloc(memstr,memlength*sizeof(char),
- "atom:memstr");
+ memory->grow(memstr,memlength,"atom:memstr");
}
strcat(memstr,padded);
diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp
index 666ba7bc3f..26bd4d0738 100644
--- a/src/atom_vec_atomic.cpp
+++ b/src/atom_vec_atomic.cpp
@@ -57,17 +57,13 @@ void AtomVecAtomic::grow(int n)
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
- tag = atom->tag = (int *)
- memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
- type = atom->type = (int *)
- memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
- mask = atom->mask = (int *)
- memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
- image = atom->image = (int *)
- memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
- x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
- v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
- f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
+ tag = memory->grow(atom->tag,nmax,"atom:tag");
+ type = memory->grow(atom->type,nmax,"atom:type");
+ mask = memory->grow(atom->mask,nmax,"atom:mask");
+ image = memory->grow(atom->image,nmax,"atom:image");
+ x = memory->grow(atom->x,nmax,3,"atom:x");
+ v = memory->grow(atom->v,nmax,3,"atom:v");
+ f = memory->grow(atom->f,nmax,3,"atom:f");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp
index 3071d5cf92..4f92be8aed 100644
--- a/src/atom_vec_charge.cpp
+++ b/src/atom_vec_charge.cpp
@@ -59,20 +59,15 @@ void AtomVecCharge::grow(int n)
if (nmax < 0 || nmax > MAXSMALLINT)
error->one("Per-processor system is too big");
- tag = atom->tag = (int *)
- memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
- type = atom->type = (int *)
- memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
- mask = atom->mask = (int *)
- memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
- image = atom->image = (int *)
- memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
- x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
- v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
- f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
-
- q = atom->q = (double *)
- memory->srealloc(atom->q,nmax*sizeof(double),"atom:q");
+ tag = memory->grow(atom->tag,nmax,"atom:tag");
+ type = memory->grow(atom->type,nmax,"atom:type");
+ mask = memory->grow(atom->mask,nmax,"atom:mask");
+ image = memory->grow(atom->image,nmax,"atom:image");
+ x = memory->grow(atom->x,nmax,3,"atom:x");
+ v = memory->grow(atom->v,nmax,3,"atom:v");
+ f = memory->grow(atom->f,nmax,3,"atom:f");
+
+ q = memory->grow(atom->q,nmax,"atom:q");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
diff --git a/src/comm.cpp b/src/comm.cpp
index 324c9d0546..10f81b6042 100644
--- a/src/comm.cpp
+++ b/src/comm.cpp
@@ -68,20 +68,18 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
// initialize comm buffers & exchange memory
maxsend = BUFMIN;
- buf_send = (double *)
- memory->smalloc((maxsend+BUFEXTRA)*sizeof(double),"comm:buf_send");
+ memory->create(buf_send,maxsend+BUFEXTRA,"comm:buf_send");
maxrecv = BUFMIN;
- buf_recv = (double *)
- memory->smalloc(maxrecv*sizeof(double),"comm:buf_recv");
+ memory->create(buf_recv,maxrecv,"comm:buf_recv");
maxswap = 6;
allocate_swap(maxswap);
sendlist = (int **) memory->smalloc(maxswap*sizeof(int *),"sendlist");
- maxsendlist = (int *) memory->smalloc(maxswap*sizeof(int),"maxsendlist");
+ memory->create(maxsendlist,maxswap,"maxsendlist");
for (int i = 0; i < maxswap; i++) {
maxsendlist[i] = BUFMIN;
- sendlist[i] = (int *) memory->smalloc(BUFMIN*sizeof(int),"sendlist[i]");
+ memory->create(sendlist[i],BUFMIN,"sendlist[i]");
}
maxforward_fix = maxreverse_fix = 0;
@@ -92,20 +90,20 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
Comm::~Comm()
{
- if (grid2proc) memory->destroy_3d_int_array(grid2proc);
+ if (grid2proc) memory->destroy(grid2proc);
free_swap();
if (style == MULTI) {
free_multi();
- memory->destroy_2d_double_array(cutghostmulti);
+ memory->destroy(cutghostmulti);
}
- memory->sfree(maxsendlist);
- if (sendlist) for (int i = 0; i < maxswap; i++) memory->sfree(sendlist[i]);
+ memory->destroy(maxsendlist);
+ if (sendlist) for (int i = 0; i < maxswap; i++) memory->destroy(sendlist[i]);
memory->sfree(sendlist);
- memory->sfree(buf_send);
- memory->sfree(buf_recv);
+ memory->destroy(buf_send);
+ memory->destroy(buf_recv);
}
/* ----------------------------------------------------------------------
@@ -121,9 +119,9 @@ void Comm::set_procs()
if (domain->dimension == 2 && procgrid[2] != 1)
error->all("Processor count in z must be 1 for 2d simulation");
