From 759ee1f3e88b16ed78e46d85c24e83e2bc9dec1b Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 14 Apr 2011 17:40:40 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5940
f3b2605a-c512-4ea7-a41b-209d697bcdaa
---
src/ASPHERE/atom_vec_ellipsoid.cpp | 116 ++++++++++++++++++----------
src/ASPHERE/atom_vec_ellipsoid.h | 12 +--
src/DIPOLE/atom_vec_dipole.cpp | 73 +++++++++++------
src/DIPOLE/atom_vec_dipole.h | 8 +-
src/MOLECULE/atom_vec_angle.cpp | 23 ++++--
src/MOLECULE/atom_vec_angle.h | 4 +-
src/MOLECULE/atom_vec_bond.cpp | 23 ++++--
src/MOLECULE/atom_vec_bond.h | 4 +-
src/MOLECULE/atom_vec_full.cpp | 28 +++++--
src/MOLECULE/atom_vec_full.h | 4 +-
src/MOLECULE/atom_vec_molecular.cpp | 23 ++++--
src/MOLECULE/atom_vec_molecular.h | 4 +-
src/PERI/atom_vec_peri.cpp | 63 ++++++++++-----
src/PERI/atom_vec_peri.h | 8 +-
src/SRD/fix_srd.cpp | 2 -
src/USER-EFF/atom_vec_electron.cpp | 86 ++++++++++++++-------
src/USER-EFF/atom_vec_electron.h | 12 +--
src/atom.cpp | 4 +-
src/atom.h | 2 +-
src/atom_vec.h | 12 +--
src/atom_vec_charge.cpp | 23 ++++--
src/atom_vec_charge.h | 4 +-
src/atom_vec_hybrid.cpp | 109 ++++++++++++++++----------
src/atom_vec_sphere.cpp | 88 ++++++++++++++-------
src/atom_vec_sphere.h | 12 +--
src/pair_dpd_tstat.cpp | 2 +-
26 files changed, 490 insertions(+), 259 deletions(-)
diff --git a/src/ASPHERE/atom_vec_ellipsoid.cpp b/src/ASPHERE/atom_vec_ellipsoid.cpp
index e6c7a127e4..50820debe8 100755
--- a/src/ASPHERE/atom_vec_ellipsoid.cpp
+++ b/src/ASPHERE/atom_vec_ellipsoid.cpp
@@ -262,13 +262,19 @@ int AtomVecEllipsoid::pack_comm_vel(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
-int AtomVecEllipsoid::pack_comm_one(int i, double *buf)
+int AtomVecEllipsoid::pack_comm_hybrid(int n, int *list, double *buf)
{
- buf[0] = quat[i][0];
- buf[1] = quat[i][1];
- buf[2] = quat[i][2];
- buf[3] = quat[i][3];
- return 4;
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = quat[i][0];
+ buf[m++] = quat[i][1];
+ buf[m++] = quat[i][2];
+ buf[m++] = quat[i][3];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -317,13 +323,19 @@ void AtomVecEllipsoid::unpack_comm_vel(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecEllipsoid::unpack_comm_one(int i, double *buf)
+int AtomVecEllipsoid::unpack_comm_hybrid(int n, int first, double *buf)
{
- quat[i][0] = buf[0];
- quat[i][1] = buf[1];
- quat[i][2] = buf[2];
- quat[i][3] = buf[3];
- return 4;
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ quat[i][0] = buf[m++];
+ quat[i][1] = buf[m++];
+ quat[i][2] = buf[m++];
+ quat[i][3] = buf[m++];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -347,12 +359,18 @@ int AtomVecEllipsoid::pack_reverse(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecEllipsoid::pack_reverse_one(int i, double *buf)
+int AtomVecEllipsoid::pack_reverse_hybrid(int n, int first, double *buf)
{
- buf[0] = torque[i][0];
- buf[1] = torque[i][1];
- buf[2] = torque[i][2];
- return 3;
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ buf[m++] = torque[i][0];
+ buf[m++] = torque[i][1];
+ buf[m++] = torque[i][2];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -375,12 +393,18 @@ void AtomVecEllipsoid::unpack_reverse(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecEllipsoid::unpack_reverse_one(int i, double *buf)
+int AtomVecEllipsoid::unpack_reverse_hybrid(int n, int *list, double *buf)
{
- torque[i][0] += buf[0];
- torque[i][1] += buf[1];
- torque[i][2] += buf[2];
- return 3;
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ torque[j][0] += buf[m++];
+ torque[j][1] += buf[m++];
+ torque[j][2] += buf[m++];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -543,16 +567,22 @@ int AtomVecEllipsoid::pack_border_vel(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
-int AtomVecEllipsoid::pack_border_one(int i, double *buf)
+int AtomVecEllipsoid::pack_border_hybrid(int n, int *list, double *buf)
{
- buf[0] = shape[i][0];
- buf[1] = shape[i][1];
- buf[2] = shape[i][2];
- buf[3] = quat[i][0];
- buf[4] = quat[i][1];
- buf[5] = quat[i][2];
- buf[6] = quat[i][3];
- return 7;
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = shape[j][0];
+ buf[m++] = shape[j][1];
+ buf[m++] = shape[j][2];
+ buf[m++] = quat[j][0];
+ buf[m++] = quat[j][1];
+ buf[m++] = quat[j][2];
+ buf[m++] = quat[j][3];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -615,16 +645,22 @@ void AtomVecEllipsoid::unpack_border_vel(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecEllipsoid::unpack_border_one(int i, double *buf)
+int AtomVecEllipsoid::unpack_border_hybrid(int n, int first, double *buf)
{
- shape[i][0] = buf[0];
- shape[i][1] = buf[1];
- shape[i][2] = buf[2];
- quat[i][0] = buf[3];
- quat[i][1] = buf[4];
- quat[i][2] = buf[5];
- quat[i][3] = buf[6];
- return 7;
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ shape[i][0] = buf[m++];
+ shape[i][1] = buf[m++];
+ shape[i][2] = buf[m++];
+ quat[i][0] = buf[m++];
+ quat[i][1] = buf[m++];
+ quat[i][2] = buf[m++];
+ quat[i][3] = buf[m++];
+ }
+ return m;
}
/* ----------------------------------------------------------------------
diff --git a/src/ASPHERE/atom_vec_ellipsoid.h b/src/ASPHERE/atom_vec_ellipsoid.h
index e3f0938047..b1a4a81341 100755
