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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@254 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2007-01-30 00:22:05 +00:00
parent 9cdbeaf9f2
commit 209f169cbc
414 changed files with 6935 additions and 10462 deletions
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6
src/CLASS2/Install.csh
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@ -1,7 +1,5 @@
# Install/unInstall package classes in LAMMPS
# pair_lj_class2_coul_long.h must always be in src
if ($1 == 1) then
cp style_class2.h ..
@ -22,7 +20,7 @@ if ($1 == 1) then
cp pair_lj_class2.h ..
cp pair_lj_class2_coul_cut.h ..
# cp pair_lj_class2_coul_long.h ..
cp pair_lj_class2_coul_long.h ..
else if ($1 == 0) then
@ -45,6 +43,6 @@ else if ($1 == 0) then
rm ../pair_lj_class2.h
rm ../pair_lj_class2_coul_cut.h
# rm ../pair_lj_class2_coul_long.h
rm ../pair_lj_class2_coul_long.h
endif

14
src/CLASS2/angle_class2.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -26,11 +26,15 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define SMALL 0.001
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
AngleClass2::AngleClass2(LAMMPS *lmp) : Angle(lmp) {}
/* ---------------------------------------------------------------------- */
AngleClass2::~AngleClass2()
{

10
src/CLASS2/angle_class2.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -17,9 +17,11 @@
#include "stdio.h"
#include "angle.h"
namespace LAMMPS_NS {
class AngleClass2 : public Angle {
public:
AngleClass2() {}
AngleClass2(class LAMMPS *);
~AngleClass2();
void compute(int, int);
void coeff(int, int, char **);
@ -36,4 +38,6 @@ class AngleClass2 : public Angle {
void allocate();
};
}
#endif

14
src/CLASS2/bond_class2.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -26,9 +26,13 @@
#include "memory.h"
#include "error.h"
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondClass2::BondClass2(LAMMPS *lmp) : Bond(lmp) {}
/* ---------------------------------------------------------------------- */
BondClass2::~BondClass2()
{

10
src/CLASS2/bond_class2.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -17,9 +17,11 @@
#include "stdio.h"
#include "bond.h"
namespace LAMMPS_NS {
class BondClass2 : public Bond {
public:
BondClass2() {}
BondClass2(class LAMMPS *);
~BondClass2();
void compute(int, int);
void coeff(int, char **);
@ -34,4 +36,6 @@ class BondClass2 : public Bond {
void allocate();
};
}
#endif

16
src/CLASS2/dihedral_class2.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -27,24 +27,22 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define TOLERANCE 0.05
#define SMALL 0.0000001
/* ----------------------------------------------------------------------
set all global defaults
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
DihedralClass2::DihedralClass2()
DihedralClass2::DihedralClass2(LAMMPS *lmp) : Dihedral(lmp)
{
PI = 4.0*atan(1.0);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
DihedralClass2::~DihedralClass2()
{

10
src/CLASS2/dihedral_class2.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -17,9 +17,11 @@
#include "stdio.h"
#include "dihedral.h"
namespace LAMMPS_NS {
class DihedralClass2 : public Dihedral {
public:
DihedralClass2();
DihedralClass2(class LAMMPS *);
~DihedralClass2();
void compute(int, int);
void coeff(int, int, char **);
@ -43,4 +45,6 @@ class DihedralClass2 : public Dihedral {
void allocate();
};
}
#endif

16
src/CLASS2/improper_class2.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -27,20 +27,18 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define SMALL 0.001
/* ----------------------------------------------------------------------
set all global defaults
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
ImproperClass2::ImproperClass2()
ImproperClass2::ImproperClass2(LAMMPS *lmp) : Improper(lmp)
{
PI = 4.0*atan(1.0);
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
ImproperClass2::~ImproperClass2()
{

10
src/CLASS2/improper_class2.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -17,9 +17,11 @@
#include "stdio.h"
#include "improper.h"
namespace LAMMPS_NS {
class ImproperClass2 : public Improper {
public:
ImproperClass2();
ImproperClass2(class LAMMPS *);
~ImproperClass2();
void compute(int, int);
void coeff(int, int, char **);
@ -38,4 +40,6 @@ class ImproperClass2 : public Improper {
double dot(double *, double *);
};
}
#endif

14
src/CLASS2/pair_lj_class2.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -23,12 +23,16 @@
#include "neighbor.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
PairLJClass2::PairLJClass2(LAMMPS *lmp) : Pair(lmp) {}
/* ---------------------------------------------------------------------- */
PairLJClass2::~PairLJClass2()
{

10
src/CLASS2/pair_lj_class2.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,9 +16,11 @@
#include "pair.h"
namespace LAMMPS_NS {
class PairLJClass2 : public Pair {
public:
PairLJClass2() {}
PairLJClass2(class LAMMPS *);
~PairLJClass2();
void compute(int, int);
void settings(int, char **);
@ -39,4 +41,6 @@ class PairLJClass2 : public Pair {
void allocate();
};
}
#endif

16
src/CLASS2/pair_lj_class2_coul_cut.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -23,12 +23,16 @@
#include "neighbor.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
PairLJClass2CoulCut::PairLJClass2CoulCut(LAMMPS *lmp) : Pair(lmp) {}
/* ---------------------------------------------------------------------- */
PairLJClass2CoulCut::~PairLJClass2CoulCut()
{
@ -333,7 +337,7 @@ void PairLJClass2CoulCut::init_style()
{
// require an atom style with charge defined
if (atom->charge_allow == 0)
if (atom->q == NULL)
error->all("Must use charged atom style with this pair style");
}

10
src/CLASS2/pair_lj_class2_coul_cut.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,9 +16,11 @@
#include "pair.h"
namespace LAMMPS_NS {
class PairLJClass2CoulCut : public Pair {
public:
PairLJClass2CoulCut() {}
PairLJClass2CoulCut(class LAMMPS *);
~PairLJClass2CoulCut();
void compute(int, int);
void settings(int, char **);
@ -41,4 +43,6 @@ class PairLJClass2CoulCut : public Pair {
void allocate();
};
}
#endif

23
src/CLASS2/pair_lj_class2_coul_long.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -25,6 +25,8 @@
#include "neighbor.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
@ -36,9 +38,11 @@
#define A4 -1.453152027
#define A5 1.061405429
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
PairLJClass2CoulLong::PairLJClass2CoulLong(LAMMPS *lmp) : Pair(lmp) {}
/* ---------------------------------------------------------------------- */
PairLJClass2CoulLong::~PairLJClass2CoulLong()
{
@ -339,7 +343,7 @@ void PairLJClass2CoulLong::init_style()
{
// require an atom style with charge defined
if (atom->charge_allow == 0)
if (atom->q == NULL)
error->all("Must use charged atom style with this pair style");
cut_coulsq = cut_coul * cut_coul;
@ -474,3 +478,10 @@ void PairLJClass2CoulLong::single(int i, int j, int itype, int jtype,
} else one.eng_vdwl = 0.0;
}
}
/* ---------------------------------------------------------------------- */
void PairLJClass2CoulLong::extract_long(double *p_cut_coul)
{
*p_cut_coul = cut_coul;
}