- if (grid2proc) memory->destroy_3d_int_array(grid2proc);
- grid2proc = memory->create_3d_int_array(procgrid[0],procgrid[1],procgrid[2],
- "comm:grid2proc");
+ if (grid2proc) memory->destroy(grid2proc);
+ memory->create(grid2proc,procgrid[0],procgrid[1],procgrid[2],
+ "comm:grid2proc");
// use MPI Cartesian routines to setup 3d grid of procs
// grid2proc[i][j][k] = proc that owns i,j,k location in grid
@@ -213,12 +211,11 @@ void Comm::init()
if (style == MULTI && multilo == NULL) {
allocate_multi(maxswap);
- cutghostmulti =
- memory->create_2d_double_array(atom->ntypes+1,3,"comm:cutghostmulti");
+ memory->create(cutghostmulti,atom->ntypes+1,3,"comm:cutghostmulti");
}
if (style == SINGLE && multilo) {
free_multi();
- memory->destroy_2d_double_array(cutghostmulti);
+ memory->destroy(cutghostmulti);
}
}
@@ -1129,13 +1126,10 @@ void Comm::grow_send(int n, int flag)
{
maxsend = static_cast<int> (BUFFACTOR * n);
if (flag)
- buf_send = (double *)
- memory->srealloc(buf_send,(maxsend+BUFEXTRA)*sizeof(double),
- "comm:buf_send");
+ memory->grow(buf_send,(maxsend+BUFEXTRA),"comm:buf_send");
else {
- memory->sfree(buf_send);
- buf_send = (double *) memory->smalloc((maxsend+BUFEXTRA)*sizeof(double),
- "comm:buf_send");
+ memory->destroy(buf_send);
+ memory->create(buf_send,maxsend+BUFEXTRA,"comm:buf_send");
}
}
@@ -1146,9 +1140,8 @@ void Comm::grow_send(int n, int flag)
void Comm::grow_recv(int n)
{
maxrecv = static_cast<int> (BUFFACTOR * n);
- memory->sfree(buf_recv);
- buf_recv = (double *) memory->smalloc(maxrecv*sizeof(double),
- "comm:buf_recv");
+ memory->destroy(buf_recv);
+ memory->create(buf_recv,maxrecv,"comm:buf_recv");
}
/* ----------------------------------------------------------------------
@@ -1158,9 +1151,7 @@ void Comm::grow_recv(int n)
void Comm::grow_list(int iswap, int n)
{
maxsendlist[iswap] = static_cast<int> (BUFFACTOR * n);
- sendlist[iswap] = (int *)
- memory->srealloc(sendlist[iswap],maxsendlist[iswap]*sizeof(int),
- "comm:sendlist[iswap]");
+ memory->grow(sendlist[iswap],maxsendlist[iswap],"comm:sendlist[iswap]");
}
/* ----------------------------------------------------------------------
@@ -1178,12 +1169,10 @@ void Comm::grow_swap(int n)
sendlist = (int **)
memory->srealloc(sendlist,n*sizeof(int *),"comm:sendlist");
- maxsendlist = (int *)
- memory->srealloc(maxsendlist,n*sizeof(int),"comm:maxsendlist");
+ memory->grow(maxsendlist,n,"comm:maxsendlist");
for (int i = maxswap; i < n; i++) {
maxsendlist[i] = BUFMIN;
- sendlist[i] = (int *)
- memory->smalloc(BUFMIN*sizeof(int),"comm:sendlist[i]");
+ memory->create(sendlist[i],BUFMIN,"comm:sendlist[i]");
}
maxswap = n;
}
@@ -1194,29 +1183,28 @@ void Comm::grow_swap(int n)
void Comm::allocate_swap(int n)
{
- sendnum = (int *) memory->smalloc(n*sizeof(int),"comm:sendnum");
- recvnum = (int *) memory->smalloc(n*sizeof(int),"comm:recvnum");
- sendproc = (int *) memory->smalloc(n*sizeof(int),"comm:sendproc");
- recvproc = (int *) memory->smalloc(n*sizeof(int),"comm:recvproc");
- size_forward_recv = (int *) memory->smalloc(n*sizeof(int),"comm:size");
- size_reverse_send = (int *) memory->smalloc(n*sizeof(int),"comm:size");
- size_reverse_recv = (int *) memory->smalloc(n*sizeof(int),"comm:size");
- slablo = (double *) memory->smalloc(n*sizeof(double),"comm:slablo");
- slabhi = (double *) memory->smalloc(n*sizeof(double),"comm:slabhi");
- firstrecv = (int *) memory->smalloc(n*sizeof(int),"comm:firstrecv");
- pbc_flag = (int *) memory->smalloc(n*sizeof(int),"comm:pbc_flag");
- pbc = (int **) memory->create_2d_int_array(n,6,"comm:pbc");
+ memory->create(sendnum,n,"comm:sendnum");
+ memory->create(recvnum,n,"comm:recvnum");
+ memory->create(sendproc,n,"comm:sendproc");
+ memory->create(recvproc,n,"comm:recvproc");
+ memory->create(size_forward_recv,n,"comm:size");
+ memory->create(size_reverse_send,n,"comm:size");
+ memory->create(size_reverse_recv,n,"comm:size");
+ memory->create(slablo,n,"comm:slablo");
+ memory->create(slabhi,n,"comm:slabhi");
+ memory->create(firstrecv,n,"comm:firstrecv");
+ memory->create(pbc_flag,n,"comm:pbc_flag");
+ memory->create(pbc,n,6,"comm:pbc");
}
-
/* ----------------------------------------------------------------------
allocation of multi-type swap info
------------------------------------------------------------------------- */
void Comm::allocate_multi(int n)
{
- multilo = memory->create_2d_double_array(n,atom->ntypes+1,"comm:multilo");
- multihi = memory->create_2d_double_array(n,atom->ntypes+1,"comm:multihi");
+ multilo = memory->create(multilo,n,atom->ntypes+1,"comm:multilo");
