diff --git a/src/DIPOLE/atom_vec_dipole.cpp b/src/DIPOLE/atom_vec_dipole.cpp
index acd35a1b9c5ee533b1dcc6e256cfd1048fde9e05..ef4f68a86c8fc1724b721dfaabeeb33d3f5bab27 100644
--- a/src/DIPOLE/atom_vec_dipole.cpp
+++ b/src/DIPOLE/atom_vec_dipole.cpp
@@ -28,8 +28,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecDipole::AtomVecDipole(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg)
+AtomVecDipole::AtomVecDipole(LAMMPS *lmp) : AtomVec(lmp)
{
molecular = 0;
mass_type = 1;
diff --git a/src/DIPOLE/atom_vec_dipole.h b/src/DIPOLE/atom_vec_dipole.h
index bdbf180a8e4e164a4bc618bc46f6b21e72f52b68..a465272e36ee3b82bf0ed28f0cea7e571a21a967 100644
--- a/src/DIPOLE/atom_vec_dipole.h
+++ b/src/DIPOLE/atom_vec_dipole.h
@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
class AtomVecDipole : public AtomVec {
public:
- AtomVecDipole(class LAMMPS *, int, char **);
+ AtomVecDipole(class LAMMPS *);
void grow(int);
void grow_reset();
void copy(int, int, int);
diff --git a/src/Depend.sh b/src/Depend.sh
index feb92c3e29bfcd8ea977044a305b6db01a0cf8fc..b5d6ff3d66a7643eaaa0680356ba956b9fc06c3c 100644
--- a/src/Depend.sh
+++ b/src/Depend.sh
@@ -46,4 +46,3 @@ elif (test $1 = 0) then
fi
fi
-
diff --git a/src/MOLECULE/atom_vec_angle.cpp b/src/MOLECULE/atom_vec_angle.cpp
index 8b1d2cd2f62a7634346e62622b6c476f0202131d..9b42d6ef1b4a11b55073da77983b4d7c90b56e3d 100644
--- a/src/MOLECULE/atom_vec_angle.cpp
+++ b/src/MOLECULE/atom_vec_angle.cpp
@@ -27,8 +27,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecAngle::AtomVecAngle(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg)
+AtomVecAngle::AtomVecAngle(LAMMPS *lmp) : AtomVec(lmp)
{
molecular = 1;
bonds_allow = angles_allow = 1;
diff --git a/src/MOLECULE/atom_vec_angle.h b/src/MOLECULE/atom_vec_angle.h
index 7a39863f222344a19277cd856944269802108258..3300106fdf5cf40b36e9b707f9d53a521515e089 100644
--- a/src/MOLECULE/atom_vec_angle.h
+++ b/src/MOLECULE/atom_vec_angle.h
@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
class AtomVecAngle : public AtomVec {
public:
- AtomVecAngle(class LAMMPS *, int, char **);
+ AtomVecAngle(class LAMMPS *);
virtual ~AtomVecAngle() {}
void grow(int);
void grow_reset();
diff --git a/src/MOLECULE/atom_vec_bond.cpp b/src/MOLECULE/atom_vec_bond.cpp
index 375c0dc7702792b435d451fa321b9f55777fff4b..2493533c443a259c5a86c5a1821b9ad5132fa635 100644
--- a/src/MOLECULE/atom_vec_bond.cpp
+++ b/src/MOLECULE/atom_vec_bond.cpp
@@ -27,8 +27,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecBond::AtomVecBond(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg)
+AtomVecBond::AtomVecBond(LAMMPS *lmp) : AtomVec(lmp)
{
molecular = 1;
bonds_allow = 1;
diff --git a/src/MOLECULE/atom_vec_bond.h b/src/MOLECULE/atom_vec_bond.h
index ed437027a10551b5968961559c983794639daa97..c94aec1eb438a256f48ff343c99021c0542650f8 100644
--- a/src/MOLECULE/atom_vec_bond.h
+++ b/src/MOLECULE/atom_vec_bond.h
@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
class AtomVecBond : public AtomVec {
public:
- AtomVecBond(class LAMMPS *, int, char **);
+ AtomVecBond(class LAMMPS *);
void grow(int);
void grow_reset();
void copy(int, int, int);
diff --git a/src/MOLECULE/atom_vec_full.cpp b/src/MOLECULE/atom_vec_full.cpp
index e7f009c569eb69512acf16a565b3dd8c339d7185..d7cecabf718e524e83613e351d4dee9d1c913342 100644
--- a/src/MOLECULE/atom_vec_full.cpp
+++ b/src/MOLECULE/atom_vec_full.cpp
@@ -27,8 +27,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecFull::AtomVecFull(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg)
+AtomVecFull::AtomVecFull(LAMMPS *lmp) : AtomVec(lmp)
{
molecular = 1;
bonds_allow = angles_allow = dihedrals_allow = impropers_allow = 1;
diff --git a/src/MOLECULE/atom_vec_full.h b/src/MOLECULE/atom_vec_full.h
index 14e25237dea6a2238f365168c6798b8e2f14a7fa..d14871271af6109c124a21df7e0743d28a565fb3 100644
--- a/src/MOLECULE/atom_vec_full.h
+++ b/src/MOLECULE/atom_vec_full.h
@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
class AtomVecFull : public AtomVec {
public:
- AtomVecFull(class LAMMPS *, int, char **);
+ AtomVecFull(class LAMMPS *);
virtual ~AtomVecFull() {}
void grow(int);
void grow_reset();
diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp
index bb21e5b0f4528b87ba638bcdafa6b221db9881eb..d85cc567ba48f0f00d657697f2ef8deb1d0242be 100644
--- a/src/MOLECULE/atom_vec_molecular.cpp
+++ b/src/MOLECULE/atom_vec_molecular.cpp
@@ -27,8 +27,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecMolecular::AtomVecMolecular(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg)
+AtomVecMolecular::AtomVecMolecular(LAMMPS *lmp) : AtomVec(lmp)
{
molecular = 1;
bonds_allow = angles_allow = dihedrals_allow = impropers_allow = 1;
diff --git a/src/MOLECULE/atom_vec_molecular.h b/src/MOLECULE/atom_vec_molecular.h
index 3da1a5fe029334e41f8507c1eb047ed35901d9f8..9ba67449702d6a790efae7bf3bfbe0a22aab5f34 100644
--- a/src/MOLECULE/atom_vec_molecular.h
+++ b/src/MOLECULE/atom_vec_molecular.h
@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
class AtomVecMolecular : public AtomVec {
public:
- AtomVecMolecular(class LAMMPS *, int, char **);
+ AtomVecMolecular(class LAMMPS *);
void grow(int);
void grow_reset();
void copy(int, int, int);
diff --git a/src/Make.sh b/src/Make.sh
index e554ba6353e69004a96a0621221d1b04c9d66c1b..47d62037e209f9359c5b93090f96ee5e801b5142 100644
--- a/src/Make.sh
+++ b/src/Make.sh
@@ -10,7 +10,7 @@
# else Make will not recreate them
style () {
- list=`grep -l $1 $2*.h`
+ list=`grep -sl $1 $2*.h`
if (test -e style_$3.tmp) then
rm -f style_$3.tmp
fi
@@ -19,8 +19,15 @@ style () {
echo "#include $qfile" >> style_$3.tmp
done
if (test ! -e style_$3.tmp) then
- rm -f style_$3.h
- touch style_$3.h
+ if (test "`cat style_$3.h`" != "") then
+ rm -f style_$3.h
+ touch style_$3.h
+ rm -f Obj_*/$4.d
+ if (test $5) then
+ rm -f Obj_*/$5.d
+ fi
+ rm -f Obj_*/lammps.d
+ fi
elif (test ! -e style_$3.h) then
mv style_$3.tmp style_$3.h
rm -f Obj_*/$4.d
@@ -50,7 +57,8 @@ style () {
if (test $1 = "style") then
style ANGLE_CLASS angle_ angle force
- style ATOM_CLASS atom_vec_ atom atom
+ style ATOM_CLASS atom_vec_ atom atom atom_vec_hybrid
+ style BODY_CLASS body_ body atom_vec_body
style BOND_CLASS bond_ bond force
style COMMAND_CLASS "" command input
style COMPUTE_CLASS compute_ compute modify
diff --git a/src/Makefile b/src/Makefile
index 35a3e4814f54fc99398cb6d4ff34c205b0635de9..d994ba4089b45e0da2c88badd969efcb085fc10a 100755
--- a/src/Makefile
+++ b/src/Makefile
@@ -13,7 +13,7 @@ OBJ = $(SRC:.cpp=.o)
# Package variables
-PACKAGE = asphere class2 colloid dipole fld gpu granular kim \
+PACKAGE = asphere body class2 colloid dipole fld gpu granular kim \
kspace manybody mc meam molecule opt peri poems reax replica \
rigid shock srd voronoi xtc
diff --git a/src/PERI/atom_vec_peri.cpp b/src/PERI/atom_vec_peri.cpp
index 8bccaf5dee8e98b9bbeda1b9cb298b0bfadd307c..21a1717d8431079aadaa46602a5941b40ba73a4e 100644
--- a/src/PERI/atom_vec_peri.cpp
+++ b/src/PERI/atom_vec_peri.cpp