4
src/CLASS2/style_class2.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

8
src/DPD/Install.csh
View File

@ -4,10 +4,10 @@ if ($1 == 1) then
cp style_dpd.h ..
cp atom_dpd.cpp ..
cp atom_vec_dpd.cpp ..
cp pair_dpd.cpp ..
cp atom_dpd.h ..
cp atom_vec_dpd.h ..
cp pair_dpd.h ..
else if ($1 == 0) then
@ -15,10 +15,10 @@ else if ($1 == 0) then
rm ../style_dpd.h
touch ../style_dpd.h
rm ../atom_dpd.cpp
rm ../atom_vec_dpd.cpp
rm ../pair_dpd.cpp
rm ../atom_dpd.h
rm ../atom_vec_dpd.h
rm ../pair_dpd.h
endif

236
src/DPD/atom_dpd.cpp
View File

@ -1,236 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "atom_dpd.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
/* ---------------------------------------------------------------------- */
AtomDPD::AtomDPD(int narg, char **arg) : Atom(narg, arg) {}
/* ---------------------------------------------------------------------- */
void AtomDPD::copy(int i, int j)
{
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
if (nextra_grow)
for (int iextra = 0; iextra < nextra_grow; iextra++)
modify->fix[extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
void AtomDPD::pack_comm(int n, int *list, double *buf, int *pbc_flags)
{
int i,j,m;
m = 0;
if (pbc_flags[0] == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + pbc_flags[1]*xprd;
buf[m++] = x[j][1] + pbc_flags[2]*yprd;
buf[m++] = x[j][2] + pbc_flags[3]*zprd;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
}
/* ---------------------------------------------------------------------- */
void AtomDPD::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
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++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomDPD::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
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];
}
}
/* ---------------------------------------------------------------------- */
void AtomDPD::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomDPD::pack_border(int n, int *list, double *buf, int *pbc_flags)
{
int i,j,m;
m = 0;
if (pbc_flags[0] == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
} else {
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + pbc_flags[1]*xprd;
buf[m++] = x[j][1] + pbc_flags[2]*yprd;
buf[m++] = x[j][2] + pbc_flags[3]*zprd;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
}
}
}
/* ---------------------------------------------------------------------- */
void AtomDPD::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
}
}
/* ----------------------------------------------------------------------
pack all atom quantities for shipping to another proc
xyz must be 1st 3 values, so that comm::exchange can test on them
------------------------------------------------------------------------- */
int AtomDPD::pack_exchange(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
if (nextra_grow)
for (int iextra = 0; iextra < nextra_grow; iextra++)
m += modify->fix[extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomDPD::unpack_exchange(double *buf)
{
if (nlocal == nmax) grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
if (nextra_grow)
for (int iextra = 0; iextra < nextra_grow; iextra++)
m += modify->fix[extra_grow[iextra]]->unpack_exchange(nlocal,&buf[m]);
nlocal++;
return m;
}

34
src/DPD/atom_dpd.h
View File

@ -1,34 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef ATOM_DPD_H
#define ATOM_DPD_H
#include "atom.h"
class AtomDPD : public Atom {
public:
AtomDPD(int, char **);
~AtomDPD() {}
void copy(int, int);
void pack_comm(int, int *, double *, int *);
void unpack_comm(int, int, double *);
void pack_reverse(int, int, double *);
void unpack_reverse(int, int *, double *);
void pack_border(int, int *, double *, int *);
void unpack_border(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
};
#endif

28
src/DPD/pair_dpd.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -28,6 +28,8 @@
#include "neighbor.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
@ -35,14 +37,12 @@
/* ---------------------------------------------------------------------- */
PairDPD::PairDPD()
PairDPD::PairDPD(LAMMPS *lmp) : Pair(lmp)
{
random = NULL;
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
PairDPD::~PairDPD()
{
@ -208,7 +208,7 @@ void PairDPD::settings(int narg, char **arg)
if (seed <= 0 || seed > 900000000)
error->all("Illegal fix pair_style command");
if (random) delete random;
random = new RanMars(seed + comm->me);
random = new RanMars(lmp,seed + comm->me);
// reset cutoffs that have been explicitly set
@ -372,7 +372,7 @@ void PairDPD::read_restart_settings(FILE *fp)
// same seed that pair_style command initially specified
if (random) delete random;
random = new RanMars(seed + comm->me);
random = new RanMars(lmp,seed + comm->me);
}
/* ---------------------------------------------------------------------- */
@ -381,15 +381,7 @@ void PairDPD::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_dpd, int eflag,
One &one)
{
double r,rinv,dot,wd,randnum,phi;
double delx = atom->x[i][0] - atom->x[j][0];
double dely = atom->x[i][1] - atom->x[j][1];
double delz = atom->x[i][2] - atom->x[j][2];
double delvx = atom->v[i][0] - atom->v[j][0];
double delvy = atom->v[i][1] - atom->v[j][1];
double delvz = atom->v[i][2] - atom->v[j][2];
double dtinvsqrt = 1.0/sqrt(update->dt);
double r,rinv,wd,phi;
r = sqrt(rsq);
if (r < EPSILON) {
@ -399,9 +391,7 @@ void PairDPD::single(int i, int j, int itype, int jtype, double rsq,
}
rinv = 1.0/r;
dot = delx*delvx + dely*delvy + delz*delvz;
wd = 1.0 - r/cut[itype][jtype];
randnum = random->gaussian();
one.fforce = a0[itype][jtype]*wd * factor_dpd*rinv;

12
src/DPD/pair_dpd.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,11 +16,11 @@
#include "pair.h"
class RanMars;
namespace LAMMPS_NS {
class PairDPD : public Pair {
public:
PairDPD();
PairDPD(class LAMMPS *);
~PairDPD();
void compute(int, int);
void settings(int, char **);
@ -39,9 +39,11 @@ class PairDPD : public Pair {
double **cut;
double **a0,**gamma;
double **sigma;
RanMars *random;
class RanMars *random;
void allocate();
};
}
#endif

8
src/DPD/style_dpd.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -12,11 +12,11 @@
------------------------------------------------------------------------- */
#ifdef AtomInclude
#include "atom_dpd.h"
#include "atom_vec_dpd.h"
#endif
#ifdef AtomClass
AtomStyle(dpd,AtomDPD)
AtomStyle(dpd,AtomVecDPD)
#endif
#ifdef PairInclude

14
src/GRANULAR/Install.csh
View File

@ -1,28 +1,24 @@
# Install/unInstall package classes in LAMMPS
# fix_shear_history.h must always be in src
if ($1 == 1) then
cp style_granular.h ..
cp atom_granular.cpp ..
cp atom_vec_granular.cpp ..
cp fix_freeze.cpp ..
cp fix_gran_diag.cpp ..
cp fix_nve_gran.cpp ..
cp fix_pour.cpp ..
cp fix_shear_history.cpp ..
cp fix_wall_gran.cpp ..
cp pair_gran_hertzian.cpp ..
cp pair_gran_history.cpp ..
cp pair_gran_no_history.cpp ..
cp atom_granular.h ..
cp atom_vec_granular.h ..
cp fix_freeze.h ..
cp fix_gran_diag.h ..
cp fix_nve_gran.h ..
cp fix_pour.h ..
# cp fix_shear_history.h ..
cp fix_wall_gran.h ..
cp pair_gran_hertzian.h ..
cp pair_gran_history.h ..
@ -33,23 +29,21 @@ else if ($1 == 0) then
rm ../style_granular.h
touch ../style_granular.h
rm ../atom_granular.cpp
rm ../atom_vec_granular.cpp
rm ../fix_freeze.cpp
rm ../fix_gran_diag.cpp
rm ../fix_nve_gran.cpp
rm ../fix_pour.cpp
rm ../fix_shear_history.cpp
rm ../fix_wall_gran.cpp
rm ../pair_gran_hertzian.cpp
rm ../pair_gran_history.cpp
rm ../pair_gran_no_history.cpp
rm ../atom_granular.h
rm ../atom_vec_granular.h
rm ../fix_freeze.h
rm ../fix_gran_diag.h
rm ../fix_nve_gran.h
rm ../fix_pour.h
# rm ../fix_shear_history.h
rm ../fix_wall_gran.h
rm ../pair_gran_hertzian.h
rm ../pair_gran_history.h