+ multihi = memory->create(multihi,n,atom->ntypes+1,"comm:multihi");
}
/* ----------------------------------------------------------------------
@@ -1225,17 +1213,17 @@ void Comm::allocate_multi(int n)
void Comm::free_swap()
{
- memory->sfree(sendnum);
- memory->sfree(recvnum);
- memory->sfree(sendproc);
- memory->sfree(recvproc);
- memory->sfree(size_forward_recv);
- memory->sfree(size_reverse_send);
- memory->sfree(size_reverse_recv);
- memory->sfree(slablo);
- memory->sfree(slabhi);
- memory->sfree(firstrecv);
- memory->sfree(pbc_flag);
+ memory->destroy(sendnum);
+ memory->destroy(recvnum);
+ memory->destroy(sendproc);
+ memory->destroy(recvproc);
+ memory->destroy(size_forward_recv);
+ memory->destroy(size_reverse_send);
+ memory->destroy(size_reverse_recv);
+ memory->destroy(slablo);
+ memory->destroy(slabhi);
+ memory->destroy(firstrecv);
+ memory->destroy(pbc_flag);
memory->destroy_2d_int_array(pbc);
}
@@ -1245,8 +1233,8 @@ void Comm::free_swap()
void Comm::free_multi()
{
- memory->destroy_2d_double_array(multilo);
- memory->destroy_2d_double_array(multihi);
+ memory->destroy(multilo);
+ memory->destroy(multihi);
}
/* ----------------------------------------------------------------------
diff --git a/src/memory.cpp b/src/memory.cpp
index b7e4c4dc4b..0f69561210 100644
--- a/src/memory.cpp
+++ b/src/memory.cpp
@@ -71,6 +71,51 @@ void *Memory::srealloc(void *ptr, int n, const char *name)
return ptr;
}
+/* ----------------------------------------------------------------------
+ newer routines
+------------------------------------------------------------------------- */
+
+void *Memory::smalloc_new(bigint nbytes, const char *name)
+{
+ if (nbytes == 0) return NULL;
+
+ void *ptr = malloc(nbytes);
+ if (ptr == NULL) {
+ char str[128];
+ sprintf(str,"Failed to allocate " BIGINT_FORMAT "bytes for array %s",
+ nbytes,name);
+ error->one(str);
+ }
+ return ptr;
+}
+
+void *Memory::srealloc_new(void *ptr, bigint nbytes, const char *name)
+{
+ if (nbytes == 0) {
+ sfree_new(ptr);
+ return NULL;
+ }
+
+ ptr = realloc(ptr,nbytes);
+ if (ptr == NULL) {
+ char str[128];
+ sprintf(str,"Failed to reallocate " BIGINT_FORMAT "bytes for array %s",
+ nbytes,name);
+ error->one(str);
+ }
+ return ptr;
+}
+
+void Memory::sfree_new(void *ptr)
+{
+ if (ptr == NULL) return;
+ free(ptr);
+}
+
+/* ----------------------------------------------------------------------
+ older routines
+------------------------------------------------------------------------- */
+
/* ----------------------------------------------------------------------
create a 1d double array with index from nlo to nhi inclusive
------------------------------------------------------------------------- */
@@ -361,7 +406,6 @@ void Memory::destroy_3d_double_array(double ***array, int n1_offset,
sfree(array + n1_offset);
}
-
/* ----------------------------------------------------------------------
create a 3d int array
------------------------------------------------------------------------- */
diff --git a/src/memory.h b/src/memory.h
index 8ed2a8e051..3a2a90775c 100644
--- a/src/memory.h
+++ b/src/memory.h
@@ -14,6 +14,7 @@
#ifndef LMP_MEMORY_H
#define LMP_MEMORY_H
+#include "lmptype.h"
#include "pointers.h"
namespace LAMMPS_NS {
@@ -22,6 +23,8 @@ class Memory : protected Pointers {
public:
Memory(class LAMMPS *);
+ // older routines
+
void *smalloc(int n, const char *);
void sfree(void *);
void *srealloc(void *, int n, const char *);
@@ -55,6 +58,345 @@ class Memory : protected Pointers {
double ****create_4d_double_array(int, int, int, int, const char *);
void destroy_4d_double_array(double ****);
+
+ // newer routines
+
+ public:
+ void *smalloc_new(bigint n, const char *);
+ void *srealloc_new(void *, bigint n, const char *);
+ void sfree_new(void *);
+
+
+/* ----------------------------------------------------------------------
+ NOTE: to avoid code bloat, only use these for int,double,float,char
+ otherwise, just use smalloc,srealloc,sfree
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ create a 1d array
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ TYPE *create(TYPE *&array, int n, const char *name)
+ {
+ bigint nbytes = sizeof(TYPE) * n;
+ array = (TYPE *) smalloc_new(nbytes,name);
+ return array;
+ };
+
+/* ----------------------------------------------------------------------
+ grow or shrink 1d array
+ if dim is 0, return NULL
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ TYPE *grow(TYPE *&array, int n, const char *name)
+ {
+ if (array == NULL) return create(array,n,name);
+ if (n == 0) {
+ destroy(array);
+ return NULL;