@@ -32,8 +32,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecPeri::AtomVecPeri(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg)
+AtomVecPeri::AtomVecPeri(LAMMPS *lmp) : AtomVec(lmp)
{
molecular = 0;
diff --git a/src/PERI/atom_vec_peri.h b/src/PERI/atom_vec_peri.h
index 185eca375c46a936e2c585f8192be881e00b0b12..9633540b95c871f636c79a4e721fb78a46c0ca66 100755
--- a/src/PERI/atom_vec_peri.h
+++ b/src/PERI/atom_vec_peri.h
@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
class AtomVecPeri : public AtomVec {
public:
- AtomVecPeri(class LAMMPS *, int, char **);
+ AtomVecPeri(class LAMMPS *);
void grow(int);
void grow_reset();
void copy(int, int, int);
diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp
index a8572f4a0498c22d2903ae77cf5ab31ef112f280..627cbe80c654b6604fcbd9731fd77b3487fbbd1e 100644
--- a/src/RIGID/fix_rigid.cpp
+++ b/src/RIGID/fix_rigid.cpp
@@ -2139,9 +2139,9 @@ void FixRigid::readfile(int which, double *vec, double **array, int *inbody)
array[id][0] = atof(values[5]);
array[id][1] = atof(values[6]);
array[id][2] = atof(values[7]);
- array[id][5] = atof(values[8]);
- array[id][4] = atof(values[9]);
array[id][3] = atof(values[10]);
+ array[id][4] = atof(values[9]);
+ array[id][5] = atof(values[8]);
}
buf = next + 1;
diff --git a/src/USER-AWPMD/atom_vec_wavepacket.cpp b/src/USER-AWPMD/atom_vec_wavepacket.cpp
index e36741e59d47cd0d695ecd52bcada5d31b32f9e3..92721e0d904fc1b60bccdbcf6b01d8267ad88eab 100644
--- a/src/USER-AWPMD/atom_vec_wavepacket.cpp
+++ b/src/USER-AWPMD/atom_vec_wavepacket.cpp
@@ -34,8 +34,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecWavepacket::AtomVecWavepacket(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg)
+AtomVecWavepacket::AtomVecWavepacket(LAMMPS *lmp) : AtomVec(lmp)
{
comm_x_only = comm_f_only = 0;
@@ -56,8 +55,6 @@ AtomVecWavepacket::AtomVecWavepacket(LAMMPS *lmp, int narg, char **arg) :
atom->ervel_flag = atom->erforce_flag = 1;
atom->cs_flag = atom->csforce_flag = atom->vforce_flag = atom->ervelforce_flag = atom->etag_flag = 1;
-
-
}
/* ----------------------------------------------------------------------
diff --git a/src/USER-AWPMD/atom_vec_wavepacket.h b/src/USER-AWPMD/atom_vec_wavepacket.h
index dd8b61c6fc2a28bd36af41c10dbeb45f04090753..41f9559137faf35e8107b460299ad50ac411875e 100644
--- a/src/USER-AWPMD/atom_vec_wavepacket.h
+++ b/src/USER-AWPMD/atom_vec_wavepacket.h
@@ -31,7 +31,7 @@ namespace LAMMPS_NS {
class AtomVecWavepacket : public AtomVec {
public:
- AtomVecWavepacket(class LAMMPS *, int, char **);
+ AtomVecWavepacket(class LAMMPS *);
~AtomVecWavepacket() {}
void grow(int);
void grow_reset();
diff --git a/src/USER-CUDA/atom_vec_angle_cuda.cpp b/src/USER-CUDA/atom_vec_angle_cuda.cpp
index f7795a3148ce1263615873d3bb801213438f8c6f..9fff3c9b6d321e4dc91f3049128abddd86e3d643 100644
--- a/src/USER-CUDA/atom_vec_angle_cuda.cpp
+++ b/src/USER-CUDA/atom_vec_angle_cuda.cpp
@@ -60,8 +60,7 @@ using namespace LAMMPS_NS;
#define BUF_FLOAT double
/* ---------------------------------------------------------------------- */
-AtomVecAngleCuda::AtomVecAngleCuda(LAMMPS *lmp, int narg, char **arg) :
- AtomVecAngle(lmp, narg, arg)
+AtomVecAngleCuda::AtomVecAngleCuda(LAMMPS *lmp) : AtomVecAngle(lmp)
{
cuda = lmp->cuda;
if(cuda == NULL)
diff --git a/src/USER-CUDA/atom_vec_angle_cuda.h b/src/USER-CUDA/atom_vec_angle_cuda.h
index 1c2956e8377c70e8ef3a4ecdeab258dc348ae886..f89b4b4bf091f35b917a943af50368ee7ec4ac58 100644
--- a/src/USER-CUDA/atom_vec_angle_cuda.h
+++ b/src/USER-CUDA/atom_vec_angle_cuda.h
@@ -37,7 +37,7 @@ namespace LAMMPS_NS {
class AtomVecAngleCuda : public AtomVecAngle {
public:
- AtomVecAngleCuda(class LAMMPS *, int, char **);
+ AtomVecAngleCuda(class LAMMPS *);
virtual ~AtomVecAngleCuda() {}
void grow_copylist(int n);
void grow_send(int n,double** buf_send,int flag);
diff --git a/src/USER-CUDA/atom_vec_atomic_cuda.cpp b/src/USER-CUDA/atom_vec_atomic_cuda.cpp
index 51ce230b8ce5e61b5f2fc458975389951a7a16b2..a6840355d775047a1a7df50069c56209387b9612 100644
--- a/src/USER-CUDA/atom_vec_atomic_cuda.cpp
+++ b/src/USER-CUDA/atom_vec_atomic_cuda.cpp
@@ -60,8 +60,7 @@ using namespace LAMMPS_NS;
#define BUF_FLOAT double
/* ---------------------------------------------------------------------- */
-AtomVecAtomicCuda::AtomVecAtomicCuda(LAMMPS *lmp, int narg, char **arg) :
- AtomVecAtomic(lmp, narg, arg)
+AtomVecAtomicCuda::AtomVecAtomicCuda(LAMMPS *lmp) : AtomVecAtomic(lmp)
{
cuda = lmp->cuda;
if(cuda == NULL)
diff --git a/src/USER-CUDA/atom_vec_atomic_cuda.h b/src/USER-CUDA/atom_vec_atomic_cuda.h
index 17b803d8ad383497ffcef1c2cc9b93a29614f469..1260971c431e9934925741259362454108d152bc 100644
--- a/src/USER-CUDA/atom_vec_atomic_cuda.h
+++ b/src/USER-CUDA/atom_vec_atomic_cuda.h
@@ -49,7 +49,7 @@ namespace LAMMPS_NS {
class AtomVecAtomicCuda : public AtomVecAtomic {
public:
- AtomVecAtomicCuda(class LAMMPS *, int, char **);
+ AtomVecAtomicCuda(class LAMMPS *);
virtual ~AtomVecAtomicCuda() {}
void grow_copylist(int n);
void grow_send(int n,double** buf_send,int flag);
diff --git a/src/USER-CUDA/atom_vec_charge_cuda.cpp b/src/USER-CUDA/atom_vec_charge_cuda.cpp
index 991038debb43e4d80a5cdbcb562c07dae62d6315..9e8a5ac373c934f8e25d10735c7eaa605ddfc835 100644
--- a/src/USER-CUDA/atom_vec_charge_cuda.cpp
+++ b/src/USER-CUDA/atom_vec_charge_cuda.cpp
@@ -59,8 +59,7 @@ using namespace LAMMPS_NS;
#define BUF_FLOAT double
/* ---------------------------------------------------------------------- */
-AtomVecChargeCuda::AtomVecChargeCuda(LAMMPS *lmp, int narg, char **arg) :
- AtomVecCharge(lmp, narg, arg)
+AtomVecChargeCuda::AtomVecChargeCuda(LAMMPS *lmp) : AtomVecCharge(lmp)
{
cuda = lmp->cuda;
if(cuda == NULL)
diff --git a/src/USER-CUDA/atom_vec_charge_cuda.h b/src/USER-CUDA/atom_vec_charge_cuda.h
index ba7b57e75f0d2d40a967cde7d277597525f2856e..b1bbabb0d1c4977a4402991430d351fe21949401 100644
--- a/src/USER-CUDA/atom_vec_charge_cuda.h
+++ b/src/USER-CUDA/atom_vec_charge_cuda.h
@@ -37,7 +37,7 @@ namespace LAMMPS_NS {
class AtomVecChargeCuda : public AtomVecCharge {
public:
- AtomVecChargeCuda(class LAMMPS *, int, char **);
+ AtomVecChargeCuda(class LAMMPS *);
virtual ~AtomVecChargeCuda() {}
void grow_copylist(int n);
void grow_send(int n,double** buf_send,int flag);
diff --git a/src/USER-EFF/atom_vec_electron.cpp b/src/USER-EFF/atom_vec_electron.cpp
index c8eb874087998080a9c414676afc7be2d4e019cb..f95ed825c64c711035768cc82e361125279d9c82 100644
--- a/src/USER-EFF/atom_vec_electron.cpp
+++ b/src/USER-EFF/atom_vec_electron.cpp
@@ -33,8 +33,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecElectron::AtomVecElectron(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg)
+AtomVecElectron::AtomVecElectron(LAMMPS *lmp) : AtomVec(lmp)
{
comm_x_only = comm_f_only = 0;
diff --git a/src/USER-EFF/atom_vec_electron.h b/src/USER-EFF/atom_vec_electron.h
index 73dd126a628df8e3ff0e27e092b7ab6d7f4b0232..c0cc5d5e4a3b811f9bbb8072ace085d8f7b2dc03 100644
--- a/src/USER-EFF/atom_vec_electron.h
+++ b/src/USER-EFF/atom_vec_electron.h
@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
class AtomVecElectron : public AtomVec {