322
src/GRANULAR/atom_granular.cpp
View File

@ -1,322 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "string.h"
#include "atom_granular.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
/* ---------------------------------------------------------------------- */
AtomGranular::AtomGranular(int narg, char **arg) : Atom(narg, arg) {}
/* ---------------------------------------------------------------------- */
void AtomGranular::copy(int i, int j)
{
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
phix[j][0] = phix[i][0];
phix[j][1] = phix[i][1];
phix[j][2] = phix[i][2];
phiv[j][0] = phiv[i][0];
phiv[j][1] = phiv[i][1];
phiv[j][2] = phiv[i][2];
radius[j] = radius[i];
density[j] = density[i];
rmass[j] = rmass[i];
if (nextra_grow)
for (int iextra = 0; iextra < nextra_grow; iextra++)
modify->fix[extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
void AtomGranular::pack_comm(int n, int *list, double *buf, int *pbc_flags)
{
int i,j,m;
m = 0;
if (pbc_flags[0] == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = phiv[j][0];
buf[m++] = phiv[j][1];
buf[m++] = phiv[j][2];
}
} else {
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + pbc_flags[1]*xprd;
buf[m++] = x[j][1] + pbc_flags[2]*yprd;
buf[m++] = x[j][2] + pbc_flags[3]*zprd;
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = phiv[j][0];
buf[m++] = phiv[j][1];
buf[m++] = phiv[j][2];
}
}
}
/* ---------------------------------------------------------------------- */
void AtomGranular::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
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++];
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
phiv[i][0] = buf[m++];
phiv[i][1] = buf[m++];
phiv[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomGranular::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
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];
buf[m++] = phia[i][0];
buf[m++] = phia[i][1];
buf[m++] = phia[i][2];
}
}
/* ---------------------------------------------------------------------- */
void AtomGranular::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
phia[j][0] += buf[m++];
phia[j][1] += buf[m++];
phia[j][2] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
void AtomGranular::pack_border(int n, int *list, double *buf, int *pbc_flags)
{
int i,j,m;
m = 0;
if (pbc_flags[0] == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = phiv[j][0];
buf[m++] = phiv[j][1];
buf[m++] = phiv[j][2];
buf[m++] = radius[j];
buf[m++] = rmass[j];
}
} else {
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + pbc_flags[1]*xprd;
buf[m++] = x[j][1] + pbc_flags[2]*yprd;
buf[m++] = x[j][2] + pbc_flags[3]*zprd;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = phiv[j][0];
buf[m++] = phiv[j][1];
buf[m++] = phiv[j][2];
buf[m++] = radius[j];
buf[m++] = rmass[j];
}
}
}
/* ---------------------------------------------------------------------- */
void AtomGranular::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
phiv[i][0] = buf[m++];
phiv[i][1] = buf[m++];
phiv[i][2] = buf[m++];
radius[i] = buf[m++];
rmass[i] = buf[m++];
}
}
/* ----------------------------------------------------------------------
pack all atom quantities for shipping to another proc
xyz must be 1st 3 values, so that comm::exchange can test on them
------------------------------------------------------------------------- */
int AtomGranular::pack_exchange(int i, double *buf)
{
int m = 1;
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
buf[m++] = v[i][0];
buf[m++] = v[i][1];
buf[m++] = v[i][2];
buf[m++] = phix[i][0];
buf[m++] = phix[i][1];
buf[m++] = phix[i][2];
buf[m++] = phiv[i][0];
buf[m++] = phiv[i][1];
buf[m++] = phiv[i][2];
buf[m++] = radius[i];
buf[m++] = density[i];
buf[m++] = rmass[i];
buf[m++] = tag[i];
buf[m++] = type[i];
buf[m++] = mask[i];
buf[m++] = image[i];
if (nextra_grow)
for (int iextra = 0; iextra < nextra_grow; iextra++)
m += modify->fix[extra_grow[iextra]]->pack_exchange(i,&buf[m]);
buf[0] = m;
return m;
}
/* ---------------------------------------------------------------------- */
int AtomGranular::unpack_exchange(double *buf)
{
if (nlocal == nmax) grow(0);
int m = 1;
x[nlocal][0] = buf[m++];
x[nlocal][1] = buf[m++];
x[nlocal][2] = buf[m++];
v[nlocal][0] = buf[m++];
v[nlocal][1] = buf[m++];
v[nlocal][2] = buf[m++];
phix[nlocal][0] = buf[m++];
phix[nlocal][1] = buf[m++];
phix[nlocal][2] = buf[m++];
phiv[nlocal][0] = buf[m++];
phiv[nlocal][1] = buf[m++];
phiv[nlocal][2] = buf[m++];
radius[nlocal] = buf[m++];
density[nlocal] = buf[m++];
rmass[nlocal] = buf[m++];
tag[nlocal] = static_cast<int> (buf[m++]);
type[nlocal] = static_cast<int> (buf[m++]);
mask[nlocal] = static_cast<int> (buf[m++]);
image[nlocal] = static_cast<int> (buf[m++]);
if (nextra_grow)
for (int iextra = 0; iextra < nextra_grow; iextra++)
m += modify->fix[extra_grow[iextra]]->unpack_exchange(nlocal,&buf[m]);
nlocal++;
return m;
}
/* ----------------------------------------------------------------------
unpack vels & phis specific to granular data file
------------------------------------------------------------------------- */
void AtomGranular::unpack_vels(int n, char *buf)
{
int m,tagtmp;
double vxtmp,vytmp,vztmp,phivxtmp,phivytmp,phivztmp;
char *next;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
sscanf(buf,"%d %lg %lg %lg %lg %lg %lg",
&tagtmp,&vxtmp,&vytmp,&vztmp,
&phivxtmp,&phivytmp,&phivztmp);
if ((m = map(tagtmp)) >= 0) {
v[m][0] = vxtmp;
v[m][1] = vytmp;
v[m][2] = vztmp;
phiv[m][0] = phivxtmp;
phiv[m][1] = phivytmp;
phiv[m][2] = phivztmp;
}
buf = next + 1;
}
}

36
src/GRANULAR/atom_granular.h
View File

@ -1,36 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef ATOM_GRANULAR_H
#define ATOM_GRANULAR_H
#include "atom.h"
class AtomGranular : public Atom {
public:
AtomGranular(int, char **);
~AtomGranular() {}
void copy(int, int);
void pack_comm(int, int *, double *, int *);
void unpack_comm(int, int, double *);
void pack_reverse(int, int, double *);
void unpack_reverse(int, int *, double *);
void pack_border(int, int *, double *, int *);
void unpack_border(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
void unpack_vels(int, char *);
};
#endif