+ }
+
+ bigint nbytes = sizeof(TYPE) * n;
+ array = (TYPE *) srealloc_new(array,nbytes,name);
+ return array;
+ };
+
+/* ----------------------------------------------------------------------
+ destroy a 1d array
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ void destroy(TYPE *array)
+ {
+ sfree_new(array);
+ };
+
+/* ----------------------------------------------------------------------
+ create a 1d array with index from nlo to nhi inclusive
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ TYPE *create(TYPE *&array, int nlo, int nhi, const char *name)
+ {
+ bigint nbytes = sizeof(TYPE) * (nhi-nlo+1);
+ array = (TYPE *) smalloc_new(nbytes,name);
+ array = array-nlo;
+ return array;
+ }
+
+/* ----------------------------------------------------------------------
+ destroy a 1d array with index offset
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ void destroy(TYPE *array, int offset)
+ {
+ if (array) sfree_new(array+offset);
+ }
+
+/* ----------------------------------------------------------------------
+ create a 2d array
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ TYPE **create(TYPE **&array, int n1, int n2, const char *name)
+ {
+ bigint nbytes = sizeof(TYPE) * n1*n2;
+ TYPE *data = (TYPE *) smalloc_new(nbytes,name);
+ nbytes = sizeof(TYPE *) * n1;
+ array = (TYPE **) smalloc_new(nbytes,name);
+
+ int n = 0;
+ for (int i = 0; i < n1; i++) {
+ array[i] = &data[n];
+ n += n2;
+ }
+ return array;
+ }
+
+/* ----------------------------------------------------------------------
+ grow or shrink 1st dim of a 2d array
+ last dim must stay the same
+ if either dim is 0, destroy it and return NULL
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ TYPE **grow(TYPE **&array, int n1, int n2, const char *name)
+ {
+ if (array == NULL) return create(array,n1,n2,name);
+ if (n1 == 0 || n2 == 0) {
+ destroy(array);
+ return NULL;
+ }
+
+ bigint nbytes = sizeof(TYPE) * n1*n2;
+ TYPE *data = (TYPE *) srealloc_new(array[0],nbytes,name);
+ nbytes = sizeof(TYPE *) * n1;
+ array = (TYPE **) srealloc_new(array,nbytes,name);
+
+ int n = 0;
+ for (int i = 0; i < n1; i++) {
+ array[i] = &data[n];
+ n += n2;
+ }
+ return array;
+ }
+
+/* ----------------------------------------------------------------------
+ destroy a 2d array
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ void destroy(TYPE **array)
+ {
+ if (array == NULL) return;
+ sfree_new(array[0]);
+ sfree_new(array);
+ }
+
+/* ----------------------------------------------------------------------
+ create a 2d array with 2nd index from n2lo to n2hi inclusive
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ TYPE **create(TYPE **&array, int n1, int n2lo, int n2hi,
+ const char *name)
+ {
+ int n2 = n2hi - n2lo + 1;
+ create(array,n1,n2,name);
+ for (int i = 0; i < n1; i++) array[i] -= n2lo;
+ return array;
+ }
+
+/* ----------------------------------------------------------------------
+ destroy a 2d array with 2nd index offset
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ void destroy(TYPE **array, int offset)
+ {
+ if (array == NULL) return;
+ sfree_new(&array[0][offset]);
+ sfree_new(array);
+ }
+
+/* ----------------------------------------------------------------------
+ create a 3d array
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ TYPE ***create(TYPE ***&array, int n1, int n2, int n3, const char *name)
+ {
+ bigint nbytes = sizeof(TYPE) * n1*n2*n3;
+ TYPE *data = (TYPE *) smalloc_new(nbytes,name);
+ nbytes = sizeof(TYPE *) * n1*n2;
+ TYPE **plane = (TYPE **) smalloc_new(nbytes,name);
+ nbytes = sizeof(TYPE **) * n1;
+ array = (TYPE ***) smalloc_new(nbytes,name);
+
+ int i,j;
+ int n = 0;
+ for (i = 0; i < n1; i++) {
+ array[i] = &plane[i*n2];
+ for (j = 0; j < n2; j++) {
+ plane[i*n2+j] = &data[n];
+ n += n3;
+ }
+ }
+ return array;
+ }
+
+/* ----------------------------------------------------------------------
+ grow or shrink 1st dim of a 3d array
+ last 2 dims must stay the same
+ if any dim is 0, destroy it and return NULL
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ TYPE ***grow(TYPE ***&array, int n1, int n2, int n3, const char *name)
+ {
+ if (array == NULL) return create(array,n1,n2,n3,name);
+ if (n1 == 0 || n2 == 0 || n3 == 0) {
+ destroy(array);
+ return NULL;
+ }
+
+ bigint nbytes = sizeof(TYPE) * n1*n2*n3;
+ TYPE *data = (TYPE *) srealloc_new(array[0][0],nbytes,name);
+ nbytes = sizeof(TYPE *) * n1*n2;
+ TYPE **plane = (TYPE **) srealloc_new(array[0],nbytes,name);
+ nbytes = sizeof(TYPE **) * n1;
+ array = (TYPE ***) srealloc_new(array,nbytes,name);