public:
- AtomVecElectron(class LAMMPS *, int, char **);
+ AtomVecElectron(class LAMMPS *);
~AtomVecElectron() {}
void grow(int);
void grow_reset();
diff --git a/src/USER-SPH/atom_vec_meso.cpp b/src/USER-SPH/atom_vec_meso.cpp
index 73cf49619f3440886c60f3f0b30bda55b6ec7afe..57c71e353f71506f6c410d6afd0fc51616a0fdd9 100644
--- a/src/USER-SPH/atom_vec_meso.cpp
+++ b/src/USER-SPH/atom_vec_meso.cpp
@@ -27,8 +27,8 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecMeso::AtomVecMeso(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg) {
+AtomVecMeso::AtomVecMeso(LAMMPS *lmp) : AtomVec(lmp)
+{
molecular = 0;
mass_type = 1;
diff --git a/src/USER-SPH/atom_vec_meso.h b/src/USER-SPH/atom_vec_meso.h
index 97ea42ac5caffebcaf7a6d9edb81040ffeb95f18..f017008d465beb64de2e66dda8e08c1a54bc1699 100644
--- a/src/USER-SPH/atom_vec_meso.h
+++ b/src/USER-SPH/atom_vec_meso.h
@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
class AtomVecMeso : public AtomVec {
public:
- AtomVecMeso(class LAMMPS *, int, char **);
+ AtomVecMeso(class LAMMPS *);
~AtomVecMeso() {}
void grow(int);
void grow_reset();
diff --git a/src/atom.cpp b/src/atom.cpp
index 3ee0d194fc04c66381ea0cbeef69b9384daf0fbb..993a239186a03ce0e2dcf7492ec0f5d55463d2d8 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -42,6 +42,7 @@ using namespace LAMMPS_NS;
#define DELTA_MEMSTR 1024
#define EPSILON 1.0e-6
#define CUDA_CHUNK 3000
+#define MAXBODY 20 // max # of lines in one body, also in ReadData class
/* ---------------------------------------------------------------------- */
@@ -190,6 +191,7 @@ Atom::~Atom()
memory->destroy(ellipsoid);
memory->destroy(line);
memory->destroy(tri);
+ memory->destroy(body);
memory->destroy(spin);
memory->destroy(eradius);
memory->destroy(ervel);
@@ -271,7 +273,8 @@ void Atom::create_avec(const char *style, int narg, char **arg, char *suffix)
vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
int sflag;
- avec = new_avec(style,narg,arg,suffix,sflag);
+ avec = new_avec(style,suffix,sflag);
+ avec->settings(narg,arg);
if (sflag) {
char estyle[256];
@@ -295,8 +298,7 @@ void Atom::create_avec(const char *style, int narg, char **arg, char *suffix)
generate an AtomVec class, first with suffix appended
------------------------------------------------------------------------- */
-AtomVec *Atom::new_avec(const char *style, int narg, char **arg,
- char *suffix, int &sflag)
+AtomVec *Atom::new_avec(const char *style, char *suffix, int &sflag)
{
if (suffix && lmp->suffix_enable) {
sflag = 1;
@@ -307,7 +309,7 @@ AtomVec *Atom::new_avec(const char *style, int narg, char **arg,
#define ATOM_CLASS
#define AtomStyle(key,Class) \
- else if (strcmp(estyle,#key) == 0) return new Class(lmp,narg,arg);
+ else if (strcmp(estyle,#key) == 0) return new Class(lmp);
#include "style_atom.h"
#undef AtomStyle
#undef ATOM_CLASS
@@ -320,7 +322,7 @@ AtomVec *Atom::new_avec(const char *style, int narg, char **arg,
#define ATOM_CLASS
#define AtomStyle(key,Class) \
- else if (strcmp(style,#key) == 0) return new Class(lmp,narg,arg);
+ else if (strcmp(style,#key) == 0) return new Class(lmp);
#include "style_atom.h"
#undef ATOM_CLASS
@@ -718,6 +720,45 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus)
delete [] values;
}
+/* ----------------------------------------------------------------------
+ unpack n lines from atom-style specific section of data file
+ check that atom IDs are > 0 and <= map_tag_max
+ call style-specific routine to parse line
+------------------------------------------------------------------------- */
+
+void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body)
+{
+ int j,m,tagdata,ninteger,ndouble;
+
+ char **ivalues = new char*[10*MAXBODY];
+ char **dvalues = new char*[10*MAXBODY];
+
+ // loop over lines of body data
+ // tokenize the lines into ivalues and dvalues
+ // if I own atom tag, unpack its values
+
+ for (int i = 0; i < n; i++) {
+ if (i == 0) tagdata = atoi(strtok(buf," \t\n\r\f"));
+ else tagdata = atoi(strtok(NULL," \t\n\r\f"));
+ ninteger = atoi(strtok(NULL," \t\n\r\f"));
+ ndouble = atoi(strtok(NULL," \t\n\r\f"));
+
+ for (j = 0; j < ninteger; j++)
+ ivalues[j] = strtok(NULL," \t\n\r\f");
+ for (j = 0; j < ndouble; j++)
+ dvalues[j] = strtok(NULL," \t\n\r\f");
+
+ if (tagdata <= 0 || tagdata > map_tag_max)
+ error->one(FLERR,"Invalid atom ID in Bodies section of data file");
+
+ if ((m = map(tagdata)) >= 0)
+ avec_body->data_body(m,ninteger,ndouble,ivalues,dvalues);
+ }
+
+ delete [] ivalues;
+ delete [] dvalues;
+}
+
/* ----------------------------------------------------------------------
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
diff --git a/src/atom.h b/src/atom.h
index a87b66fed5eaadbada16ef8162526947fc616ec2..03c9a4c47bbbd246c052ecd63574b000c9ebc1c7 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -53,7 +53,7 @@ class Atom : protected Pointers {
double **omega,**angmom,**torque;
double *radius,*rmass,*vfrac,*s0;
double **x0;
- int *ellipsoid,*line,*tri;
+ int *ellipsoid,*line,*tri,*body;
int *spin;
double *eradius,*ervel,*erforce,*ervelforce;
double *cs,*csforce,*vforce;
@@ -89,7 +89,8 @@ class Atom : protected Pointers {
// atom style and per-atom array existence flags
// customize by adding new flag
- int sphere_flag,ellipsoid_flag,line_flag,tri_flag,peri_flag,electron_flag;
+ int sphere_flag,ellipsoid_flag,line_flag,tri_flag,body_flag;
+ int peri_flag,electron_flag;
int ecp_flag;
int wavepacket_flag,sph_flag;
@@ -135,7 +136,7 @@ class Atom : protected Pointers {
void settings(class Atom *);
void create_avec(const char *, int, char **, char *suffix = NULL);
- class AtomVec *new_avec(const char *, int, char **, char *, int &);
+ class AtomVec *new_avec(const char *, char *, int &);
void init();
void setup();
@@ -150,6 +151,7 @@ class Atom : protected Pointers {
void data_atoms(int, char *);
void data_vels(int, char *);
void data_bonus(int, char *, class AtomVec *);
+ void data_bodies(int, char *, class AtomVecBody *);
void data_bonds(int, char *);
void data_angles(int, char *);
diff --git a/src/atom_vec.cpp b/src/atom_vec.cpp
index e33fb007bc43917751aa4f59651b821acaf22afb..7b0e4984031f0d67c5594ea8215555f09ea4179c 100644
--- a/src/atom_vec.cpp
+++ b/src/atom_vec.cpp
@@ -21,7 +21,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVec::AtomVec(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
+AtomVec::AtomVec(LAMMPS *lmp) : Pointers(lmp)
{
nmax = 0;
bonds_allow = angles_allow = dihedrals_allow = impropers_allow = 0;
@@ -30,6 +30,15 @@ AtomVec::AtomVec(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
cudable = false;
}
+/* ----------------------------------------------------------------------
+ no additional args by default
+------------------------------------------------------------------------- */
+
+void AtomVec::settings(int narg, char **arg)
+{
+ if (narg) error->all(FLERR,"Invalid atom_style command");
+}
+
/* ----------------------------------------------------------------------
copy of velocity remap settings from Domain