9
src/GRANULAR/fix_freeze.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -18,9 +18,12 @@
#include "comm.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixFreeze::FixFreeze(int narg, char **arg) : Fix(narg, arg)
FixFreeze::FixFreeze(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 3) error->all("Illegal fix freeze command");

11
src/GRANULAR/fix_freeze.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,14 +16,17 @@
#include "fix.h"
namespace LAMMPS_NS {
class FixFreeze : public Fix {
public:
FixFreeze(int, char **);
~FixFreeze() {}
FixFreeze(class LAMMPS *, int, char **);
int setmask();
void init();
void setup();
void post_force(int);
};
}
#endif

76
src/GRANULAR/fix_gran_diag.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -17,28 +17,29 @@
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "fix_gran_diag.h"
#include "update.h"
#include "force.h"
#include "pair_gran_no_history.h"
#include "pair_gran_history.h"
#include "pair_gran_hertzian.h"
#include "pair.h"
#include "atom.h"
#include "neighbor.h"
#include "modify.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
#define NO_HISTORY 1
#define HISTORY 2
#define HERTZIAN 3
enum{NO_HISTORY,HISTORY,HERTZIAN};
/* ---------------------------------------------------------------------- */
FixGranDiag::FixGranDiag(int narg, char **arg) : Fix(narg, arg)
FixGranDiag::FixGranDiag(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 6) error->all("Illegal fix gran/diag command");
nevery = atoi(arg[3]);
@ -112,37 +113,38 @@ int FixGranDiag::setmask()
void FixGranDiag::init()
{
// insure use of granular pair_style
// set local values from Pair values
Pair *pair = force->pair_match("gran");
if (pair == NULL)
error->all("Fix gran/diag is incompatible with Pair style");
int dampflag;
double gamman;
pair->extract_gran(&xkk,&gamman,&xmu,&dampflag);
// same initialization as in pair_gran_history::init_style()
xkkt = xkk * 2.0/7.0;
dt = update->dt;
double gammas = 0.5*gamman;
if (dampflag == 0) gammas = 0.0;
gamman_dl = gamman/dt;
gammas_dl = gammas/dt;
// set constants from pair style
// set pairstyle from granular pair style
Pair *anypair;
if (anypair = force->pair_match("gran/no_history")) {
pairstyle = NO_HISTORY;
xkk = ((PairGranNoHistory *) anypair)->xkk;
xkkt = ((PairGranNoHistory *) anypair)->xkkt;
xmu = ((PairGranNoHistory *) anypair)->xmu;
gamman_dl = ((PairGranNoHistory *) anypair)->gamman_dl;
gammas_dl = ((PairGranNoHistory *) anypair)->gammas_dl;
freeze_group_bit = ((PairGranNoHistory *) anypair)->freeze_group_bit;
} else if (anypair = force->pair_match("gran/history")) {
pairstyle = HISTORY;
xkk = ((PairGranHistory *) anypair)->xkk;
xkkt = ((PairGranHistory *) anypair)->xkkt;
xmu = ((PairGranHistory *) anypair)->xmu;
gamman_dl = ((PairGranHistory *) anypair)->gamman_dl;
gammas_dl = ((PairGranHistory *) anypair)->gammas_dl;
freeze_group_bit = ((PairGranNoHistory *) anypair)->freeze_group_bit;
} else if (anypair = force->pair_match("gran/hertzian")) {
pairstyle = HERTZIAN;
xkk = ((PairGranHertzian *) anypair)->xkk;
xkkt = ((PairGranHertzian *) anypair)->xkkt;
xmu = ((PairGranHertzian *) anypair)->xmu;
gamman_dl = ((PairGranHertzian *) anypair)->gamman_dl;
gammas_dl = ((PairGranHertzian *) anypair)->gammas_dl;
freeze_group_bit = ((PairGranNoHistory *) anypair)->freeze_group_bit;
} else
error->all("Must use fix gran/diag with granular pair style");
if (force->pair_match("gran/no_history")) pairstyle = NO_HISTORY;
else if (force->pair_match("gran/history")) pairstyle = HISTORY;
else if (force->pair_match("gran/hertzian")) pairstyle = HERTZIAN;
// check for freeze Fix and set freeze_group_bit
int i;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"freeze") == 0) break;
if (i < modify->nfix) freeze_group_bit = modify->fix[i]->groupbit;
else freeze_group_bit = 0;
}
/* ---------------------------------------------------------------------- */

10
src/GRANULAR/fix_gran_diag.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -17,9 +17,11 @@
#include "stdio.h"
#include "fix.h"
namespace LAMMPS_NS {
class FixGranDiag : public Fix {
public:
FixGranDiag(int, char **);
FixGranDiag(class LAMMPS *, int, char **);
~FixGranDiag();
int setmask();
void init();
@ -50,4 +52,6 @@ class FixGranDiag : public Fix {
void stress_hertzian();
};
}
#endif

9
src/GRANULAR/fix_nve_gran.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -19,6 +19,8 @@
#include "force.h"
#include "error.h"
using namespace LAMMPS_NS;
// moments of inertia for sphere and disk
#define INERTIA3D 0.4
@ -26,7 +28,8 @@
/* ---------------------------------------------------------------------- */
FixNVEGran::FixNVEGran(int narg, char **arg) : Fix(narg, arg)
FixNVEGran::FixNVEGran(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 3) error->all("Illegal fix nve/gran command");

11
src/GRANULAR/fix_nve_gran.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,10 +16,11 @@
#include "fix.h"
namespace LAMMPS_NS {
class FixNVEGran : public Fix {
public:
FixNVEGran(int, char **);
~FixNVEGran() {}
FixNVEGran(class LAMMPS *, int, char **);
int setmask();
void init();
void initial_integrate();
@ -29,4 +30,6 @@ class FixNVEGran : public Fix {
double dtv,dtf,dtfphi;
};
}
#endif

25
src/GRANULAR/fix_pour.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,6 +16,7 @@
#include "string.h"
#include "fix_pour.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "update.h"
#include "comm.h"
@ -30,11 +31,14 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define EPSILON 0.001
/* ---------------------------------------------------------------------- */
FixPour::FixPour(int narg, char **arg) : Fix(narg, arg)
FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 6) error->all("Illegal fix pour command");
@ -151,7 +155,7 @@ FixPour::FixPour(int narg, char **arg) : Fix(narg, arg)
// random number generator, same for all procs
random = new RanPark(seed);
random = new RanPark(lmp,seed);
// allgather arrays
@ -269,10 +273,11 @@ void FixPour::init()
// check if a shear history fix exists
ifix_history = -1;
fix_history = NULL;
if (force->pair_match("gran/history") || force->pair_match("gran/hertzian"))
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"SHEAR_HISTORY") == 0) ifix_history = i;
if (strcmp(modify->fix[i]->style,"SHEAR_HISTORY") == 0)
fix_history = (FixShearHistory *) modify->fix[i];
}
/* ----------------------------------------------------------------------
@ -403,7 +408,7 @@ void FixPour::pre_exchange()
error->warning("Less insertions than requested");
// check if new atom is in my sub-box or above it if I'm highest proc
// if so, add to my list via create_one()
// if so, add to my list via create_atom()
// initialize info about the atom
// type, diameter, density set from fix parameters
// group mask set to "all" plus fix group
@ -412,6 +417,7 @@ void FixPour::pre_exchange()
// this gives continuous stream of atoms
// set npartner for new atom to 0 (assume not touching any others)
AtomVec *avec = atom->avec;
int m,flag;
double denstmp,vxtmp,vytmp,vztmp;
double g = 1.0;
@ -445,7 +451,7 @@ void FixPour::pre_exchange()
xtmp >= domain->subxlo && xtmp < domain->subxhi) flag = 1;
if (flag) {
atom->create_one(ntype,xtmp,ytmp,ztmp);
avec->create_atom(ntype,xtmp,ytmp,ztmp,0);
m = atom->nlocal - 1;
atom->type[m] = ntype;
atom->radius[m] = radtmp;
@ -458,8 +464,7 @@ void FixPour::pre_exchange()
atom->v[m][0] = vxtmp;
atom->v[m][1] = vytmp;
atom->v[m][2] = vztmp;
if (ifix_history >= 0)
((FixShearHistory *) modify->fix[ifix_history])->npartner[m] = 0;
if (fix_history) fix_history->npartner[m] = 0;
}
}