+
+ int i,j;
+ int n = 0;
+ for (i = 0; i < n1; i++) {
+ array[i] = &plane[i*n2];
+ for (j = 0; j < n2; j++) {
+ plane[i*n2+j] = &data[n];
+ n += n3;
+ }
+ }
+ return array;
+ }
+
+/* ----------------------------------------------------------------------
+ destroy a 3d array
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ void destroy(TYPE ***array)
+ {
+ if (array == NULL) return;
+ sfree_new(array[0][0]);
+ sfree_new(array[0]);
+ sfree_new(array);
+ }
+
+/* ----------------------------------------------------------------------
+ create a 3d array with 1st index from n1lo to n1hi inclusive
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ TYPE ***create(TYPE ***&array, int n1lo, int n1hi,
+ int n2, int n3, const char *name)
+ {
+ int n1 = n1hi - n1lo + 1;
+ create(array,n1,n2,n3,name);
+ return array-n1lo;
+ }
+
+/* ----------------------------------------------------------------------
+ free a 3d array with 1st index offset
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ void destroy(TYPE ***array, int offset)
+ {
+ if (array) destroy(array+offset);
+ }
+
+/* ----------------------------------------------------------------------
+ create a 3d array with
+ 1st index from n1lo to n1hi inclusive,
+ 2nd index from n2lo to n2hi inclusive,
+ 3rd index from n3lo to n3hi inclusive
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ TYPE ***create(TYPE ***&array, int n1lo, int n1hi, int n2lo, int n2hi,
+ int n3lo, int n3hi, const char *name)
+ {
+ int n1 = n1hi - n1lo + 1;
+ int n2 = n2hi - n2lo + 1;
+ int n3 = n3hi - n3lo + 1;
+ create(array,n1,n2,n3,name);
+
+ for (int i = 0; i < n1*n2; i++) array[0][i] -= n3lo;
+ for (int i = 0; i < n1; i++) array[i] -= n2lo;
+ return array-n1lo;
+ }
+
+/* ----------------------------------------------------------------------
+ free a 3d array with all 3 indices offset
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ void destroy(TYPE ***array, int n1_offset, int n2_offset, int n3_offset)
+ {
+ if (array == NULL) return;
+ sfree_new(&array[n1_offset][n2_offset][n3_offset]);
+ sfree_new(&array[n1_offset][n2_offset]);
+ sfree_new(array + n1_offset);
+ }
+
+/* ----------------------------------------------------------------------
+ create a 4d array
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ TYPE ****create(TYPE ****&array, int n1, int n2, int n3, int n4,
+ const char *name)
+ {
+ bigint nbytes = sizeof(TYPE) * n1*n2*n3*n4;
+ TYPE *data = (double *) smalloc_new(nbytes,name);
+ nbytes = sizeof(TYPE *) * n1*n2*n3;
+ TYPE **cube = (double **) smalloc_new(nbytes,name);
+ nbytes = sizeof(TYPE **) * n1*n2;
+ TYPE ***plane = (double ***) smalloc_new(nbytes,name);
+ nbytes = sizeof(TYPE ***) * n1;
+ array = (double ****) smalloc_new(nbytes,name);
+
+ int i,j,k;
+ int n = 0;
+ for (i = 0; i < n1; i++) {
+ array[i] = &plane[i*n2];
+ for (j = 0; j < n2; j++) {
+ plane[i*n2+j] = &cube[i*n2*n3+j*n3];
+ for (k = 0; k < n3; k++) {
+ cube[i*n2*n3+j*n3+k] = &data[n];
+ n += n4;
+ }
+ }
+ }
+ return array;
+ }
+
+/* ----------------------------------------------------------------------
+ destroy a 4d array
+------------------------------------------------------------------------- */
+
+ template <typename TYPE>
+ void destroy(TYPE ****array)
+ {
+ if (array == NULL) return;
+ sfree_new(array[0][0][0]);
+ sfree_new(array[0][0]);
+ sfree_new(array[0]);
+ sfree_new(array);
+ }
};
}
diff --git a/src/neigh_bond.cpp b/src/neigh_bond.cpp
index 2ef6b89507..b16598011e 100644
--- a/src/neigh_bond.cpp
+++ b/src/neigh_bond.cpp
@@ -51,8 +51,7 @@ void Neighbor::bond_all()
if (newton_bond || i < atom1) {
if (nbondlist == maxbond) {
maxbond += BONDDELTA;
- bondlist = memory->grow_2d_int_array(bondlist,maxbond,3,
- "neighbor:bondlist");
+ memory->grow(bondlist,maxbond,3,"neighbor:bondlist");
}
bondlist[nbondlist][0] = i;
bondlist[nbondlist][1] = atom1;
@@ -91,8 +90,7 @@ void Neighbor::bond_partial()
if (newton_bond || i < atom1) {
if (nbondlist == maxbond) {
maxbond += BONDDELTA;
- bondlist = memory->grow_2d_int_array(bondlist,maxbond,3,
- "neighbor:bondlist");
+ memory->grow(bondlist,maxbond,3,"neighbor:bondlist");
}
bondlist[nbondlist][0] = i;
bondlist[nbondlist][1] = atom1;
@@ -135,8 +133,7 @@ void Neighbor::angle_all()
if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
if (nanglelist == maxangle) {
maxangle += BONDDELTA;
- anglelist = memory->grow_2d_int_array(anglelist,maxangle,4,
- "neighbor:anglelist");
+ memory->grow(anglelist,maxangle,4,"neighbor:anglelist");
}
anglelist[nanglelist][0] = atom1;
anglelist[nanglelist][1] = atom2;