------------------------------------------------------------------------- */
diff --git a/src/atom_vec.h b/src/atom_vec.h
index 75627a42ef5bde16a5417726c3bdd7ec0a50a3f6..58e215120a8bca9671264024e667d28b35cb3c2c 100644
--- a/src/atom_vec.h
+++ b/src/atom_vec.h
@@ -14,6 +14,7 @@
#ifndef LMP_ATOM_VEC_H
#define LMP_ATOM_VEC_H
+#include "stdio.h"
#include "pointers.h"
namespace LAMMPS_NS {
@@ -41,8 +42,9 @@ class AtomVec : protected Pointers {
int cudable; // 1 if atom style is CUDA-enabled
int *maxsend; // CUDA-specific variable
- AtomVec(class LAMMPS *, int, char **);
+ AtomVec(class LAMMPS *);
virtual ~AtomVec() {}
+ virtual void settings(int, char **);
virtual void init();
virtual void grow(int) = 0;
@@ -76,6 +78,9 @@ class AtomVec : protected Pointers {
virtual int pack_restart(int, double *) = 0;
virtual int unpack_restart(double *) = 0;
+ virtual void write_restart_settings(FILE *) {}
+ virtual void read_restart_settings(FILE *) {}
+
virtual void create_atom(int, double *) = 0;
virtual void data_atom(double *, tagint, char **) = 0;
virtual void data_atom_bonus(int, char **) {}
diff --git a/src/atom_vec_atomic.cpp b/src/atom_vec_atomic.cpp
index b57b443cc01afe5fa033ac85b627e345cd4526d4..d3097b85568c9ad443f220cd08517bb6cbab3540 100644
--- a/src/atom_vec_atomic.cpp
+++ b/src/atom_vec_atomic.cpp
@@ -27,8 +27,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecAtomic::AtomVecAtomic(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg)
+AtomVecAtomic::AtomVecAtomic(LAMMPS *lmp) : AtomVec(lmp)
{
molecular = 0;
mass_type = 1;
diff --git a/src/atom_vec_atomic.h b/src/atom_vec_atomic.h
index 97e6c66887b2d3bc24dbbc2367de7e1c30fa4cce..5166bf3d7408b1e7136df5af488272a5034af198 100644
--- a/src/atom_vec_atomic.h
+++ b/src/atom_vec_atomic.h
@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
class AtomVecAtomic : public AtomVec {
public:
- AtomVecAtomic(class LAMMPS *, int, char **);
+ AtomVecAtomic(class LAMMPS *);
virtual ~AtomVecAtomic() {}
void grow(int);
void grow_reset();
diff --git a/src/atom_vec_charge.cpp b/src/atom_vec_charge.cpp
index 247912d6ac22ee6eba702ed34f016c431e2416a0..66efec1952b4c903420c2c2fc88bee74ccf6920a 100644
--- a/src/atom_vec_charge.cpp
+++ b/src/atom_vec_charge.cpp
@@ -27,8 +27,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecCharge::AtomVecCharge(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg)
+AtomVecCharge::AtomVecCharge(LAMMPS *lmp) : AtomVec(lmp)
{
molecular = 0;
mass_type = 1;
diff --git a/src/atom_vec_charge.h b/src/atom_vec_charge.h
index 41ee4e214c9871bafb722ce58f5bd449e9f4245b..69f68cc3396d548758570d793a545b88d3d5077d 100644
--- a/src/atom_vec_charge.h
+++ b/src/atom_vec_charge.h
@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
class AtomVecCharge : public AtomVec {
public:
- AtomVecCharge(class LAMMPS *, int, char **);
+ AtomVecCharge(class LAMMPS *);
virtual ~AtomVecCharge() {}
void grow(int);
void grow_reset();
diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp
index 0e88e3472a013e6e18800e457dc7655048b690ec..c30cbaa0b9d114d42b09b2d251b276cffdb66310 100755
--- a/src/atom_vec_ellipsoid.cpp
+++ b/src/atom_vec_ellipsoid.cpp
@@ -36,8 +36,7 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-AtomVecEllipsoid::AtomVecEllipsoid(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg)
+AtomVecEllipsoid::AtomVecEllipsoid(LAMMPS *lmp) : AtomVec(lmp)
{
molecular = 0;
@@ -107,6 +106,7 @@ void AtomVecEllipsoid::grow_reset()
mask = atom->mask; image = atom->image;
x = atom->x; v = atom->v; f = atom->f;
rmass = atom->rmass; angmom = atom->angmom; torque = atom->torque;
+ ellipsoid = atom->ellipsoid;
}
/* ----------------------------------------------------------------------
@@ -145,16 +145,16 @@ void AtomVecEllipsoid::copy(int i, int j, int delflag)
angmom[j][1] = angmom[i][1];
angmom[j][2] = angmom[i][2];
- // if delflag and atom J has bonus data, then delete it
+ // if deleting atom J via delflag and J has bonus data, then delete it
if (delflag && ellipsoid[j] >= 0) {
copy_bonus(nlocal_bonus-1,ellipsoid[j]);
nlocal_bonus--;
}
- // if atom I has bonus data and not deleting I, repoint I's bonus to J
+ // if atom I has bonus data, reset I's bonus.ilocal to loc J
- if (ellipsoid[i] >= 0 && i != j) bonus[ellipsoid[i]].ilocal = j;
+ if (ellipsoid[i] >= 0) bonus[ellipsoid[i]].ilocal = j;
ellipsoid[j] = ellipsoid[i];
if (atom->nextra_grow)
diff --git a/src/atom_vec_ellipsoid.h b/src/atom_vec_ellipsoid.h
index ef13f6dbd7f970a2ee577ff87b8ba38f8b12f066..379fd36e6e0ac3b9aff2607462acf67fd0d59859 100755
--- a/src/atom_vec_ellipsoid.h
+++ b/src/atom_vec_ellipsoid.h
@@ -33,7 +33,7 @@ class AtomVecEllipsoid : public AtomVec {
};
struct Bonus *bonus;
- AtomVecEllipsoid(class LAMMPS *, int, char **);
+ AtomVecEllipsoid(class LAMMPS *);
~AtomVecEllipsoid();
void grow(int);
void grow_reset();
diff --git a/src/atom_vec_hybrid.cpp b/src/atom_vec_hybrid.cpp
index 05351cf7650af86b2f2f048b3eeb10b4596a6895..0bda19c251d1309b6b5f79b663ec9bc845d44e8a 100644
--- a/src/atom_vec_hybrid.cpp
+++ b/src/atom_vec_hybrid.cpp
@@ -27,30 +27,62 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg)
+AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp) : AtomVec(lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+AtomVecHybrid::~AtomVecHybrid()
{
- int i,k,dummy;
+ for (int k = 0; k < nstyles; k++) delete styles[k];
+ delete [] styles;
+ for (int k = 0; k < nstyles; k++) delete [] keywords[k];
+ delete [] keywords;
+}
- if (narg < 1) error->all(FLERR,"Illegal atom_style command");
+/* ----------------------------------------------------------------------
+ process sub-style args
+------------------------------------------------------------------------- */
- // create sub-styles
+void AtomVecHybrid::settings(int narg, char **arg)
+{
+ // build list of all known atom styles
- nstyles = narg;
- styles = new AtomVec*[nstyles];
- keywords = new char*[nstyles];
+ build_styles();
- for (i = 0; i < narg; i++) {
- for (k = 0; k < i; k++)
- if (strcmp(arg[i],keywords[k]) == 0)
- error->all(FLERR,"Atom style hybrid cannot use same atom style twice");
- if (strcmp(arg[i],"hybrid") == 0)
+ // allocate list of sub-styles as big as possibly needed if no extra args
+
+ styles = new AtomVec*[narg];
+ keywords = new char*[narg];
+
+ // allocate each sub-style
+ // call settings() with set of args that are not atom style names
+ // use known_style() to determine which args these are
+
+ int i,jarg,dummy;
+
+ int iarg = 0;
+ nstyles = 0;
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"hybrid") == 0)
error->all(FLERR,"Atom style hybrid cannot have hybrid as an argument");
- styles[i] = atom->new_avec(arg[i],0,NULL,NULL,dummy);
- keywords[i] = new char[strlen(arg[i])+1];
- strcpy(keywords[i],arg[i]);
+ for (i = 0; i < nstyles; i++)
+ if (strcmp(arg[iarg],keywords[i]) == 0)
+ error->all(FLERR,"Atom style hybrid cannot use same atom style twice");
+ styles[nstyles] = atom->new_avec(arg[iarg],NULL,dummy);
+ keywords[nstyles] = new char[strlen(arg[iarg])+1];
+ strcpy(keywords[nstyles],arg[iarg]);