--- a/src/ASPHERE/atom_vec_ellipsoid.h
+++ b/src/ASPHERE/atom_vec_ellipsoid.h
@@ -33,20 +33,20 @@ class AtomVecEllipsoid : public AtomVec {
void copy(int, int);
int pack_comm(int, int *, double *, int, int *);
int pack_comm_vel(int, int *, double *, int, int *);
- int pack_comm_one(int, double *);
+ int pack_comm_hybrid(int, int *, double *);
void unpack_comm(int, int, double *);
void unpack_comm_vel(int, int, double *);
- int unpack_comm_one(int, double *);
+ int unpack_comm_hybrid(int, int, double *);
int pack_reverse(int, int, double *);
- int pack_reverse_one(int, double *);
+ int pack_reverse_hybrid(int, int, double *);
void unpack_reverse(int, int *, double *);
- int unpack_reverse_one(int, double *);
+ int unpack_reverse_hybrid(int, int *, double *);
int pack_border(int, int *, double *, int, int *);
int pack_border_vel(int, int *, double *, int, int *);
- int pack_border_one(int, double *);
+ int pack_border_hybrid(int, int *, double *);
void unpack_border(int, int, double *);
void unpack_border_vel(int, int, double *);
- int unpack_border_one(int, double *);
+ int unpack_border_hybrid(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
int size_restart();
diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp
index 7a1bc6be14..71c9d1407b 100644
--- a/src/DIPOLE/atom_vec_dipole.cpp
+++ b/src/DIPOLE/atom_vec_dipole.cpp
@@ -44,7 +44,6 @@ AtomVecDipole::AtomVecDipole(LAMMPS *lmp, int narg, char **arg) :
size_data_vel = 7;
xcol_data = 4;
- atom->dipole_flag = 1;
atom->q_flag = atom->mu_flag = 1;
}
@@ -232,12 +231,18 @@ int AtomVecDipole::pack_comm_vel(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
-int AtomVecDipole::pack_comm_one(int i, double *buf)
+int AtomVecDipole::pack_comm_hybrid(int n, int *list, double *buf)
{
- buf[0] = mu[i][0];
- buf[1] = mu[i][1];
- buf[2] = mu[i][2];
- return 3;
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = mu[j][0];
+ buf[m++] = mu[j][1];
+ buf[m++] = mu[j][2];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -281,12 +286,18 @@ void AtomVecDipole::unpack_comm_vel(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecDipole::unpack_comm_one(int i, double *buf)
+int AtomVecDipole::unpack_comm_hybrid(int n, int first, double *buf)
{
- mu[i][0] = buf[0];
- mu[i][1] = buf[1];
- mu[i][2] = buf[2];
- return 3;
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ mu[i][0] = buf[m++];
+ mu[i][1] = buf[m++];
+ mu[i][2] = buf[m++];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -461,14 +472,20 @@ int AtomVecDipole::pack_border_vel(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
-int AtomVecDipole::pack_border_one(int i, double *buf)
+int AtomVecDipole::pack_border_hybrid(int n, int *list, double *buf)
{
- buf[0] = q[i];
- buf[1] = mu[i][0];
- buf[2] = mu[i][1];
- buf[3] = mu[i][2];
- buf[4] = mu[i][3];
- return 5;
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = q[j];
+ buf[m++] = mu[j][0];
+ buf[m++] = mu[j][1];
+ buf[m++] = mu[j][2];
+ buf[m++] = mu[j][3];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -524,14 +541,20 @@ void AtomVecDipole::unpack_border_vel(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecDipole::unpack_border_one(int i, double *buf)
+int AtomVecDipole::unpack_border_hybrid(int n, int first, double *buf)
{
- q[i] = buf[0];
- mu[i][0] = buf[1];
- mu[i][1] = buf[2];
- mu[i][2] = buf[3];
- mu[i][3] = buf[4];
- return 5;
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ q[i] = buf[m++];
+ mu[i][0] = buf[m++];
+ mu[i][1] = buf[m++];
+ mu[i][2] = buf[m++];
+ mu[i][3] = buf[m++];
+ }
+ return m;
}
/* ----------------------------------------------------------------------
diff --git a/src/DIPOLE/atom_vec_dipole.h b/src/DIPOLE/atom_vec_dipole.h
index 5cfd54c3d1..8e8c77bdc8 100644
--- a/src/DIPOLE/atom_vec_dipole.h
+++ b/src/DIPOLE/atom_vec_dipole.h
@@ -32,18 +32,18 @@ class AtomVecDipole : public AtomVec {
void copy(int, int);
int pack_comm(int, int *, double *, int, int *);
int pack_comm_vel(int, int *, double *, int, int *);
- int pack_comm_one(int, double *);
+ int pack_comm_hybrid(int, int *, double *);
void unpack_comm(int, int, double *);
void unpack_comm_vel(int, int, double *);
- int unpack_comm_one(int, double *);
+ int unpack_comm_hybrid(int, int, double *);
int pack_reverse(int, int, double *);
void unpack_reverse(int, int *, double *);
int pack_border(int, int *, double *, int, int *);
int pack_border_vel(int, int *, double *, int, int *);
- int pack_border_one(int, double *);
+ int pack_border_hybrid(int, int *, double *);
void unpack_border(int, int, double *);
void unpack_border_vel(int, int, double *);
- int unpack_border_one(int, double *);
+ int unpack_border_hybrid(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
int size_restart();
diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp
index 54c5cc6746..26e3968bcf 100644
--- a/src/MOLECULE/atom_vec_angle.cpp
+++ b/src/MOLECULE/atom_vec_angle.cpp
@@ -428,10 +428,16 @@ int AtomVecAngle::pack_border_vel(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
-int AtomVecAngle::pack_border_one(int i, double *buf)
+int AtomVecAngle::pack_border_hybrid(int n, int *list, double *buf)
{
- buf[0] = molecule[i];
- return 1;