15
src/GRANULAR/fix_pour.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,7 +16,7 @@
#include "fix.h"
class RanPark;
namespace LAMMPS_NS {
class FixPour : public Fix {
friend class PairGranHistory;
@ -24,7 +24,7 @@ class FixPour : public Fix {
friend class PairGranNoHistory;
public:
FixPour(int, char **);
FixPour(class LAMMPS *, int, char **);
~FixPour();
int setmask();
void init();
@ -47,12 +47,13 @@ class FixPour : public Fix {
double PI;
int nfreq,nfirst,ninserted,nper;
double lo_current,hi_current;
int ifix_history;
RanPark *random;
class FixShearHistory *fix_history;
class RanPark *random;
int overlap(int);
void xyz_random(double, double &, double &, double &);
};
}
#endif

282
src/GRANULAR/fix_shear_history.cpp
View File

@ -1,282 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "string.h"
#include "stdio.h"
#include "fix_shear_history.h"
#include "atom.h"
#include "neighbor.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "memory.h"
#include "error.h"
#define MAXTOUCH 15
/* ---------------------------------------------------------------------- */
FixShearHistory::FixShearHistory(int narg, char **arg) : Fix(narg, arg)
{
restart_peratom = 1;
// perform initial allocation of atom-based arrays
// register with atom class
npartner = NULL;
partner = NULL;
shearpartner = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
atom->add_callback(1);
// initialize npartner to 0 so neighbor list creation is OK the 1st time
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) npartner[i] = 0;
}
/* ---------------------------------------------------------------------- */
FixShearHistory::~FixShearHistory()
{
// if atom class still exists:
// unregister this fix so atom class doesn't invoke it any more
if (atom) atom->delete_callback(id,0);
if (atom) atom->delete_callback(id,1);
// delete locally stored arrays
memory->sfree(npartner);
memory->destroy_2d_int_array(partner);
memory->destroy_3d_double_array(shearpartner);
}
/* ---------------------------------------------------------------------- */
int FixShearHistory::setmask()
{
int mask = 0;
mask |= PRE_EXCHANGE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixShearHistory::init()
{
if (atom->tag_enable == 0)
error->all("Pair style granular with history requires atoms have IDs");
}
/* ----------------------------------------------------------------------
copy shear partner info from neighbor lists to atom arrays
so can be exchanged with atoms
------------------------------------------------------------------------- */
void FixShearHistory::pre_exchange()
{
int i,j,k,m;
// zero npartners for all current atoms
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) npartner[i] = 0;
// copy shear info from neighbor list atoms to atom arrays
// nlocal = nlocal_neighbor = nlocal when neighbor list last built,
// which might be pre-insert on this step
int numneigh;
int *neighs,*touch;
double *firstshear,*shear;
int *tag = atom->tag;
nlocal = neighbor->nlocal_neighbor;
for (i = 0; i < nlocal; i++) {
neighs = neighbor->firstneigh[i];
touch = neighbor->firsttouch[i];
firstshear = neighbor->firstshear[i];
numneigh = neighbor->numneigh[i];
for (k = 0; k < numneigh; k++) {
if (touch[k]) {
shear = &firstshear[3*k];
j = neighs[k];
if (npartner[i] < MAXTOUCH) {
m = npartner[i];
partner[i][m] = tag[j];
shearpartner[i][m][0] = shear[0];
shearpartner[i][m][1] = shear[1];
shearpartner[i][m][2] = shear[2];
}
npartner[i]++;
if (j < nlocal) {
if (npartner[j] < MAXTOUCH) {
m = npartner[j];
partner[j][m] = tag[i];
shearpartner[j][m][0] = -shear[0];
shearpartner[j][m][1] = -shear[1];
shearpartner[j][m][2] = -shear[2];
}
npartner[j]++;
}
}
}
}
// test for too many touching neighbors
int flag = 0;
for (i = 0; i < nlocal; i++)
if (npartner[i] >= MAXTOUCH) flag = 1;
int flag_all;
MPI_Allreduce(&flag,&flag_all,1,MPI_INT,MPI_SUM,world);
if (flag_all) error->all("Too many touching neighbors - boost MAXTOUCH");
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
int FixShearHistory::memory_usage()
{
int nmax = atom->nmax;
int bytes = nmax * sizeof(int);
bytes += nmax*MAXTOUCH * sizeof(int);
bytes += nmax*MAXTOUCH*3 * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixShearHistory::grow_arrays(int nmax)
{
npartner = (int *) memory->srealloc(npartner,nmax*sizeof(int),
"shear_history:npartner");
partner = memory->grow_2d_int_array(partner,nmax,MAXTOUCH,
"shear_history:partner");
shearpartner =
memory->grow_3d_double_array(shearpartner,nmax,MAXTOUCH,3,
"shear_history:shearpartner");
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixShearHistory::copy_arrays(int i, int j)
{
npartner[j] = npartner[i];
for (int m = 0; m < npartner[j]; m++) {
partner[j][m] = partner[i][m];
shearpartner[j][m][0] = shearpartner[i][m][0];
shearpartner[j][m][1] = shearpartner[i][m][1];
shearpartner[j][m][2] = shearpartner[i][m][2];
}
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixShearHistory::pack_exchange(int i, double *buf)
{
int m = 0;
buf[m++] = npartner[i];
for (int n = 0; n < npartner[i]; n++) {
buf[m++] = partner[i][n];
buf[m++] = shearpartner[i][n][0];
buf[m++] = shearpartner[i][n][1];
buf[m++] = shearpartner[i][n][2];
}
return m;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixShearHistory::unpack_exchange(int nlocal, double *buf)
{
int m = 0;
npartner[nlocal] = static_cast<int> (buf[m++]);
for (int n = 0; n < npartner[nlocal]; n++) {
partner[nlocal][n] = static_cast<int> (buf[m++]);
shearpartner[nlocal][n][0] = buf[m++];
shearpartner[nlocal][n][1] = buf[m++];
shearpartner[nlocal][n][2] = buf[m++];
}
return m;
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixShearHistory::pack_restart(int i, double *buf)
{
int m = 0;
buf[m++] = 4*npartner[i] + 2;
buf[m++] = npartner[i];
for (int n = 0; n < npartner[i]; n++) {
buf[m++] = partner[i][n];
buf[m++] = shearpartner[i][n][0];
buf[m++] = shearpartner[i][n][1];
buf[m++] = shearpartner[i][n][2];
}
return m;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void FixShearHistory::unpack_restart(int nlocal, int nth)
{
double **extra = atom->extra;
// skip to Nth set of extra values
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++;
npartner[nlocal] = static_cast<int> (extra[nlocal][m++]);
for (int n = 0; n < npartner[nlocal]; n++) {
partner[nlocal][n] = static_cast<int> (extra[nlocal][m++]);
shearpartner[nlocal][n][0] = extra[nlocal][m++];
shearpartner[nlocal][n][1] = extra[nlocal][m++];
shearpartner[nlocal][n][2] = extra[nlocal][m++];
}
}
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixShearHistory::maxsize_restart()
{
return 4*MAXTOUCH + 2;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixShearHistory::size_restart(int nlocal)
{
return 4*npartner[nlocal] + 2;
}