+ jarg = iarg + 1;
+ while (jarg < narg && !known_style(arg[jarg])) jarg++;
+ styles[nstyles]->settings(jarg-iarg-1,&arg[iarg+1]);
+ iarg = jarg;
+ nstyles++;
}
+ // free allstyles created by build_styles()
+
+ for (int i = 0; i < nallstyles; i++) delete [] allstyles[i];
+ delete [] allstyles;
+
// hybrid settings are MAX or MIN of sub-style settings
// hybrid sizes are minimial values plus extra values for each sub-style
@@ -64,7 +96,7 @@ AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp, int narg, char **arg) :
size_data_vel = 4;
xcol_data = 3;
- for (k = 0; k < nstyles; k++) {
+ for (int k = 0; k < nstyles; k++) {
molecular = MAX(molecular,styles[k]->molecular);
bonds_allow = MAX(bonds_allow,styles[k]->bonds_allow);
angles_allow = MAX(angles_allow,styles[k]->angles_allow);
@@ -89,16 +121,6 @@ AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
-AtomVecHybrid::~AtomVecHybrid()
-{
- for (int k = 0; k < nstyles; k++) delete styles[k];
- delete [] styles;
- for (int k = 0; k < nstyles; k++) delete [] keywords[k];
- delete [] keywords;
-}
-
-/* ---------------------------------------------------------------------- */
-
void AtomVecHybrid::init()
{
AtomVec::init();
@@ -780,6 +802,22 @@ int AtomVecHybrid::unpack_restart(double *buf)
return m;
}
+/* ---------------------------------------------------------------------- */
+
+void AtomVecHybrid::write_restart_settings(FILE *fp)
+{
+ for (int k = 0; k < nstyles; k++)
+ styles[k]->write_restart_settings(fp);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AtomVecHybrid::read_restart_settings(FILE *fp)
+{
+ for (int k = 0; k < nstyles; k++)
+ styles[k]->read_restart_settings(fp);
+}
+
/* ----------------------------------------------------------------------
create one atom of itype at coord
create each sub-style one after the other
@@ -863,6 +901,45 @@ void AtomVecHybrid::data_vel(int m, char **values)
n += styles[k]->data_vel_hybrid(m,&values[n]);
}
+/* ----------------------------------------------------------------------
+ allstyles = list of all atom styles in this LAMMPS executable
+------------------------------------------------------------------------- */
+
+void AtomVecHybrid::build_styles()
+{
+ nallstyles = 0;
+#define ATOM_CLASS
+#define AtomStyle(key,Class) nallstyles++;
+#include "style_atom.h"
+#undef AtomStyle
+#undef ATOM_CLASS
+
+ allstyles = new char*[nallstyles];
+
+ int n;
+ nallstyles = 0;
+#define ATOM_CLASS
+#define AtomStyle(key,Class) \
+ n = strlen(#key) + 1; \
+ allstyles[nallstyles] = new char[n]; \
+ strcpy(allstyles[nallstyles],#key); \
+ nallstyles++;
+#include "style_atom.h"
+#undef AtomStyle
+#undef ATOM_CLASS
+}
+
+/* ----------------------------------------------------------------------
+ allstyles = list of all known atom styles
+------------------------------------------------------------------------- */
+
+int AtomVecHybrid::known_style(char *str)
+{
+ for (int i = 0; i < nallstyles; i++)
+ if (strcmp(str,allstyles[i]) == 0) return 1;
+ return 0;
+}
+
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
------------------------------------------------------------------------- */
diff --git a/src/atom_vec_hybrid.h b/src/atom_vec_hybrid.h
index da9956d6957e207ba0690e987d45cfed7ebfa054..df3d410efc8034484d302bcfc358195292c63846 100644
--- a/src/atom_vec_hybrid.h
+++ b/src/atom_vec_hybrid.h
@@ -20,6 +20,7 @@ AtomStyle(hybrid,AtomVecHybrid)
#ifndef LMP_ATOM_VEC_HYBRID_H
#define LMP_ATOM_VEC_HYBRID_H
+#include "stdio.h"
#include "atom_vec.h"
namespace LAMMPS_NS {
@@ -30,8 +31,9 @@ class AtomVecHybrid : public AtomVec {
class AtomVec **styles;
char **keywords;
- AtomVecHybrid(class LAMMPS *, int, char **);
+ AtomVecHybrid(class LAMMPS *);
~AtomVecHybrid();
+ void settings(int, char **);
void init();
void grow(int);
void grow_reset();
@@ -52,6 +54,8 @@ class AtomVecHybrid : public AtomVec {
int size_restart();
int pack_restart(int, double *);
int unpack_restart(double *);
+ void write_restart_settings(FILE *);
+ void read_restart_settings(FILE *);
void create_atom(int, double *);
void data_atom(double *, tagint, char **);
int data_atom_hybrid(int, char **) {return 0;}
@@ -63,6 +67,12 @@ class AtomVecHybrid : public AtomVec {
tagint *image;
double **x,**v,**f;
double **omega,**angmom;
+
+ int nallstyles;
+ char **allstyles;
+
+ void build_styles();
+ int known_style(char *);
};
}
diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp
index 9da8c139dc2ede564b0eb5b24c72c63e2c0bcbdb..000f38b4af77b265a3d146fef9818ff5a81f5c21 100644
--- a/src/atom_vec_line.cpp
+++ b/src/atom_vec_line.cpp
@@ -32,8 +32,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecLine::AtomVecLine(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg)
+AtomVecLine::AtomVecLine(LAMMPS *lmp) : AtomVec(lmp)
{
molecular = 0;
@@ -116,6 +115,7 @@ void AtomVecLine::grow_reset()
x = atom->x; v = atom->v; f = atom->f;
molecule = atom->molecule; rmass = atom->rmass;
omega = atom->omega; torque = atom->torque;
+ line = atom->line;
}
/* ----------------------------------------------------------------------
@@ -155,16 +155,16 @@ void AtomVecLine::copy(int i, int j, int delflag)
omega[j][1] = omega[i][1];
omega[j][2] = omega[i][2];
- // if delflag and atom J has bonus data, then delete it
+ // if deleting atom J via delflag and J has bonus data, then delete it
if (delflag && line[j] >= 0) {
copy_bonus(nlocal_bonus-1,line[j]);
nlocal_bonus--;
}
- // if atom I has bonus data and not deleting I, repoint I's bonus to J
+ // if atom I has bonus data, reset I's bonus.ilocal to loc J
- if (line[i] >= 0 && i != j) bonus[line[i]].ilocal = j;
+ if (line[i] >= 0) bonus[line[i]].ilocal = j;
line[j] = line[i];
if (atom->nextra_grow)
diff --git a/src/atom_vec_line.h b/src/atom_vec_line.h
index b94a63ad3f10c5a2afc5db38d180df7d2c8d5612..72e871f5422292ccc1d5c7f4f149bf66c3456fd6 100644
--- a/src/atom_vec_line.h
+++ b/src/atom_vec_line.h
@@ -32,7 +32,7 @@ class AtomVecLine : public AtomVec {
};
struct Bonus *bonus;
- AtomVecLine(class LAMMPS *, int, char **);
+ AtomVecLine(class LAMMPS *);
~AtomVecLine();
void init();
void grow(int);
diff --git a/src/atom_vec_sphere.cpp b/src/atom_vec_sphere.cpp
index c8f00743bb653a7e04fb358a07bd3bd491b84a6d..7cc92d5202e18f8e9ab6e4aa1a93d09e6c932056 100644
--- a/src/atom_vec_sphere.cpp
+++ b/src/atom_vec_sphere.cpp
@@ -33,8 +33,7 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
-AtomVecSphere::AtomVecSphere(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg)
+AtomVecSphere::AtomVecSphere(LAMMPS *lmp) : AtomVec(lmp)
{
molecular = 0;
diff --git a/src/atom_vec_sphere.h b/src/atom_vec_sphere.h
index 02ba050b43452dc4f53bd78ccc3114da438e2a46..1501ce791f9c267b373f7015721a2b0e38cb8631 100644
--- a/src/atom_vec_sphere.h
+++ b/src/atom_vec_sphere.h
@@ -26,7 +26,7 @@ namespace LAMMPS_NS {
class AtomVecSphere : public AtomVec {
public:
- AtomVecSphere(class LAMMPS *, int, char **);
+ AtomVecSphere(class LAMMPS *);
~AtomVecSphere() {}
void init();
void grow(int);
diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp