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = molecule[j];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -479,10 +485,15 @@ void AtomVecAngle::unpack_border_vel(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecAngle::unpack_border_one(int i, double *buf)
+int AtomVecAngle::unpack_border_hybrid(int n, int first, double *buf)
{
- molecule[i] = static_cast<int> (buf[0]);
- return 1;
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++)
+ molecule[i] = static_cast<int> (buf[m++]);
+ return m;
}
/* ----------------------------------------------------------------------
diff --git a/src/MOLECULE/atom_vec_angle.h b/src/MOLECULE/atom_vec_angle.h
index bd73a7ef38..009a38d8eb 100644
--- a/src/MOLECULE/atom_vec_angle.h
+++ b/src/MOLECULE/atom_vec_angle.h
@@ -38,10 +38,10 @@ class AtomVecAngle : public AtomVec {
void unpack_reverse(int, int *, double *);
int pack_border(int, int *, double *, int, int *);
int pack_border_vel(int, int *, double *, int, int *);
- int pack_border_one(int, double *);
+ int pack_border_hybrid(int, int *, double *);
void unpack_border(int, int, double *);
void unpack_border_vel(int, int, double *);
- int unpack_border_one(int, double *);
+ int unpack_border_hybrid(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
int size_restart();
diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp
index 5900aa4609..81660e1e2f 100644
--- a/src/MOLECULE/atom_vec_bond.cpp
+++ b/src/MOLECULE/atom_vec_bond.cpp
@@ -421,10 +421,16 @@ int AtomVecBond::pack_border_vel(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
-int AtomVecBond::pack_border_one(int i, double *buf)
+int AtomVecBond::pack_border_hybrid(int n, int *list, double *buf)
{
- buf[0] = molecule[i];
- return 1;
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = molecule[j];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -472,10 +478,15 @@ void AtomVecBond::unpack_border_vel(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecBond::unpack_border_one(int i, double *buf)
+int AtomVecBond::unpack_border_hybrid(int n, int first, double *buf)
{
- molecule[i] = static_cast<int> (buf[0]);
- return 1;
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++)
+ molecule[i] = static_cast<int> (buf[m++]);
+ return m;
}
/* ----------------------------------------------------------------------
diff --git a/src/MOLECULE/atom_vec_bond.h b/src/MOLECULE/atom_vec_bond.h
index 5a6648651c..3274e3a0cf 100644
--- a/src/MOLECULE/atom_vec_bond.h
+++ b/src/MOLECULE/atom_vec_bond.h
@@ -38,10 +38,10 @@ class AtomVecBond : public AtomVec {
void unpack_reverse(int, int *, double *);
int pack_border(int, int *, double *, int, int *);
int pack_border_vel(int, int *, double *, int, int *);
- int pack_border_one(int, double *);
+ int pack_border_hybrid(int, int *, double *);
void unpack_border(int, int, double *);
void unpack_border_vel(int, int, double *);
- int unpack_border_one(int, double *);
+ int unpack_border_hybrid(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
int size_restart();
diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp
index 8261b4317e..428c8957ca 100644
--- a/src/MOLECULE/atom_vec_full.cpp
+++ b/src/MOLECULE/atom_vec_full.cpp
@@ -506,11 +506,17 @@ int AtomVecFull::pack_border_vel(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
-int AtomVecFull::pack_border_one(int i, double *buf)
+int AtomVecFull::pack_border_hybrid(int n, int *list, double *buf)
{
- buf[0] = q[i];
- buf[1] = molecule[i];
- return 2;
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = q[j];
+ buf[m++] = molecule[j];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -560,11 +566,17 @@ void AtomVecFull::unpack_border_vel(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecFull::unpack_border_one(int i, double *buf)
+int AtomVecFull::unpack_border_hybrid(int n, int first, double *buf)
{
- q[i] = buf[0];
- molecule[i] = static_cast<int> (buf[1]);
- return 2;
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ q[i] = buf[m++];
+ molecule[i] = static_cast<int> (buf[m++]);
+ }
+ return m;
}
/* ----------------------------------------------------------------------
diff --git a/src/MOLECULE/atom_vec_full.h b/src/MOLECULE/atom_vec_full.h
index 4fea6a5ea5..c2c23881d7 100644
--- a/src/MOLECULE/atom_vec_full.h
+++ b/src/MOLECULE/atom_vec_full.h
@@ -38,10 +38,10 @@ class AtomVecFull : public AtomVec {
void unpack_reverse(int, int *, double *);
int pack_border(int, int *, double *, int, int *);
int pack_border_vel(int, int *, double *, int, int *);
- int pack_border_one(int, double *);
+ int pack_border_hybrid(int, int *, double *);
void unpack_border(int, int, double *);
void unpack_border_vel(int, int, double *);
- int unpack_border_one(int, double *);
+ int unpack_border_hybrid(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
int size_restart();
diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp
index 84bfa9f27a..ac26f00c49 100644
--- a/src/MOLECULE/atom_vec_molecular.cpp
+++ b/src/MOLECULE/atom_vec_molecular.cpp
@@ -499,10 +499,16 @@ int AtomVecMolecular::pack_border_vel(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
-int AtomVecMolecular::pack_border_one(int i, double *buf)
+int AtomVecMolecular::pack_border_hybrid(int n, int *list, double *buf)