71
src/GRANULAR/fix_wall_gran.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -22,21 +22,15 @@
#include "atom.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "modify.h"
#include "pair_gran_no_history.h"
#include "pair_gran_history.h"
#include "pair_gran_hertzian.h"
#include "memory.h"
#include "error.h"
#define XPLANE 1
#define YPLANE 2
#define ZPLANE 3
#define ZCYLINDER 4
using namespace LAMMPS_NS;
#define NO_HISTORY 1
#define HISTORY 2
#define HERTZIAN 3
enum{XPLANE,YPLANE,ZPLANE,ZCYLINDER};
enum{NO_HISTORY,HISTORY,HERTZIAN};
#define BIG 1.0e20
@ -45,7 +39,8 @@
/* ---------------------------------------------------------------------- */
FixWallGran::FixWallGran(int narg, char **arg) : Fix(narg, arg)
FixWallGran::FixWallGran(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 4) error->all("Illegal fix wall/gran command");
@ -125,7 +120,7 @@ FixWallGran::FixWallGran(int narg, char **arg) : Fix(narg, arg)
}
// perform initial allocation of atom-based arrays
// register with atom class
// register with Atom class
shear = NULL;
grow_arrays(atom->nmax);
@ -143,11 +138,10 @@ FixWallGran::FixWallGran(int narg, char **arg) : Fix(narg, arg)
FixWallGran::~FixWallGran()
{
// if atom class still exists:
// unregister this fix so atom class doesn't invoke it any more
// unregister callbacks to this fix from Atom class
if (atom) atom->delete_callback(id,0);
if (atom) atom->delete_callback(id,1);
atom->delete_callback(id,0);
atom->delete_callback(id,1);
// delete locally stored arrays
@ -167,32 +161,29 @@ int FixWallGran::setmask()
void FixWallGran::init()
{
// set constants that depend on pair style
// insure use of granular pair_style
// set local values from Pair values
Pair *anypair;
if (anypair = force->pair_match("gran/no_history")) {
historystyle = 0;
pairstyle = NO_HISTORY;
xkk = ((PairGranNoHistory *) anypair)->xkk;
xkkt = ((PairGranNoHistory *) anypair)->xkkt;
} else if (anypair = force->pair_match("gran/history")) {
historystyle = 1;
pairstyle = HISTORY;
xkk = ((PairGranHistory *) anypair)->xkk;
xkkt = ((PairGranHistory *) anypair)->xkkt;
} else if (anypair = force->pair_match("gran/hertzian")) {
historystyle = 1;
pairstyle = HERTZIAN;
xkk = ((PairGranHertzian *) anypair)->xkk;
xkkt = ((PairGranHertzian *) anypair)->xkkt;
} else
error->all("Fix wall/gran can only be used with granular pair style");
Pair *pair = force->pair_match("gran");
if (pair == NULL)
error->all("Fix wall/gran is incompatible with Pair style");
int itmp;
double tmp1,tmp2;
pair->extract_gran(&xkk,&tmp1,&tmp2,&itmp);
// friction coeffs
// same initialization as in pair_gran_history::init_style()
xkkt = xkk * 2.0/7.0;
dt = update->dt;
double gammas = 0.5*gamman;
gamman_dl = gamman/dt;
gammas_dl = 0.5*gamman_dl;
gammas_dl = gammas/dt;
// set pairstyle from granular pair style
if (force->pair_match("gran/no_history")) pairstyle = NO_HISTORY;
else if (force->pair_match("gran/history")) pairstyle = HISTORY;
else if (force->pair_match("gran/hertzian")) pairstyle = HERTZIAN;
}
/* ---------------------------------------------------------------------- */
@ -274,7 +265,7 @@ void FixWallGran::post_force(int vflag)
rsq = dx*dx + dy*dy + dz*dz;
if (rsq > radius[i]*radius[i]) {
if (historystyle) {
if (pairstyle != NO_HISTORY) {
shear[i][0] = 0.0;
shear[i][1] = 0.0;
shear[i][2] = 0.0;

12
src/GRANULAR/fix_wall_gran.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,9 +16,11 @@
#include "fix.h"
namespace LAMMPS_NS {
class FixWallGran : public Fix {
public:
FixWallGran(int, char **);
FixWallGran(class LAMMPS *, int, char **);
~FixWallGran();
int setmask();
void init();
@ -36,7 +38,7 @@ class FixWallGran : public Fix {
int maxsize_restart();
private:
int wallstyle,pairstyle,historystyle,wiggle,axis;
int wallstyle,pairstyle,wiggle,axis;
double xkk,xkkt,gamman,xmu;
double lo,hi,cylradius;
double dt,gamman_dl,gammas_dl;
@ -55,4 +57,6 @@ class FixWallGran : public Fix {
double *);
};
}
#endif

13
src/GRANULAR/pair_gran_hertzian.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -23,11 +23,20 @@
#include "force.h"
#include "neighbor.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
PairGranHertzian::PairGranHertzian(LAMMPS *lmp) : PairGranHistory(lmp)
{
history = 1;
}
/* ---------------------------------------------------------------------- */
void PairGranHertzian::compute(int eflag, int vflag)
{
int i,j,k,numneigh;

9
src/GRANULAR/pair_gran_hertzian.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,9 +16,14 @@
#include "pair_gran_history.h"
namespace LAMMPS_NS {
class PairGranHertzian : public PairGranHistory {
public:
PairGranHertzian(class LAMMPS *);
void compute(int, int);
};
}
#endif