index 0aab80bba9a7edc370a1777d9144f94e69b4cbb3..fc405d2fd5b60680d72e454aaff22bdc7b5f75aa 100644
--- a/src/atom_vec_tri.cpp
+++ b/src/atom_vec_tri.cpp
@@ -33,8 +33,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-AtomVecTri::AtomVecTri(LAMMPS *lmp, int narg, char **arg) :
- AtomVec(lmp, narg, arg)
+AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp)
{
molecular = 0;
@@ -117,6 +116,7 @@ void AtomVecTri::grow_reset()
x = atom->x; v = atom->v; f = atom->f;
molecule = atom->molecule; rmass = atom->rmass;
angmom = atom->angmom; torque = atom->torque;
+ tri = atom->tri;
}
/* ----------------------------------------------------------------------
@@ -157,16 +157,16 @@ void AtomVecTri::copy(int i, int j, int delflag)
angmom[j][1] = angmom[i][1];
angmom[j][2] = angmom[i][2];
- // if delflag and atom J has bonus data, then delete it
+ // if deleting atom J via delflag and J has bonus data, then delete it
if (delflag && tri[j] >= 0) {
copy_bonus(nlocal_bonus-1,tri[j]);
nlocal_bonus--;
}
- // if atom I has bonus data and not deleting I, repoint I's bonus to J
+ // if atom I has bonus data, reset I's bonus.ilocal to loc J
- if (tri[i] >= 0 && i != j) bonus[tri[i]].ilocal = j;
+ if (tri[i] >= 0) bonus[tri[i]].ilocal = j;
tri[j] = tri[i];
if (atom->nextra_grow)
@@ -1320,7 +1320,7 @@ void AtomVecTri::create_atom(int itype, double *coord)
}
/* ----------------------------------------------------------------------
- unpack one tri from Atoms section of data file
+ unpack one line from Atoms section of data file
initialize other atom quantities
------------------------------------------------------------------------- */
@@ -1387,7 +1387,7 @@ int AtomVecTri::data_atom_hybrid(int nlocal, char **values)
}
/* ----------------------------------------------------------------------
- unpack one tri from Tris section of data file
+ unpack one line from Tris section of data file
------------------------------------------------------------------------- */
void AtomVecTri::data_atom_bonus(int m, char **values)
@@ -1511,7 +1511,7 @@ void AtomVecTri::data_atom_bonus(int m, char **values)
}
/* ----------------------------------------------------------------------
- unpack one tri from Velocities section of data file
+ unpack one line from Velocities section of data file
------------------------------------------------------------------------- */
void AtomVecTri::data_vel(int m, char **values)
@@ -1555,7 +1555,8 @@ bigint AtomVecTri::memory_usage()
if (atom->memcheck("molecule")) bytes += memory->usage(molecule,nmax);
if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax);
if (atom->memcheck("angmom")) bytes += memory->usage(angmom,nmax,3);
- if (atom->memcheck("torque")) bytes += memory->usage(torque,nmax*comm->nthreads,3);
+ if (atom->memcheck("torque")) bytes +=
+ memory->usage(torque,nmax*comm->nthreads,3);
if (atom->memcheck("tri")) bytes += memory->usage(tri,nmax);
bytes += nmax_bonus*sizeof(Bonus);
diff --git a/src/atom_vec_tri.h b/src/atom_vec_tri.h
index 245c32dde1db777ea95c1ea54de2b71b1f8bf89b..bdc5a8bca557a039160a19b6cefee8054f21529d 100644
--- a/src/atom_vec_tri.h
+++ b/src/atom_vec_tri.h
@@ -34,7 +34,7 @@ class AtomVecTri : public AtomVec {
};
struct Bonus *bonus;
- AtomVecTri(class LAMMPS *, int, char **);
+ AtomVecTri(class LAMMPS *);
~AtomVecTri();
void init();
void grow(int);
diff --git a/src/comm.cpp b/src/comm.cpp
index 45eefcec2b82bd35d4bc48e2cb578277dad5417d..46d937edbaf923c79cab4a4b6ea5586cbd080ff3 100644
--- a/src/comm.cpp
+++ b/src/comm.cpp
@@ -798,10 +798,13 @@ void Comm::exchange()
// clear global->local map for owned and ghost atoms
// b/c atoms migrate to new procs in exchange() and
- // new ghosts are created in borders()
+ // new ghosts are created in borders()
// map_set() is done at end of borders()
+ // clear ghost count and any ghost bonus data internal to AtomVec
if (map_style) atom->map_clear();
+ atom->nghost = 0;
+ atom->avec->clear_bonus();
// subbox bounds for orthogonal or triclinic
@@ -836,6 +839,7 @@ void Comm::exchange()
}
atom->nlocal = nlocal;
+
// send/recv atoms in both directions
// if 1 proc in dimension, no send/recv, set recv buf to send buf
// if 2 procs in dimension, single send/recv
@@ -907,11 +911,6 @@ void Comm::borders()
MPI_Status status;
AtomVec *avec = atom->avec;
- // clear old ghosts and any ghost bonus data internal to AtomVec
-
- atom->nghost = 0;
- atom->avec->clear_bonus();
-
// do swaps over all 3 dimensions
iswap = 0;
diff --git a/src/compute_property_atom.cpp b/src/compute_property_atom.cpp
index d3ae7171f45742f6b1dfb31df0516d7302f07241..382286fec61b9643745aaf78167003c07f3c9e3b 100644
--- a/src/compute_property_atom.cpp
+++ b/src/compute_property_atom.cpp
@@ -19,6 +19,7 @@
#include "atom_vec_ellipsoid.h"
#include "atom_vec_line.h"
#include "atom_vec_tri.h"
+#include "atom_vec_body.h"
#include "update.h"
#include "domain.h"
#include "memory.h"
@@ -191,26 +192,36 @@ ComputePropertyAtom::ComputePropertyAtom(LAMMPS *lmp, int narg, char **arg) :
if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
"atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_shapez;
+
} else if (strcmp(arg[iarg],"quatw") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
- if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ avec_body = (AtomVecBody *) atom->style_match("body");
+ if (!avec_ellipsoid && !avec_body)
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_quatw;
} else if (strcmp(arg[iarg],"quati") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
- if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ avec_body = (AtomVecBody *) atom->style_match("body");
+ if (!avec_ellipsoid && !avec_body)
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_quati;
} else if (strcmp(arg[iarg],"quatj") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
- if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ avec_body = (AtomVecBody *) atom->style_match("body");
+ if (!avec_ellipsoid && !avec_body)
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_quatj;
} else if (strcmp(arg[iarg],"quatk") == 0) {
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
- if (!avec_ellipsoid) error->all(FLERR,"Compute property/atom for "
- "atom property that isn't allocated");
+ avec_body = (AtomVecBody *) atom->style_match("body");
+ if (!avec_ellipsoid && !avec_body)
+ error->all(FLERR,"Compute property/atom for "
+ "atom property that isn't allocated");
pack_choice[i] = &ComputePropertyAtom::pack_quatk;
+
} else if (strcmp(arg[iarg],"tqx") == 0) {
if (!atom->torque_flag)
error->all(FLERR,"Compute property/atom for "
@@ -349,6 +360,7 @@ void ComputePropertyAtom::init()
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
avec_line = (AtomVecLine *) atom->style_match("line");
avec_tri = (AtomVecTri *) atom->style_match("tri");
+ avec_body = (AtomVecBody *) atom->style_match("body");
}
/* ---------------------------------------------------------------------- */
@@ -1136,16 +1148,31 @@ void ComputePropertyAtom::pack_shapez(int n)
void ComputePropertyAtom::pack_quatw(int n)