{
- buf[0] = molecule[i];
- return 1;
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = molecule[j];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -550,10 +556,15 @@ void AtomVecMolecular::unpack_border_vel(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecMolecular::unpack_border_one(int i, double *buf)
+int AtomVecMolecular::unpack_border_hybrid(int n, int first, double *buf)
{
- molecule[i] = static_cast<int> (buf[0]);
- return 1;
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++)
+ molecule[i] = static_cast<int> (buf[m++]);
+ return m;
}
/* ----------------------------------------------------------------------
diff --git a/src/MOLECULE/atom_vec_molecular.h b/src/MOLECULE/atom_vec_molecular.h
index 2f1ce1006f..6249b8bf1e 100644
--- a/src/MOLECULE/atom_vec_molecular.h
+++ b/src/MOLECULE/atom_vec_molecular.h
@@ -38,10 +38,10 @@ class AtomVecMolecular : public AtomVec {
void unpack_reverse(int, int *, double *);
int pack_border(int, int *, double *, int, int *);
int pack_border_vel(int, int *, double *, int, int *);
- int pack_border_one(int, double *);
+ int pack_border_hybrid(int, int *, double *);
void unpack_border(int, int, double *);
void unpack_border_vel(int, int, double *);
- int unpack_border_one(int, double *);
+ int unpack_border_hybrid(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
int size_restart();
diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp
index d23fe810f3..b4d94e3fa8 100644
--- a/src/PERI/atom_vec_peri.cpp
+++ b/src/PERI/atom_vec_peri.cpp
@@ -231,10 +231,16 @@ int AtomVecPeri::pack_comm_vel(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
-int AtomVecPeri::pack_comm_one(int i, double *buf)
+int AtomVecPeri::pack_comm_hybrid(int n, int *list, double *buf)
{
- buf[0] = s0[i];
- return 1;
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = s0[i];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -274,10 +280,15 @@ void AtomVecPeri::unpack_comm_vel(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecPeri::unpack_comm_one(int i, double *buf)
+int AtomVecPeri::unpack_comm_hybrid(int n, int first, double *buf)
{
- s0[i] = buf[0];
- return 1;
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++)
+ s0[i] = buf[m++];
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -452,14 +463,20 @@ int AtomVecPeri::pack_border_vel(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
-int AtomVecPeri::pack_border_one(int i, double *buf)
+int AtomVecPeri::pack_border_hybrid(int n, int *list, double *buf)
{
- buf[0] = vfrac[i];
- buf[1] = s0[i];
- buf[2] = x0[i][0];
- buf[3] = x0[i][1];
- buf[4] = x0[i][2];
- return 5;
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = vfrac[j];
+ buf[m++] = s0[j];
+ buf[m++] = x0[j][0];
+ buf[m++] = x0[j][1];
+ buf[m++] = x0[j][2];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -515,14 +532,20 @@ void AtomVecPeri::unpack_border_vel(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecPeri::unpack_border_one(int i, double *buf)
+int AtomVecPeri::unpack_border_hybrid(int n, int first, double *buf)
{
- vfrac[i] = buf[0];
- s0[i] = buf[1];
- x0[i][0] = buf[2];
- x0[i][1] = buf[3];
- x0[i][2] = buf[4];
- return 5;
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ vfrac[i] = buf[m++];
+ s0[i] = buf[m++];
+ x0[i][0] = buf[m++];
+ x0[i][1] = buf[m++];
+ x0[i][2] = buf[m++];
+ }
+ return m;
}
/* ----------------------------------------------------------------------
diff --git a/src/PERI/atom_vec_peri.h b/src/PERI/atom_vec_peri.h
index 333e452b5a..4b14c04b42 100755
--- a/src/PERI/atom_vec_peri.h
+++ b/src/PERI/atom_vec_peri.h
@@ -32,18 +32,18 @@ class AtomVecPeri : public AtomVec {
void copy(int, int);
int pack_comm(int, int *, double *, int, int *);
int pack_comm_vel(int, int *, double *, int, int *);
- int pack_comm_one(int, double *);
+ int pack_comm_hybrid(int, int *, double *);
void unpack_comm(int, int, double *);
void unpack_comm_vel(int, int, double *);
- int unpack_comm_one(int, double *);
+ int unpack_comm_hybrid(int, int, double *);
int pack_reverse(int, int, double *);
void unpack_reverse(int, int *, double *);
int pack_border(int, int *, double *, int, int *);
int pack_border_vel(int, int *, double *, int, int *);
- int pack_border_one(int, double *);
+ int pack_border_hybrid(int, int *, double *);
void unpack_border(int, int, double *);
void unpack_border_vel(int, int, double *);
- int unpack_border_one(int, double *);
+ int unpack_border_hybrid(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
int size_restart();
diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp
index 41f9040625..ec8716f403 100644
--- a/src/SRD/fix_srd.cpp
+++ b/src/SRD/fix_srd.cpp
@@ -291,8 +291,6 @@ void FixSRD::init()
if (bigexist && !atom->sphere_flag && !atom->ellipsoid_flag)
error->all("Fix SRD requires atom style sphere or ellipsoid");
- if (bigexist && atom->angmom_flag && atom->omega_flag)
- error->all("Fix SRD cannot have both atom attributes angmom and omega");
if (bigexist && collidestyle == NOSLIP && !atom->torque_flag)
error->all("Fix SRD no-slip requires atom attribute torque");
diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp
index 7ddb37d004..0a13aa1a76 100644