@@ -181,8 +178,7 @@ void Neighbor::angle_partial()
if (newton_bond || (i <= atom1 && i <= atom2 && i <= atom3)) {
if (nanglelist == maxangle) {
maxangle += BONDDELTA;
- anglelist = memory->grow_2d_int_array(anglelist,maxangle,4,
- "neighbor:anglelist");
+ memory->grow(anglelist,maxangle,4,"neighbor:anglelist");
}
anglelist[nanglelist][0] = atom1;
anglelist[nanglelist][1] = atom2;
@@ -230,9 +226,7 @@ void Neighbor::dihedral_all()
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (ndihedrallist == maxdihedral) {
maxdihedral += BONDDELTA;
- dihedrallist =
- memory->grow_2d_int_array(dihedrallist,maxdihedral,5,
- "neighbor:dihedrallist");
+ memory->grow(dihedrallist,maxdihedral,5,"neighbor:dihedrallist");
}
dihedrallist[ndihedrallist][0] = atom1;
dihedrallist[ndihedrallist][1] = atom2;
@@ -282,9 +276,7 @@ void Neighbor::dihedral_partial()
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (ndihedrallist == maxdihedral) {
maxdihedral += BONDDELTA;
- dihedrallist =
- memory->grow_2d_int_array(dihedrallist,maxdihedral,5,
- "neighbor:dihedrallist");
+ memory->grow(dihedrallist,maxdihedral,5,"neighbor:dihedrallist");
}
dihedrallist[ndihedrallist][0] = atom1;
dihedrallist[ndihedrallist][1] = atom2;
@@ -333,9 +325,7 @@ void Neighbor::improper_all()
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (nimproperlist == maximproper) {
maximproper += BONDDELTA;
- improperlist =
- memory->grow_2d_int_array(improperlist,maximproper,5,
- "neighbor:improperlist");
+ memory->grow(improperlist,maximproper,5,"neighbor:improperlist");
}
improperlist[nimproperlist][0] = atom1;
improperlist[nimproperlist][1] = atom2;
@@ -385,9 +375,7 @@ void Neighbor::improper_partial()
(i <= atom1 && i <= atom2 && i <= atom3 && i <= atom4)) {
if (nimproperlist == maximproper) {
maximproper += BONDDELTA;
- improperlist =
- memory->grow_2d_int_array(improperlist,maximproper,5,
- "neighbor:improperlist");
+ memory->grow(improperlist,maximproper,5,"neighbor:improperlist");
}
improperlist[nimproperlist][0] = atom1;
improperlist[nimproperlist][1] = atom2;
diff --git a/src/neigh_list.cpp b/src/neigh_list.cpp
index 9426c3df68..c5bd04b3f7 100644
--- a/src/neigh_list.cpp
+++ b/src/neigh_list.cpp
@@ -70,27 +70,27 @@ NeighList::NeighList(LAMMPS *lmp, int size) : Pointers(lmp)
NeighList::~NeighList()
{
if (!listcopy) {
- memory->sfree(ilist);
- memory->sfree(numneigh);
+ memory->destroy(ilist);
+ memory->destroy(numneigh);
memory->sfree(firstneigh);
memory->sfree(firstdouble);
- for (int i = 0; i < maxpage; i++) memory->sfree(pages[i]);
+ for (int i = 0; i < maxpage; i++) memory->destroy(pages[i]);
memory->sfree(pages);
if (dnum) {
- for (int i = 0; i < maxpage; i++) memory->sfree(dpages[i]);
+ for (int i = 0; i < maxpage; i++) memory->destroy(dpages[i]);
memory->sfree(dpages);
}
}
delete [] iskip;
- memory->destroy_2d_int_array(ijskip);
+ memory->destroy(ijskip);
- if (maxstencil) memory->sfree(stencil);
+ if (maxstencil) memory->destroy(stencil);
if (maxstencil_multi) {
for (int i = 1; i <= atom->ntypes; i++) {
- memory->sfree(stencil_multi[i]);
- memory->sfree(distsq_multi[i]);
+ memory->destroy(stencil_multi[i]);
+ memory->destroy(distsq_multi[i]);
}
delete [] nstencil_multi;
delete [] stencil_multi;
@@ -110,13 +110,11 @@ void NeighList::grow(int nmax)
if (nmax <= maxlocal) return;
maxlocal = nmax;
- memory->sfree(ilist);
- memory->sfree(numneigh);
+ memory->destroy(ilist);
+ memory->destroy(numneigh);
memory->sfree(firstneigh);
- ilist = (int *)
- memory->smalloc(maxlocal*sizeof(int),"neighlist:ilist");
- numneigh = (int *)
- memory->smalloc(maxlocal*sizeof(int),"neighlist:numneigh");
+ memory->create(ilist,maxlocal,"neighlist:ilist");
+ memory->create(numneigh,maxlocal,"neighlist:numneigh");
firstneigh = (int **)
memory->smalloc(maxlocal*sizeof(int *),"neighlist:firstneigh");
@@ -137,8 +135,8 @@ void NeighList::stencil_allocate(int smax, int style)
if (style == BIN) {
if (smax > maxstencil) {
maxstencil = smax;
- memory->sfree(stencil);
- stencil = (int *) memory->smalloc(smax*sizeof(int),"neighlist:stencil");
+ memory->destroy(stencil);
+ memory->create(stencil,smax,"neighlist:stencil");
}
} else {
@@ -156,12 +154,10 @@ void NeighList::stencil_allocate(int smax, int style)
if (smax > maxstencil_multi) {
maxstencil_multi = smax;
for (i = 1; i <= n; i++) {
- memory->sfree(stencil_multi[i]);
- memory->sfree(distsq_multi[i]);
- stencil_multi[i] = (int *)
- memory->smalloc(smax*sizeof(int),"neighlist:stencil_multi");
- distsq_multi[i] = (double *) memory->smalloc(smax*sizeof(double),
- "neighlist:distsq_multi");