{
- AtomVecEllipsoid::Bonus *bonus = avec_ellipsoid->bonus;
- int *ellipsoid = atom->ellipsoid;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
+ if (avec_ellipsoid) {
+ AtomVecEllipsoid::Bonus *bonus = avec_ellipsoid->bonus;
+ int *ellipsoid = atom->ellipsoid;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
- for (int i = 0; i < nlocal; i++) {
- if ((mask[i] & groupbit) && ellipsoid[i] >= 0)
- buf[n] = bonus[ellipsoid[i]].quat[0];
- else buf[n] = 0.0;
- n += nvalues;
+ for (int i = 0; i < nlocal; i++) {
+ if ((mask[i] & groupbit) && ellipsoid[i] >= 0)
+ buf[n] = bonus[ellipsoid[i]].quat[0];
+ else buf[n] = 0.0;
+ n += nvalues;
+ }
+
+ } else {
+ AtomVecBody::Bonus *bonus = avec_body->bonus;
+ int *body = atom->body;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int i = 0; i < nlocal; i++) {
+ if ((mask[i] & groupbit) && body[i] >= 0)
+ buf[n] = bonus[body[i]].quat[0];
+ else buf[n] = 0.0;
+ n += nvalues;
+ }
}
}
@@ -1153,16 +1180,31 @@ void ComputePropertyAtom::pack_quatw(int n)
void ComputePropertyAtom::pack_quati(int n)
{
- AtomVecEllipsoid::Bonus *bonus = avec_ellipsoid->bonus;
- int *ellipsoid = atom->ellipsoid;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
+ if (avec_ellipsoid) {
+ AtomVecEllipsoid::Bonus *bonus = avec_ellipsoid->bonus;
+ int *ellipsoid = atom->ellipsoid;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
- for (int i = 0; i < nlocal; i++) {
- if ((mask[i] & groupbit) && ellipsoid[i] >= 0)
- buf[n] = bonus[ellipsoid[i]].quat[1];
- else buf[n] = 0.0;
- n += nvalues;
+ for (int i = 0; i < nlocal; i++) {
+ if ((mask[i] & groupbit) && ellipsoid[i] >= 0)
+ buf[n] = bonus[ellipsoid[i]].quat[1];
+ else buf[n] = 0.0;
+ n += nvalues;
+ }
+
+ } else {
+ AtomVecBody::Bonus *bonus = avec_body->bonus;
+ int *body = atom->body;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int i = 0; i < nlocal; i++) {
+ if ((mask[i] & groupbit) && body[i] >= 0)
+ buf[n] = bonus[body[i]].quat[1];
+ else buf[n] = 0.0;
+ n += nvalues;
+ }
}
}
@@ -1170,16 +1212,31 @@ void ComputePropertyAtom::pack_quati(int n)
void ComputePropertyAtom::pack_quatj(int n)
{
- AtomVecEllipsoid::Bonus *bonus = avec_ellipsoid->bonus;
- int *ellipsoid = atom->ellipsoid;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
+ if (avec_ellipsoid) {
+ AtomVecEllipsoid::Bonus *bonus = avec_ellipsoid->bonus;
+ int *ellipsoid = atom->ellipsoid;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
- for (int i = 0; i < nlocal; i++) {
- if ((mask[i] & groupbit) && ellipsoid[i] >= 0)
- buf[n] = bonus[ellipsoid[i]].quat[2];
- else buf[n] = 0.0;
- n += nvalues;
+ for (int i = 0; i < nlocal; i++) {
+ if ((mask[i] & groupbit) && ellipsoid[i] >= 0)
+ buf[n] = bonus[ellipsoid[i]].quat[2];
+ else buf[n] = 0.0;
+ n += nvalues;
+ }
+
+ } else {
+ AtomVecBody::Bonus *bonus = avec_body->bonus;
+ int *body = atom->body;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int i = 0; i < nlocal; i++) {
+ if ((mask[i] & groupbit) && body[i] >= 0)
+ buf[n] = bonus[body[i]].quat[2];
+ else buf[n] = 0.0;
+ n += nvalues;
+ }
}
}
@@ -1187,16 +1244,31 @@ void ComputePropertyAtom::pack_quatj(int n)
void ComputePropertyAtom::pack_quatk(int n)
{
- AtomVecEllipsoid::Bonus *bonus = avec_ellipsoid->bonus;
- int *ellipsoid = atom->ellipsoid;
- int *mask = atom->mask;
- int nlocal = atom->nlocal;
+ if (avec_ellipsoid) {
+ AtomVecEllipsoid::Bonus *bonus = avec_ellipsoid->bonus;
+ int *ellipsoid = atom->ellipsoid;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
- for (int i = 0; i < nlocal; i++) {
- if ((mask[i] & groupbit) && ellipsoid[i] >= 0)
- buf[n] = bonus[ellipsoid[i]].quat[3];
- else buf[n] = 0.0;
- n += nvalues;
+ for (int i = 0; i < nlocal; i++) {
+ if ((mask[i] & groupbit) && ellipsoid[i] >= 0)
+ buf[n] = bonus[ellipsoid[i]].quat[3];
+ else buf[n] = 0.0;
+ n += nvalues;
+ }
+
+ } else {
+ AtomVecBody::Bonus *bonus = avec_body->bonus;
+ int *body = atom->body;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+
+ for (int i = 0; i < nlocal; i++) {
+ if ((mask[i] & groupbit) && body[i] >= 0)
+ buf[n] = bonus[body[i]].quat[3];
+ else buf[n] = 0.0;
+ n += nvalues;
+ }
}
}
diff --git a/src/compute_property_atom.h b/src/compute_property_atom.h
index b709e180775ec08969fadf8ea3db414c4073eded..bc8a4b0528cca8ca7bb5f04086fc01d531721df3 100644
--- a/src/compute_property_atom.h
+++ b/src/compute_property_atom.h
@@ -41,6 +41,7 @@ class ComputePropertyAtom : public Compute {
class AtomVecEllipsoid *avec_ellipsoid;
class AtomVecLine *avec_line;
class AtomVecTri *avec_tri;
+ class AtomVecBody *avec_body;
typedef void (ComputePropertyAtom::*FnPtrPack)(int);
FnPtrPack *pack_choice; // ptrs to pack functions
diff --git a/src/dump_local.cpp b/src/dump_local.cpp
index 331ee1e4d41b14de05925c9cc6feb01891d43f04..e865a3f70baa43406b59bf82cd7328331217a3fe 100644
--- a/src/dump_local.cpp
+++ b/src/dump_local.cpp
@@ -194,6 +194,17 @@ void DumpLocal::write_header(bigint ndump)
fprintf(fp,BIGINT_FORMAT "\n",update->ntimestep);
fprintf(fp,"ITEM: NUMBER OF %s\n",label);
fprintf(fp,BIGINT_FORMAT "\n",ndump);
+ if (domain->triclinic) {
+ fprintf(fp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
+ fprintf(fp,"%g %g %g\n",boxxlo,boxxhi,boxxy);
+ fprintf(fp,"%g %g %g\n",boxylo,boxyhi,boxxz);
+ fprintf(fp,"%g %g %g\n",boxzlo,boxzhi,boxyz);
+ } else {
+ fprintf(fp,"ITEM: BOX BOUNDS %s\n",boundstr);
+ fprintf(fp,"%g %g\n",boxxlo,boxxhi);
+ fprintf(fp,"%g %g\n",boxylo,boxyhi);
+ fprintf(fp,"%g %g\n",boxzlo,boxzhi);
+ }
fprintf(fp,"ITEM: %s %s\n",label,columns);
}
}
@@ -223,13 +234,15 @@ int DumpLocal::count()
for (int i = 0; i < ncompute; i++) {
if (nmine < 0) nmine = compute[i]->size_local_rows;
else if (nmine != compute[i]->size_local_rows)
- error->one(FLERR,"Dump local count is not consistent across input fields");
+ error->one(FLERR,
+ "Dump local count is not consistent across input fields");
}
for (int i = 0; i < nfix; i++) {
if (nmine < 0) nmine = fix[i]->size_local_rows;
else if (nmine != fix[i]->size_local_rows)
- error->one(FLERR,"Dump local count is not consistent across input fields");
+ error->one(FLERR,
+ "Dump local count is not consistent across input fields");
}
return nmine;
diff --git a/src/math_extra.h b/src/math_extra.h
index 515e55f5f8b297fde581ea3b3be21d223ea77231..d1691f395b03147f1912b8b24730a7950f89ec75 100755
--- a/src/math_extra.h
+++ b/src/math_extra.h
@@ -55,7 +55,7 @@ namespace MathExtra {
const double mat2[3][3],
double ans[3][3]);
inline void invert3(const double mat[3][3], double ans[3][3]);
- inline void matvec(const double mat[3][3], const double*vec, double *ans);
+ inline void matvec(const double mat[3][3], const double *vec, double *ans);
inline void matvec(const double *ex, const double *ey, const double *ez,
const double *vec, double *ans);
inline void transpose_matvec(const double mat[3][3], const double*vec,
diff --git a/src/read_data.cpp b/src/read_data.cpp
index d14d5084ad11f5d7f04443fdc0a971ac1482ee4c..0065472021aabb172a61f1a2b6e4810edc0fbc2a 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -44,9 +44,10 @@ using namespace LAMMPS_NS;