--- a/src/USER-EFF/atom_vec_electron.cpp
+++ b/src/USER-EFF/atom_vec_electron.cpp
@@ -228,6 +228,20 @@ int AtomVecElectron::pack_comm_vel(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
+int AtomVecElectron::pack_comm_hybrid(int n, int *list, double *buf)
+{
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = eradius[i];
+ }
+ return m;
+}
+
+/* ---------------------------------------------------------------------- */
+
void AtomVecElectron::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
@@ -263,18 +277,15 @@ void AtomVecElectron::unpack_comm_vel(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecElectron::pack_comm_one(int i, double *buf)
+int AtomVecElectron::unpack_comm_hybrid(int n, int first, double *buf)
{
- buf[0] = eradius[i];
- return 1;
-}
-
-/* ---------------------------------------------------------------------- */
+ int i,m,last;
-int AtomVecElectron::unpack_comm_one(int i, double *buf)
-{
- eradius[i] = buf[0];
- return 1;
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++)
+ eradius[i] = buf[m++];
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -296,10 +307,15 @@ int AtomVecElectron::pack_reverse(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecElectron::pack_reverse_one(int i, double *buf)
+int AtomVecElectron::pack_reverse_hybrid(int n, int first, double *buf)
{
- buf[0] = erforce[i];
- return 1;
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++)
+ buf[m++] = erforce[i];
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -320,10 +336,16 @@ void AtomVecElectron::unpack_reverse(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecElectron::unpack_reverse_one(int i, double *buf)
+int AtomVecElectron::unpack_reverse_hybrid(int n, int *list, double *buf)
{
- erforce[i] += buf[0];
- return 1;
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ erforce[j] += buf[m++];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -457,12 +479,18 @@ int AtomVecElectron::pack_border_vel(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
-int AtomVecElectron::pack_border_one(int i, double *buf)
+int AtomVecElectron::pack_border_hybrid(int n, int *list, double *buf)
{
- buf[0] = q[i];
- buf[1] = spin[i];
- buf[2] = eradius[i];
- return 3;
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = q[j];
+ buf[m++] = spin[j];
+ buf[m++] = eradius[j];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -514,12 +542,18 @@ void AtomVecElectron::unpack_border_vel(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecElectron::unpack_border_one(int i, double *buf)
+int AtomVecElectron::unpack_border_hybrid(int n, int first, double *buf)
{
- q[i] = buf[0];
- spin[i] = static_cast<int> (buf[1]);
- eradius[i] = buf[2];
- return 3;
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ q[i] = buf[m++];
+ spin[i] = static_cast<int> (buf[m++]);
+ eradius[i] = buf[m++];
+ }
+ return m;
}
/* ----------------------------------------------------------------------
diff --git a/src/USER-EFF/atom_vec_electron.h b/src/USER-EFF/atom_vec_electron.h
index 3670958c16..3ae836ae23 100644
--- a/src/USER-EFF/atom_vec_electron.h
+++ b/src/USER-EFF/atom_vec_electron.h
@@ -33,20 +33,20 @@ class AtomVecElectron : public AtomVec {
void copy(int, int);
int pack_comm(int, int *, double *, int, int *);
int pack_comm_vel(int, int *, double *, int, int *);
- int pack_comm_one(int, double *);
+ int pack_comm_hybrid(int, int *, double *);
void unpack_comm(int, int, double *);
void unpack_comm_vel(int, int, double *);
- int unpack_comm_one(int, double *);
+ int unpack_comm_hybrid(int, int, double *);
int pack_reverse(int, int, double *);
- int pack_reverse_one(int, double *);
+ int pack_reverse_hybrid(int, int, double *);
void unpack_reverse(int, int *, double *);
- int unpack_reverse_one(int, double *);
+ int unpack_reverse_hybrid(int, int *, double *);
int pack_border(int, int *, double *, int, int *);
int pack_border_vel(int, int *, double *, int, int *);
- int pack_border_one(int, double *);
+ int pack_border_hybrid(int, int *, double *);
void unpack_border(int, int, double *);
void unpack_border_vel(int, int, double *);
- int unpack_border_one(int, double *);
+ int unpack_border_hybrid(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
int size_restart();
diff --git a/src/atom.cpp b/src/atom.cpp
index d31f20c1e3..81ca000a40 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -99,7 +99,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
// initialize atom style and array existence flags
// customize by adding new flag
- sphere_flag = ellipsoid_flag = peri_flag = dipole_flag = electron_flag = 0;
+ sphere_flag = ellipsoid_flag = peri_flag = electron_flag = 0;
molecule_flag = q_flag = mu_flag = 0;
rmass_flag = radius_flag = omega_flag = torque_flag = 0;
@@ -253,7 +253,7 @@ void Atom::create_avec(const char *style, int narg, char **arg)
// may have been set by old avec
// customize by adding new flag
- sphere_flag = ellipsoid_flag = peri_flag = dipole_flag = electron_flag = 0;
+ sphere_flag = ellipsoid_flag = peri_flag = electron_flag = 0;
molecule_flag = q_flag = mu_flag = 0;
rmass_flag = radius_flag = omega_flag = torque_flag = 0;
diff --git a/src/atom.h b/src/atom.h