+ memory->destroy(stencil_multi[i]);
+ memory->destroy(distsq_multi[i]);
+ memory->create(stencil_multi[i],smax,"neighlist:stencil_multi");
+ memory->create(distsq_multi[i],smax,"neighlist:distsq_multi");
}
}
}
@@ -179,15 +175,13 @@ int **NeighList::add_pages()
pages = (int **)
memory->srealloc(pages,maxpage*sizeof(int *),"neighlist:pages");
for (int i = npage; i < maxpage; i++)
- pages[i] = (int *) memory->smalloc(pgsize*sizeof(int),
- "neighlist:pages[i]");
+ memory->create(pages[i],pgsize,"neighlist:pages[i]");
if (dnum) {
dpages = (double **)
memory->srealloc(dpages,maxpage*sizeof(double *),"neighlist:dpages");
for (int i = npage; i < maxpage; i++)
- dpages[i] = (double *) memory->smalloc(dnum*pgsize*sizeof(double),
- "neighlist:dpages[i]");
+ memory->create(dpages[i],dnum*pgsize,"neighlist:dpages[i]");
}
return pages;
@@ -201,8 +195,7 @@ void NeighList::copy_skip_info(int *rq_iskip, int **rq_ijskip)
{
int ntypes = atom->ntypes;
iskip = new int[ntypes+1];
- ijskip = memory->create_2d_int_array(ntypes+1,ntypes+1,
- "neigh_list:ijskip");
+ memory->create(ijskip,ntypes+1,ntypes+1,"neigh_list:ijskip");
int i,j;
for (i = 1; i <= ntypes; i++) iskip[i] = rq_iskip[i];
for (i = 1; i <= ntypes; i++)
diff --git a/src/neigh_request.cpp b/src/neigh_request.cpp
index 4eb2a73a56..bd55b6e79f 100644
--- a/src/neigh_request.cpp
+++ b/src/neigh_request.cpp
@@ -64,7 +64,7 @@ NeighRequest::NeighRequest(LAMMPS *lmp) : Pointers(lmp)
NeighRequest::~NeighRequest()
{
delete [] iskip;
- memory->destroy_2d_int_array(ijskip);
+ memory->destroy(ijskip);
}
/* ----------------------------------------------------------------------
diff --git a/src/neigh_stencil.cpp b/src/neigh_stencil.cpp
index 7f2170a022..8c41021782 100644
--- a/src/neigh_stencil.cpp
+++ b/src/neigh_stencil.cpp
@@ -14,7 +14,6 @@
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
-#include "memory.h"
using namespace LAMMPS_NS;
diff --git a/src/neighbor.cpp b/src/neighbor.cpp
index bddea6484b..76ec425b72 100644
--- a/src/neighbor.cpp
+++ b/src/neighbor.cpp
@@ -138,26 +138,26 @@ Neighbor::Neighbor(LAMMPS *lmp) : Pointers(lmp)
Neighbor::~Neighbor()
{
- memory->destroy_2d_double_array(cutneighsq);
+ memory->destroy(cutneighsq);
delete [] cuttype;
delete [] cuttypesq;
delete [] fixchecklist;
- memory->destroy_2d_double_array(xhold);
+ memory->destroy(xhold);
- memory->sfree(binhead);
- memory->sfree(bins);
+ memory->destroy(binhead);
+ memory->destroy(bins);
- memory->sfree(ex1_type);
- memory->sfree(ex2_type);
- memory->destroy_2d_int_array(ex_type);
+ memory->destroy(ex1_type);
+ memory->destroy(ex2_type);
+ memory->destroy(ex_type);
- memory->sfree(ex1_group);
- memory->sfree(ex2_group);
+ memory->destroy(ex1_group);
+ memory->destroy(ex2_group);
delete [] ex1_bit;
delete [] ex2_bit;
- memory->sfree(ex_mol_group);
+ memory->destroy(ex_mol_group);
delete [] ex_mol_bit;
for (int i = 0; i < nlist; i++) delete lists[i];
@@ -173,10 +173,10 @@ Neighbor::~Neighbor()
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->destroy(bondlist);
+ memory->destroy(anglelist);
+ memory->destroy(dihedrallist);
+ memory->destroy(improperlist);
}
/* ---------------------------------------------------------------------- */
@@ -225,7 +225,7 @@ void Neighbor::init()
n = atom->ntypes;
if (cutneighsq == NULL) {
- cutneighsq = memory->create_2d_double_array(n+1,n+1,"neigh:cutneighsq");
+ memory->create(cutneighsq,n+1,n+1,"neigh:cutneighsq");
cuttype = new double[n+1];
cuttypesq = new double[n+1];
}
@@ -326,14 +326,14 @@ void Neighbor::init()
// free xhold and bins if not needed for this run
if (dist_check == 0) {
- memory->destroy_2d_double_array(xhold);
+ memory->destroy(xhold);
maxhold = 0;
xhold = NULL;
}
if (style == NSQ) {
- memory->sfree(bins);
- memory->sfree(binhead);
+ memory->destroy(bins);
+ memory->destroy(binhead);
maxbin = maxhead = 0;
binhead = NULL;
bins = NULL;
@@ -344,14 +344,14 @@ void Neighbor::init()
if (dist_check) {
if (maxhold == 0) {
maxhold = atom->nmax;
- xhold = memory->create_2d_double_array(maxhold,3,"neigh:xhold");
+ memory->create(xhold,maxhold,3,"neigh:xhold");
}
}
if (style != NSQ) {
if (maxbin == 0) {
maxbin = atom->nmax;
- bins = (int *) memory->smalloc(maxbin*sizeof(int),"bins");
+ memory->create(bins,maxbin,"bins");
}
}
@@ -363,8 +363,8 @@ void Neighbor::init()
else exclude = 1;
if (nex_type) {
- memory->destroy_2d_int_array(ex_type);
- ex_type = (int **) memory->create_2d_int_array(n+1,n+1,"neigh:ex_type");
+ memory->destroy(ex_type);
+ memory->create(ex_type,n+1,n+1,"neigh:ex_type");
for (i = 1; i <= n; i++)