#define LB_FACTOR 1.1
#define CHUNK 1024
#define DELTA 4 // must be 2 or larger
+#define MAXBODY 20 // max # of lines in one body, also in Atom class
// customize for new sections
-#define NSECTIONS 23 // change when add to header::section_keywords
+#define NSECTIONS 24 // change when add to header::section_keywords
/* ---------------------------------------------------------------------- */
@@ -68,6 +69,8 @@ ReadData::ReadData(LAMMPS *lmp) : Pointers(lmp)
avec_line = (AtomVecLine *) atom->style_match("line");
ntris = 0;
avec_tri = (AtomVecTri *) atom->style_match("tri");
+ nbodies = 0;
+ avec_body = (AtomVecBody *) atom->style_match("body");
}
/* ---------------------------------------------------------------------- */
@@ -219,6 +222,11 @@ void ReadData::command(int narg, char **arg)
error->all(FLERR,"Invalid data file section: Triangles");
if (atomflag == 0) error->all(FLERR,"Must read Atoms before Triangles");
bonus(ntris,(AtomVec *) avec_tri,"triangles");
+ } else if (strcmp(keyword,"Bodies") == 0) {
+ if (!avec_body)
+ error->all(FLERR,"Invalid data file section: Bodies");
+ if (atomflag == 0) error->all(FLERR,"Must read Atoms before Bodies");
+ bodies();
} else if (strcmp(keyword,"Bonds") == 0) {
if (atom->avec->bonds_allow == 0)
@@ -377,7 +385,7 @@ void ReadData::header(int flag)
// customize for new sections
const char *section_keywords[NSECTIONS] =
- {"Atoms","Velocities","Ellipsoids","Lines","Triangles",
+ {"Atoms","Velocities","Ellipsoids","Lines","Triangles","Bodies",
"Bonds","Angles","Dihedrals","Impropers",
"Masses","Pair Coeffs","Bond Coeffs","Angle Coeffs",
"Dihedral Coeffs","Improper Coeffs",
@@ -452,6 +460,10 @@ void ReadData::header(int flag)
if (!avec_tri && me == 0)
error->one(FLERR,"No triangles allowed with this atom style");
sscanf(line,BIGINT_FORMAT,&ntris);
+ } else if (strstr(line,"bodies")) {
+ if (!avec_body && me == 0)
+ error->one(FLERR,"No bodies allowed with this atom style");
+ sscanf(line,BIGINT_FORMAT,&nbodies);
}
else if (strstr(line,"bonds")) sscanf(line,BIGINT_FORMAT,&atom->nbonds);
@@ -718,6 +730,86 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
}
}
+/* ----------------------------------------------------------------------
+ read all body data
+ variable amount of info per body, described by ninteger and ndouble
+ to find atoms, must build atom map if not a molecular system
+------------------------------------------------------------------------- */
+
+void ReadData::bodies()
+{
+ int i,m,nchunk,nmax,ninteger,ndouble,tmp,onebody;
+ char *eof;
+
+ int mapflag = 0;
+ if (atom->map_style == 0) {
+ mapflag = 1;
+ atom->map_style = 1;
+ atom->map_init();
+ atom->map_set();
+ }
+
+ // nmax = max # of bodies to read in this chunk
+ // nchunk = actual # readr
+
+ bigint nread = 0;
+ bigint natoms = nbodies;
+
+ while (nread < natoms) {
+ if (natoms-nread > CHUNK) nmax = CHUNK;
+ else nmax = natoms-nread;
+
+ if (me == 0) {
+ nchunk = 0;
+ nlines = 0;
+ m = 0;
+
+ while (nchunk < nmax && nlines <= CHUNK-MAXBODY) {
+ eof = fgets(&buffer[m],MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ sscanf(&buffer[m],"%d %d %d",&tmp,&ninteger,&ndouble);
+ m += strlen(&buffer[m]);
+
+ onebody = 0;
+ if (ninteger) onebody += (ninteger-1)/10 + 1;
+ if (ndouble) onebody += (ndouble-1)/10 + 1;
+ if (onebody+1 > MAXBODY)
+ error->one(FLERR,
+ "Too many lines in one body in data file - boost MAXBODY");
+
+ for (i = 0; i < onebody; i++) {
+ eof = fgets(&buffer[m],MAXLINE,fp);
+ if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
+ m += strlen(&buffer[m]);
+ }
+
+ nchunk++;
+ nlines += onebody+1;
+ }
+
+ if (buffer[m-1] != '\n') strcpy(&buffer[m++],"\n");
+ m++;
+ }
+
+ MPI_Bcast(&nchunk,1,MPI_INT,0,world);
+ MPI_Bcast(&m,1,MPI_INT,0,world);
+ MPI_Bcast(buffer,m,MPI_CHAR,0,world);
+
+ atom->data_bodies(nchunk,buffer,avec_body);
+ nread += nchunk;
+ }
+
+ if (mapflag) {
+ atom->map_delete();
+ atom->map_style = 0;
+ }
+
+ if (me == 0) {
+ if (screen) fprintf(screen," " BIGINT_FORMAT " bodies\n",natoms);
+ if (logfile) fprintf(logfile," " BIGINT_FORMAT " bodies\n",natoms);
+ }
+}
+
/* ---------------------------------------------------------------------- */
void ReadData::bonds()
@@ -1157,6 +1249,7 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
int ellipsoid_flag = 0;
int line_flag = 0;
int tri_flag = 0;
+ int body_flag = 0;
// customize for new sections
// allocate topology counting vector
@@ -1203,6 +1296,10 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
if (!avec_tri) error->one(FLERR,"Invalid data file section: Triangles");
tri_flag = 1;
skip_lines(ntris);
+ } else if (strcmp(keyword,"Bodies") == 0) {
+ if (!avec_body) error->one(FLERR,"Invalid data file section: Bodies");
+ body_flag = 1;
+ skip_lines(nbodies);
} else if (strcmp(keyword,"Pair Coeffs") == 0) {
if (force->pair == NULL)
@@ -1434,6 +1531,8 @@ void ReadData::scan(int &bond_per_atom, int &angle_per_atom,
error->one(FLERR,"Needed bonus data not in data file");
if (ntris && !tri_flag)
error->one(FLERR,"Needed bonus data not in data file");
+ if (nbodies && !body_flag)
+ error->one(FLERR,"Needed bonus data not in data file");
}
/* ----------------------------------------------------------------------
diff --git a/src/read_data.h b/src/read_data.h
index df28fa2448905bfb18084a383ac82e53bcb2789b..07bc716d4598e50c2cb5d5b094afeb4965dc445d 100644
--- a/src/read_data.h
+++ b/src/read_data.h
@@ -49,6 +49,8 @@ class ReadData : protected Pointers {
class AtomVecLine *avec_line;
bigint ntris;
class AtomVecTri *avec_tri;
+ bigint nbodies;
+ class AtomVecBody *avec_body;
void open(char *);
void scan(int &, int &, int &, int &);
@@ -61,6 +63,7 @@ class ReadData : protected Pointers {
void atoms();
void velocities();
void bonus(bigint, class AtomVec *, const char *);
+ void bodies();
void bonds();
void angles();
diff --git a/src/read_restart.cpp b/src/read_restart.cpp
index 3afd4c42e21de2ba830e120b65e1c4b67af6ca99..072a13c878140ff13af6ace991c9d236af9a991f 100644
--- a/src/read_restart.cpp
+++ b/src/read_restart.cpp
@@ -627,6 +627,8 @@ void ReadRestart::header()
}
atom->create_avec(style,nwords,words);
+ atom->avec->read_restart_settings(fp);
+
for (int i = 0; i < nwords; i++) delete [] words[i];
delete [] words;
delete [] style;
diff --git a/src/write_restart.cpp b/src/write_restart.cpp
index 8305413f8904b17ced92cc9304b8da74167ffe9b..77f2bed05ff8958a67f749b7e59218002db919ac 100644
--- a/src/write_restart.cpp
+++ b/src/write_restart.cpp
@@ -326,6 +326,7 @@ void WriteRestart::header()
// atom_style must be written before atom class values
// so read_restart can create class before reading class values
// if style = hybrid, also write sub-class styles
+ // avec->write_restart() writes atom_style specific info
write_char(ATOM_STYLE,atom->atom_style);
@@ -341,6 +342,8 @@ void WriteRestart::header()
}
}
+ if (me == 0) atom->avec->write_restart_settings(fp);
+
write_bigint(NATOMS,natoms);
write_int(NTYPES,atom->ntypes);
write_bigint(NBONDS,atom->nbonds);