index e05929eaa5..47bad27ffe 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -78,7 +78,7 @@ class Atom : protected Pointers {
// atom style and per-atom array existence flags
// customize by adding new flag
- int sphere_flag,ellipsoid_flag,peri_flag,dipole_flag,electron_flag;
+ int sphere_flag,ellipsoid_flag,peri_flag,electron_flag;
int molecule_flag,q_flag,mu_flag;
int rmass_flag,radius_flag,omega_flag,torque_flag;
diff --git a/src/atom_vec.h b/src/atom_vec.h
index 7c399bf44b..594931507e 100644
--- a/src/atom_vec.h
+++ b/src/atom_vec.h
@@ -47,22 +47,22 @@ class AtomVec : protected Pointers {
virtual int pack_comm(int, int *, double *, int, int *) = 0;
virtual int pack_comm_vel(int, int *, double *, int, int *) = 0;
- virtual int pack_comm_one(int, double *) {return 0;}
+ virtual int pack_comm_hybrid(int, int *, double *) {return 0;}
virtual void unpack_comm(int, int, double *) = 0;
virtual void unpack_comm_vel(int, int, double *) = 0;
- virtual int unpack_comm_one(int, double *) {return 0;}
+ virtual int unpack_comm_hybrid(int, int, double *) {return 0;}
virtual int pack_reverse(int, int, double *) = 0;
- virtual int pack_reverse_one(int, double *) {return 0;}
+ virtual int pack_reverse_hybrid(int, int, double *) {return 0;}
virtual void unpack_reverse(int, int *, double *) = 0;
- virtual int unpack_reverse_one(int, double *) {return 0;}
+ virtual int unpack_reverse_hybrid(int, int *, double *) {return 0;}
virtual int pack_border(int, int *, double *, int, int *) = 0;
virtual int pack_border_vel(int, int *, double *, int, int *) = 0;
- virtual int pack_border_one(int, double *) {return 0;}
+ virtual int pack_border_hybrid(int, int *, double *) {return 0;}
virtual void unpack_border(int, int, double *) = 0;
virtual void unpack_border_vel(int, int, double *) = 0;
- virtual int unpack_border_one(int, double *) {return 0;}
+ virtual int unpack_border_hybrid(int, int, double *) {return 0;}
virtual int pack_exchange(int, double *) = 0;
virtual int unpack_exchange(double *) = 0;
diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp
index e2f6ac4c03..5088361cbd 100644
--- a/src/atom_vec_charge.cpp
+++ b/src/atom_vec_charge.cpp
@@ -392,10 +392,16 @@ int AtomVecCharge::pack_border_vel(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
-int AtomVecCharge::pack_border_one(int i, double *buf)
+int AtomVecCharge::pack_border_hybrid(int n, int *list, double *buf)
{
- buf[0] = q[i];
- return 1;
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = q[j];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -443,10 +449,15 @@ void AtomVecCharge::unpack_border_vel(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecCharge::unpack_border_one(int i, double *buf)
+int AtomVecCharge::unpack_border_hybrid(int n, int first, double *buf)
{
- q[i] = buf[0];
- return 1;
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++)
+ q[i] = buf[m++];
+ return m;
}
/* ----------------------------------------------------------------------
diff --git a/src/atom_vec_charge.h b/src/atom_vec_charge.h
index 80786edc48..a25641f76d 100644
--- a/src/atom_vec_charge.h
+++ b/src/atom_vec_charge.h
@@ -38,10 +38,10 @@ class AtomVecCharge : public AtomVec {
void unpack_reverse(int, int *, double *);
int pack_border(int, int *, double *, int, int *);
int pack_border_vel(int, int *, double *, int, int *);
- int pack_border_one(int, double *);
+ int pack_border_hybrid(int, int *, double *);
void unpack_border(int, int, double *);
void unpack_border_vel(int, int, double *);
- int unpack_border_one(int, double *);
+ int unpack_border_hybrid(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
int size_restart();
diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp
index f630b67557..d4e148245c 100644
--- a/src/atom_vec_hybrid.cpp
+++ b/src/atom_vec_hybrid.cpp
@@ -187,8 +187,6 @@ int AtomVecHybrid::pack_comm(int n, int *list, double *buf,
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
- for (k = 0; k < nstyles; k++)
- m += styles[k]->pack_comm_one(j,&buf[m]);
}
} else {
if (domain->triclinic == 0) {
@@ -205,10 +203,14 @@ int AtomVecHybrid::pack_comm(int n, int *list, double *buf,
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
buf[m++] = x[j][2] + dz;
- for (k = 0; k < nstyles; k++)
- m += styles[k]->pack_comm_one(j,&buf[m]);
}
}
+
+ // pack sub-style contributions as contiguous chunks
+
+ for (k = 0; k < nstyles; k++)
+ m += styles[k]->pack_comm_hybrid(n,list,&buf[m]);
+
return m;
}
@@ -242,8 +244,6 @@ int AtomVecHybrid::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
- for (k = 0; k < nstyles; k++)
- m += styles[k]->pack_comm_one(j,&buf[m]);
}
} else {
if (domain->triclinic == 0) {
@@ -274,8 +274,6 @@ int AtomVecHybrid::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
- for (k = 0; k < nstyles; k++)
- m += styles[k]->pack_comm_one(j,&buf[m]);
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
@@ -305,11 +303,15 @@ int AtomVecHybrid::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
- for (k = 0; k < nstyles; k++)
- m += styles[k]->pack_comm_one(j,&buf[m]);
}
}
}
+
+ // pack sub-style contributions as contiguous chunks
+
+ for (k = 0; k < nstyles; k++)
+ m += styles[k]->pack_comm_hybrid(n,list,&buf[m]);