41
src/GRANULAR/pair_gran_history.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -32,24 +32,27 @@
#include "neighbor.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
PairGranHistory::PairGranHistory()
PairGranHistory::PairGranHistory(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
for (int i = 0; i < 6; i++) virial[i] = 0.0;
ifix_history = -1;
history = 1;
fix_history = NULL;
}
/* ---------------------------------------------------------------------- */
PairGranHistory::~PairGranHistory()
{
if (ifix_history >= 0) modify->delete_fix("SHEAR_HISTORY");
if (fix_history) modify->delete_fix("SHEAR_HISTORY");
if (allocated) {
memory->destroy_2d_int_array(setflag);
@ -335,32 +338,21 @@ void PairGranHistory::init_style()
if (atom->check_style("granular") == 0)
error->all("Must use atom style granular with pair style granular");
// for pair choices with shear history:
// if shear history is stored:
// check if newton flag is valid
// if first init, create Fix needed for storing shear history
int history = 0;
if (force->pair_match("gran/history") || force->pair_match("gran/hertzian"))
history = 1;
if (history && force->newton_pair == 1)
error->all("Potential with shear history requires newton pair off");
if (history && ifix_history == -1) {
if (history && fix_history == NULL) {
char **fixarg = new char*[3];
fixarg[0] = "SHEAR_HISTORY";
fixarg[1] = "all";
fixarg[2] = "SHEAR_HISTORY";
modify->add_fix(3,fixarg);
delete [] fixarg;
}
// find associated SHEAR_HISTORY fix that must exist
// could have changed locations in fix list since created
if (history) {
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"SHEAR_HISTORY") == 0) ifix_history = i;
fix_history = (FixShearHistory *) modify->fix[modify->nfix-1];
}
// check for freeze Fix and set freeze_group_bit
@ -452,3 +444,14 @@ void PairGranHistory::read_restart_settings(FILE *fp)
MPI_Bcast(&xmu,1,MPI_DOUBLE,0,world);
MPI_Bcast(&dampflag,1,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
void PairGranHistory::extract_gran(double *p_xkk, double *p_gamman,
double *p_xmu, int *p_dampflag)
{
*p_xkk = xkk;
*p_gamman = gamman;
*p_xmu = xmu;
*p_dampflag = dampflag;
}

20
src/GRANULAR/pair_gran_history.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,13 +16,11 @@
#include "pair.h"
class PairGranHistory : public Pair {
friend class Neighbor;
friend class FixWallGran;
friend class FixGranDiag;
namespace LAMMPS_NS {
class PairGranHistory : public Pair {
public:
PairGranHistory();
PairGranHistory(class LAMMPS *);
~PairGranHistory();
virtual void compute(int, int);
void settings(int, char **);
@ -34,14 +32,20 @@ class PairGranHistory : public Pair {
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
void extract_gran(double *, double *, double *, int *);
protected:
double xkk,xkkt,xmu;
int dampflag;
double gamman;
double dt,gamman_dl,gammas_dl;
int ifix_history,freeze_group_bit;
int freeze_group_bit;
int history;
class FixShearHistory *fix_history;
void allocate();
};
}
#endif

13
src/GRANULAR/pair_gran_no_history.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -23,11 +23,20 @@
#include "force.h"
#include "neighbor.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
PairGranNoHistory::PairGranNoHistory(LAMMPS *lmp) : PairGranHistory(lmp)
{
history = 0;
}
/* ---------------------------------------------------------------------- */
void PairGranNoHistory::compute(int eflag, int vflag)
{
int i,j,k,numneigh;

9
src/GRANULAR/pair_gran_no_history.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,9 +16,14 @@
#include "pair_gran_history.h"
namespace LAMMPS_NS {
class PairGranNoHistory : public PairGranHistory {
public:
PairGranNoHistory(class LAMMPS *);
void compute(int, int);
};
}
#endif

8
src/GRANULAR/style_granular.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -12,11 +12,11 @@
------------------------------------------------------------------------- */
#ifdef AtomInclude
#include "atom_granular.h"
#include "atom_vec_granular.h"
#endif
#ifdef AtomClass
AtomStyle(granular,AtomGranular)
AtomStyle(granular,AtomVecGranular)
# endif
#ifdef FixInclude

6
src/KSPACE/Install.csh
View File

@ -1,7 +1,5 @@
# Install/unInstall package classes in LAMMPS
# pair_lj_charmm_coul_long.h must always be in src
if ($1 == 1) then
cp style_kspace.h ..
@ -24,7 +22,7 @@ if ($1 == 1) then
cp pair_buck_coul_long.h ..
cp pair_lj_cut_coul_long.h ..
cp pair_lj_cut_coul_long_tip4p.h ..
# cp pair_lj_charmm_coul_long.h ..
cp pair_lj_charmm_coul_long.h ..
cp fft3d.h ..
cp fft3d_wrap.h ..
cp remap.h ..
@ -53,7 +51,7 @@ else if ($1 == 0) then
rm ../pair_buck_coul_long.h
rm ../pair_lj_cut_coul_long.h
rm ../pair_lj_cut_coul_long_tip4p.h
# rm ../pair_lj_charmm_coul_long.h
rm ../pair_lj_charmm_coul_long.h
rm ../fft3d.h
rm ../fft3d_wrap.h
rm ../remap.h

37
src/KSPACE/ewald.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -23,21 +23,19 @@
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "pair_buck_coul_long.h"
#include "pair_lj_cut_coul_long.h"
#include "pair_lj_charmm_coul_long.h"
#include "pair_lj_class2_coul_long.h"
#include "pair_table.h"
#include "pair.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
Ewald::Ewald(int narg, char **arg) : KSpace(narg, arg)
Ewald::Ewald(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
{
if (narg != 1) error->all("Illegal kspace_style ewald command");
@ -90,27 +88,16 @@ void Ewald::init()
error->all("Incorrect boundaries with slab Ewald");
}
// insure use of pair_style with long-range Coulombics
// set cutoff to short-range Coulombic cutoff
// insure use of long (or table) pair_style with long-range Coulombics
// set cutoff to Pair's short-range Coulombic cutoff
qqrd2e = force->qqrd2e;
Pair *pair = force->pair_match("long");
if (pair == NULL) pair = force->pair_match("table");
if (pair == NULL) error->all("KSpace style is incompatible with Pair style");
double cutoff;
Pair *anypair;
if (force->pair == NULL)
error->all("KSpace style is incompatible with Pair style");
else if (anypair = force->pair_match("buck/coul/long"))
cutoff = ((PairBuckCoulLong *) anypair)->cut_coul;
else if (anypair = force->pair_match("lj/cut/coul/long"))
cutoff = ((PairLJCutCoulLong *) anypair)->cut_coul;
else if (anypair = force->pair_match("lj/charmm/coul/long"))
cutoff = ((PairLJCharmmCoulLong *) anypair)->cut_coul;
else if (anypair = force->pair_match("lj/class2/coul/long"))
cutoff = ((PairLJClass2CoulLong *) anypair)->cut_coul;
else if (anypair = force->pair_match("table"))
cutoff = ((PairTable *) anypair)->cut_coul();
else error->all("KSpace style is incompatible with Pair style");
pair->extract_long(&cutoff);
// compute qsum & qsqsum

10
src/KSPACE/ewald.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,9 +16,11 @@
#include "kspace.h"
namespace LAMMPS_NS {
class Ewald : public KSpace {
public:
Ewald(int, char **);
Ewald(class LAMMPS *, int, char **);
~Ewald();
void init();
void setup();
@ -49,4 +51,6 @@ class Ewald : public KSpace {
};
#endif
}