for (j = 1; j <= n; j++)
@@ -647,7 +647,7 @@ void Neighbor::init()
// 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);
+ memory->destroy(old_requests);
old_nrequest = nrequest;
old_requests = requests;
nrequest = maxrequest = 0;
@@ -663,29 +663,27 @@ void Neighbor::init()
if (atom->molecular && atom->nbonds && maxbond == 0) {
if (nprocs == 1) maxbond = atom->nbonds;
else maxbond = static_cast<int> (LB_FACTOR * atom->nbonds / nprocs);
- bondlist = memory->create_2d_int_array(maxbond,3,"neigh:bondlist");
+ memory->create(bondlist,maxbond,3,"neigh:bondlist");
}
if (atom->molecular && atom->nangles && maxangle == 0) {
if (nprocs == 1) maxangle = atom->nangles;
else maxangle = static_cast<int> (LB_FACTOR * atom->nangles / nprocs);
- anglelist = memory->create_2d_int_array(maxangle,4,"neigh:anglelist");
+ memory->create(anglelist,maxangle,4,"neigh:anglelist");
}
if (atom->molecular && atom->ndihedrals && maxdihedral == 0) {
if (nprocs == 1) maxdihedral = atom->ndihedrals;
else maxdihedral = static_cast<int>
(LB_FACTOR * atom->ndihedrals / nprocs);
- dihedrallist =
- memory->create_2d_int_array(maxdihedral,5,"neigh:dihedrallist");
+ memory->create(dihedrallist,maxdihedral,5,"neigh:dihedrallist");
}
if (atom->molecular && atom->nimpropers && maximproper == 0) {
if (nprocs == 1) maximproper = atom->nimpropers;
else maximproper = static_cast<int>
(LB_FACTOR * atom->nimpropers / nprocs);
- improperlist =
- memory->create_2d_int_array(maximproper,5,"neigh:improperlist");
+ memory->create(improperlist,maximproper,5,"neigh:improperlist");
}
// set flags that determine which topology neighboring routines to use
@@ -1093,8 +1091,8 @@ void Neighbor::build()
if (includegroup) nlocal = atom->nfirst;
if (nlocal > maxhold) {
maxhold = atom->nmax;
- memory->destroy_2d_double_array(xhold);
- xhold = memory->create_2d_double_array(maxhold,3,"neigh:xhold");
+ memory->destroy(xhold);
+ memory->create(xhold,maxhold,3,"neigh:xhold");
}
for (i = 0; i < nlocal; i++) {
xhold[i][0] = x[i][0];
@@ -1133,8 +1131,8 @@ void Neighbor::build()
if (style != NSQ && atom->nmax > maxbin) {
maxbin = atom->nmax;
- memory->sfree(bins);
- bins = (int *) memory->smalloc(maxbin*sizeof(int),"bins");
+ memory->destroy(bins);
+ memory->create(bins,maxbin,"bins");
}
// check that pairwise lists with special bond weighting will not overflow
@@ -1179,8 +1177,8 @@ void Neighbor::build_one(int i)
if (style != NSQ && atom->nmax > maxbin) {
maxbin = atom->nmax;
- memory->sfree(bins);
- bins = (int *) memory->smalloc(maxbin*sizeof(int),"bins");
+ memory->destroy(bins);
+ memory->create(bins,maxbin,"bins");
}
// this condition can cause LAMMPS to crash
@@ -1354,8 +1352,8 @@ void Neighbor::setup_bins()
mbins = bbin;
if (mbins > maxhead) {
maxhead = mbins;
- memory->sfree(binhead);
- binhead = (int *) memory->smalloc(maxhead*sizeof(int),"neigh:binhead");
+ memory->destroy(binhead);
+ memory->create(binhead,maxhead,"neigh:binhead");
}
// create stencil of bins to search over in neighbor list construction
@@ -1481,10 +1479,8 @@ void Neighbor::modify_params(int narg, char **arg)
if (iarg+4 > narg) error->all("Illegal neigh_modify command");
if (nex_type == maxex_type) {
maxex_type += EXDELTA;
- ex1_type = (int *) memory->srealloc(ex1_type,maxex_type*sizeof(int),
- "neigh:ex1_type");
- ex2_type = (int *) memory->srealloc(ex2_type,maxex_type*sizeof(int),
- "neigh:ex2_type");
+ memory->grow(ex1_type,maxex_type,"neigh:ex1_type");
+ memory->grow(ex2_type,maxex_type,"neigh:ex2_type");
}
ex1_type[nex_type] = atoi(arg[iarg+2]);
ex2_type[nex_type] = atoi(arg[iarg+3]);
@@ -1495,12 +1491,8 @@ void Neighbor::modify_params(int narg, char **arg)
if (iarg+4 > narg) error->all("Illegal neigh_modify command");
if (nex_group == maxex_group) {
maxex_group += EXDELTA;
- ex1_group =
- (int *) memory->srealloc(ex1_group,maxex_group*sizeof(int),
- "neigh:ex1_group");
- ex2_group =
- (int *) memory->srealloc(ex2_group,maxex_group*sizeof(int),
- "neigh:ex2_group");
+ memory->grow(ex1_group,maxex_group,"neigh:ex1_group");
+ memory->grow(ex2_group,maxex_group,"neigh:ex2_group");
}
ex1_group[nex_group] = group->find(arg[iarg+2]);
ex2_group[nex_group] = group->find(arg[iarg+3]);
@@ -1518,9 +1510,7 @@ void Neighbor::modify_params(int narg, char **arg)
}
if (nex_mol == maxex_mol) {
maxex_mol += EXDELTA;
- ex_mol_group =
- (int *) memory->srealloc(ex_mol_group,maxex_mol*sizeof(int),
- "neigh:ex_mol_group");
+ memory->grow(ex_mol_group,maxex_mol,"neigh:ex_mol_group");
}
ex_mol_group[nex_mol] = group->find(arg[iarg+2]);
if (ex_mol_group[nex_mol] == -1)
--
GitLab