+
return m;
}
@@ -317,28 +319,31 @@ int AtomVecHybrid::pack_comm_vel(int n, int *list, double *buf,
void AtomVecHybrid::unpack_comm(int n, int first, double *buf)
{
- int i,k,last;
+ int i,k,m,last;
- int m = 0;
+ m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
- for (k = 0; k < nstyles; k++)
- m += styles[k]->unpack_comm_one(i,&buf[m]);
}
+
+ // unpack sub-style contributions as contiguous chunks
+
+ for (k = 0; k < nstyles; k++)
+ m += styles[k]->unpack_comm_hybrid(n,first,&buf[m]);
}
/* ---------------------------------------------------------------------- */
void AtomVecHybrid::unpack_comm_vel(int n, int first, double *buf)
{
- int i,k,last;
+ int i,k,m,last;
int omega_flag = atom->omega_flag;
int angmom_flag = atom->angmom_flag;
- int m = 0;
+ m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
@@ -357,26 +362,33 @@ void AtomVecHybrid::unpack_comm_vel(int n, int first, double *buf)
angmom[i][1] = buf[m++];
angmom[i][2] = buf[m++];
}
- for (k = 0; k < nstyles; k++)
- m += styles[k]->unpack_comm_one(i,&buf[m]);
}
+
+ // unpack sub-style contributions as contiguous chunks
+
+ for (k = 0; k < nstyles; k++)
+ m += styles[k]->unpack_comm_hybrid(n,first,&buf[m]);
}
/* ---------------------------------------------------------------------- */
int AtomVecHybrid::pack_reverse(int n, int first, double *buf)
{
- int i,k,last;
+ int i,k,m,last;
- int m = 0;
+ m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
- for (k = 0; k < nstyles; k++)
- m += styles[k]->pack_reverse_one(i,&buf[m]);
}
+
+ // pack sub-style contributions as contiguous chunks
+
+ for (k = 0; k < nstyles; k++)
+ m += styles[k]->pack_reverse_hybrid(n,first,&buf[m]);
+
return m;
}
@@ -392,9 +404,12 @@ void AtomVecHybrid::unpack_reverse(int n, int *list, double *buf)
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
- for (k = 0; k < nstyles; k++)
- m += styles[k]->unpack_reverse_one(j,&buf[m]);
}
+
+ // unpack sub-style contributions as contiguous chunks
+
+ for (k = 0; k < nstyles; k++)
+ m += styles[k]->unpack_reverse_hybrid(n,list,&buf[m]);
}
/* ---------------------------------------------------------------------- */
@@ -415,8 +430,6 @@ int AtomVecHybrid::pack_border(int n, int *list, double *buf,
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
- for (k = 0; k < nstyles; k++)
- m += styles[k]->pack_border_one(j,&buf[m]);
}
} else {
if (domain->triclinic == 0) {
@@ -436,10 +449,14 @@ int AtomVecHybrid::pack_border(int n, int *list, double *buf,
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
- for (k = 0; k < nstyles; k++)
- m += styles[k]->pack_border_one(j,&buf[m]);
}
}
+
+ // pack sub-style contributions as contiguous chunks
+
+ for (k = 0; k < nstyles; k++)
+ m += styles[k]->pack_border_hybrid(n,list,&buf[m]);
+
return m;
}
@@ -476,8 +493,6 @@ int AtomVecHybrid::pack_border_vel(int n, int *list, double *buf,
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
- for (k = 0; k < nstyles; k++)
- m += styles[k]->pack_border_one(j,&buf[m]);
}
} else {
if (domain->triclinic == 0) {
@@ -511,8 +526,6 @@ int AtomVecHybrid::pack_border_vel(int n, int *list, double *buf,
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
- for (k = 0; k < nstyles; k++)
- m += styles[k]->pack_border_one(j,&buf[m]);
}
} else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
@@ -545,11 +558,15 @@ int AtomVecHybrid::pack_border_vel(int n, int *list, double *buf,
buf[m++] = angmom[j][1];
buf[m++] = angmom[j][2];
}
- for (k = 0; k < nstyles; k++)
- m += styles[k]->pack_border_one(j,&buf[m]);
}
}
}
+
+ // pack sub-style contributions as contiguous chunks
+
+ for (k = 0; k < nstyles; k++)
+ m += styles[k]->pack_border_hybrid(n,list,&buf[m]);
+
return m;
}
@@ -569,9 +586,12 @@ void AtomVecHybrid::unpack_border(int n, int first, double *buf)
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
- for (k = 0; k < nstyles; k++)
- m += styles[k]->unpack_border_one(i,&buf[m]);
}
+
+ // unpack sub-style contributions as contiguous chunks
+
+ for (k = 0; k < nstyles; k++)
+ m += styles[k]->unpack_border_hybrid(n,first,&buf[m]);
}
/* ---------------------------------------------------------------------- */
@@ -605,9 +625,12 @@ void AtomVecHybrid::unpack_border_vel(int n, int first, double *buf)
angmom[i][1] = buf[m++];
angmom[i][2] = buf[m++];
}
- for (k = 0; k < nstyles; k++)
- m += styles[k]->unpack_border_one(i,&buf[m]);
}
+
+ // unpack sub-style contributions as contiguous chunks
+
+ for (k = 0; k < nstyles; k++)
+ m += styles[k]->unpack_border_hybrid(n,first,&buf[m]);
}
/* ----------------------------------------------------------------------
@@ -617,12 +640,12 @@ void AtomVecHybrid::unpack_border_vel(int n, int first, double *buf)
int AtomVecHybrid::pack_exchange(int i, double *buf)
{
- int k;
+ int k,m;
int tmp = atom->nextra_grow;
atom->nextra_grow = 0;
- int m = 0;
+ m = 0;
for (k = 0; k < nstyles; k++)
m += styles[k]->pack_exchange(i,&buf[m]);
@@ -644,14 +667,16 @@ int AtomVecHybrid::pack_exchange(int i, double *buf)
int AtomVecHybrid::unpack_exchange(double *buf)
{
+ int k,m;
+
int nlocal = atom->nlocal;
if (nlocal == nmax) grow(0);
int tmp = atom->nextra_grow;
atom->nextra_grow = 0;
- int m = 0;
- for (int k = 0; k < nstyles; k++) {
+ m = 0;
+ for (k = 0; k < nstyles; k++) {
m += styles[k]->unpack_exchange(&buf[m]);
atom->nlocal--;
}
diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp
index 6b7ff6eb18..1aa886c7ed 100644
--- a/src/atom_vec_sphere.cpp
+++ b/src/atom_vec_sphere.cpp
@@ -363,13 +363,19 @@ int AtomVecSphere::pack_comm_vel(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
-int AtomVecSphere::pack_comm_one(int i, double *buf)
+int AtomVecSphere::pack_comm_hybrid(int n, int *list, double *buf)
{
+ int i,j,m;
+
if (radvary == 0) return 0;
- buf[0] = radius[i];
- buf[1] = rmass[i];
- return 2;
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = radius[i];
+ buf[m++] = rmass[i];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -440,13 +446,19 @@ void AtomVecSphere::unpack_comm_vel(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecSphere::unpack_comm_one(int i, double *buf)
+int AtomVecSphere::unpack_comm_hybrid(int n, int first, double *buf)
{
+ int i,m,last;
+
if (radvary == 0) return 0;
- radius[i] = buf[0];
- rmass[i] = buf[1];
- return 2;
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ radius[i] = buf[m++];
+ rmass[i] = buf[m++];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -470,12 +482,18 @@ int AtomVecSphere::pack_reverse(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecSphere::pack_reverse_one(int i, double *buf)
+int AtomVecSphere::pack_reverse_hybrid(int n, int first, double *buf)
{
- buf[0] = torque[i][0];
- buf[1] = torque[i][1];
- buf[2] = torque[i][2];
- return 3;
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ buf[m++] = torque[i][0];
+ buf[m++] = torque[i][1];
+ buf[m++] = torque[i][2];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -498,12 +516,18 @@ void AtomVecSphere::unpack_reverse(int n, int *list, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecSphere::unpack_reverse_one(int i, double *buf)
+int AtomVecSphere::unpack_reverse_hybrid(int n, int *list, double *buf)
{
- torque[i][0] += buf[0];
- torque[i][1] += buf[1];
- torque[i][2] += buf[2];
- return 3;
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ torque[j][0] += buf[m++];
+ torque[j][1] += buf[m++];
+ torque[j][2] += buf[m++];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -641,11 +665,17 @@ int AtomVecSphere::pack_border_vel(int n, int *list, double *buf,
/* ---------------------------------------------------------------------- */
-int AtomVecSphere::pack_border_one(int i, double *buf)
+int AtomVecSphere::pack_border_hybrid(int n, int *list, double *buf)
{
- buf[0] = radius[i];
- buf[1] = rmass[i];
- return 2;
+ int i,j,m;
+
+ m = 0;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = radius[j];
+ buf[m++] = rmass[j];
+ }
+ return m;
}
/* ---------------------------------------------------------------------- */
@@ -699,11 +729,17 @@ void AtomVecSphere::unpack_border_vel(int n, int first, double *buf)
/* ---------------------------------------------------------------------- */
-int AtomVecSphere::unpack_border_one(int i, double *buf)
+int AtomVecSphere::unpack_border_hybrid(int n, int first, double *buf)
{
- radius[i] = buf[0];
- rmass[i] = buf[1];
- return 2;
+ int i,m,last;
+
+ m = 0;
+ last = first + n;
+ for (i = first; i < last; i++) {
+ radius[i] = buf[m++];
+ rmass[i] = buf[m++];
+ }
+ return m;
}
/* ----------------------------------------------------------------------
diff --git a/src/atom_vec_sphere.h b/src/atom_vec_sphere.h
index d1fa9ba42b..566db3ff96 100644
--- a/src/atom_vec_sphere.h
+++ b/src/atom_vec_sphere.h
@@ -34,20 +34,20 @@ class AtomVecSphere : public AtomVec {
void copy(int, int);
int pack_comm(int, int *, double *, int, int *);
int pack_comm_vel(int, int *, double *, int, int *);
- int pack_comm_one(int, double *);
+ int pack_comm_hybrid(int, int *, double *);
void unpack_comm(int, int, double *);
void unpack_comm_vel(int, int, double *);
- int unpack_comm_one(int, double *);
+ int unpack_comm_hybrid(int, int, double *);
int pack_reverse(int, int, double *);
- int pack_reverse_one(int, double *);
+ int pack_reverse_hybrid(int, int, double *);
void unpack_reverse(int, int *, double *);
- int unpack_reverse_one(int, double *);
+ int unpack_reverse_hybrid(int, int *, double *);
int pack_border(int, int *, double *, int, int *);
int pack_border_vel(int, int *, double *, int, int *);
- int pack_border_one(int, double *);
+ int pack_border_hybrid(int, int *, double *);
void unpack_border(int, int, double *);
void unpack_border_vel(int, int, double *);
- int unpack_border_one(int, double *);
+ int unpack_border_hybrid(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
int size_restart();
diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp
index b64ff6b0f2..1546d22340 100644
--- a/src/pair_dpd_tstat.cpp
+++ b/src/pair_dpd_tstat.cpp
@@ -56,7 +56,7 @@ void PairDPDTstat::compute(int eflag, int vflag)
temperature = t_start + delta * (t_stop-t_start);
double boltz = force->boltz;
for (i = 1; i <= atom->ntypes; i++)
- for (j = i+1; j <= atom->ntypes; j++)
+ for (j = i; j <= atom->ntypes; j++)
sigma[i][j] = sigma[j][i] = sqrt(2.0*boltz*temperature*gamma[i][j]);
}
--
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