4
src/KSPACE/fft3d.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

4
src/KSPACE/fft3d.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

10
src/KSPACE/fft3d_wrap.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -15,14 +15,16 @@
#include "fft3d_wrap.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FFT3d::FFT3d(MPI_Comm comm, int nfast, int nmid, int nslow,
FFT3d::FFT3d(LAMMPS *lmp, MPI_Comm comm, int nfast, int nmid, int nslow,
int in_ilo, int in_ihi, int in_jlo, int in_jhi,
int in_klo, int in_khi,
int out_ilo, int out_ihi, int out_jlo, int out_jhi,
int out_klo, int out_khi,
int scaled, int permute, int *nbuf)
int scaled, int permute, int *nbuf) : Pointers(lmp)
{
plan = fft_3d_create_plan(comm,nfast,nmid,nslow,
in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,

14
src/KSPACE/fft3d_wrap.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -14,12 +14,14 @@
#ifndef FFT3D_WRAP_H
#define FFT3D_WRAP_H
#include "lammps.h"
#include "pointers.h"
#include "fft3d.h"
class FFT3d : public LAMMPS {
namespace LAMMPS_NS {
class FFT3d : protected Pointers {
public:
FFT3d(MPI_Comm,int,int,int,int,int,int,int,int,int,
FFT3d(class LAMMPS *, MPI_Comm,int,int,int,int,int,int,int,int,int,
int,int,int,int,int,int,int,int,int *);
~FFT3d();
void compute(double *, double *, int);
@ -29,4 +31,6 @@ class FFT3d : public LAMMPS {
struct fft_plan_3d *plan;
};
}
#endif

24
src/KSPACE/pair_buck_coul_long.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -25,6 +25,8 @@
#include "neighbor.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
@ -36,9 +38,11 @@
#define A4 -1.453152027
#define A5 1.061405429
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
PairBuckCoulLong::PairBuckCoulLong(LAMMPS *lmp) : Pair(lmp) {}
/* ---------------------------------------------------------------------- */
PairBuckCoulLong::~PairBuckCoulLong()
{
@ -305,7 +309,7 @@ void PairBuckCoulLong::init_style()
{
// require an atom style with charge defined
if (atom->charge_allow == 0)
if (atom->q == NULL)
error->all("Must use charged atom style with this pair style");
cut_coulsq = cut_coul * cut_coul;
@ -444,3 +448,11 @@ void PairBuckCoulLong::single(int i, int j, int itype, int jtype,
} else one.eng_vdwl = 0.0;
}
}
/* ---------------------------------------------------------------------- */
void PairBuckCoulLong::extract_long(double *p_cut_coul)
{
*p_cut_coul = cut_coul;
}

16
src/KSPACE/pair_buck_coul_long.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,11 +16,11 @@
#include "pair.h"
namespace LAMMPS_NS {
class PairBuckCoulLong : public Pair {
public:
double cut_coul;
PairBuckCoulLong() {}
PairBuckCoulLong(class LAMMPS *);
~PairBuckCoulLong();
void compute(int, int);
void settings(int, char **);
@ -33,10 +33,12 @@ class PairBuckCoulLong : public Pair {
void read_restart_settings(FILE *);
void single(int, int, int, int, double, double, double, int, One &);
void extract_long(double *);
private:
double cut_lj_global;
double **cut_lj,**cut_ljsq;
double cut_coulsq;
double cut_coul,cut_coulsq;
double **a,**rho,**c;
double **rhoinv,**buck1,**buck2,**offset;
double g_ewald;
@ -44,4 +46,6 @@ class PairBuckCoulLong : public Pair {
void allocate();
};
}
#endif

32
src/KSPACE/pair_lj_charmm_coul_long.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -31,6 +31,8 @@
#include "neighbor.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
@ -44,7 +46,7 @@
/* ---------------------------------------------------------------------- */
PairLJCharmmCoulLong::PairLJCharmmCoulLong()
PairLJCharmmCoulLong::PairLJCharmmCoulLong(LAMMPS *lmp) : Pair(lmp)
{
respa_enable = 1;
ftable = NULL;
@ -763,7 +765,7 @@ void PairLJCharmmCoulLong::init_style()
{
// require an atom style with charge defined
if (atom->charge_allow == 0)
if (atom->q == NULL)
error->all("Must use charged atom style with this pair style");
// require cut_lj_inner < cut_lj
@ -1158,3 +1160,25 @@ void PairLJCharmmCoulLong::single(int i, int j, int itype, int jtype,
} else one.eng_vdwl = 0.0;
}
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulLong::extract_charmm(double ***p_lj14_1,
double ***p_lj14_2,
double ***p_lj14_3,
double ***p_lj14_4,
int *p_implicit_flag)
{
*p_lj14_1 = lj14_1;
*p_lj14_2 = lj14_2;
*p_lj14_3 = lj14_3;
*p_lj14_4 = lj14_4;
*p_implicit_flag = 0;
}
/* ---------------------------------------------------------------------- */
void PairLJCharmmCoulLong::extract_long(double *p_cut_coul)
{
*p_cut_coul = cut_coul;
}

21
src/KSPACE/pair_lj_cut_coul_long.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -31,6 +31,8 @@
#include "neighbor.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
@ -44,15 +46,13 @@
/* ---------------------------------------------------------------------- */
PairLJCutCoulLong::PairLJCutCoulLong()
PairLJCutCoulLong::PairLJCutCoulLong(LAMMPS *lmp) : Pair(lmp)
{
respa_enable = 1;
ftable = NULL;
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
PairLJCutCoulLong::~PairLJCutCoulLong()
{
@ -739,7 +739,7 @@ void PairLJCutCoulLong::init_style()
// require an atom style with charge defined
if (atom->charge_allow == 0)
if (atom->q == NULL)
error->all("Must use charged atom style with this pair style");
cut_coulsq = cut_coul * cut_coul;
@ -1102,3 +1102,10 @@ void PairLJCutCoulLong::single(int i, int j, int itype, int jtype,
} else one.eng_vdwl = 0.0;
}
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLong::extract_long(double *p_cut_coul)
{
*p_cut_coul = cut_coul;
}

15
src/KSPACE/pair_lj_cut_coul_long.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,11 +16,11 @@
#include "pair.h"
namespace LAMMPS_NS {
class PairLJCutCoulLong : public Pair {
public:
double cut_coul;
PairLJCutCoulLong();
PairLJCutCoulLong(class LAMMPS *);
~PairLJCutCoulLong();
virtual void compute(int, int);
virtual void settings(int, char **);
@ -36,11 +36,12 @@ class PairLJCutCoulLong : public Pair {
void compute_inner();
void compute_middle();
void compute_outer(int, int);
void extract_long(double *);
protected:
double cut_lj_global;
double **cut_lj,**cut_ljsq;
double cut_coulsq;
double cut_coul,cut_coulsq;
double **epsilon,**sigma;
double **lj1,**lj2,**lj3,**lj4,**offset;
double *cut_respa;
@ -56,4 +57,6 @@ class PairLJCutCoulLong : public Pair {
void free_tables();
};
}
#endif

24
src/KSPACE/pair_lj_cut_coul_long_tip4p.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -33,6 +33,8 @@
#include "neighbor.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
@ -46,7 +48,8 @@
/* ---------------------------------------------------------------------- */
PairLJCutCoulLongTIP4P::PairLJCutCoulLongTIP4P()
PairLJCutCoulLongTIP4P::PairLJCutCoulLongTIP4P(LAMMPS *lmp) :
PairLJCutCoulLong(lmp)
{
single_enable = 0;
}
@ -407,7 +410,7 @@ void PairLJCutCoulLongTIP4P::init_style()
error->all("Pair style lj/cut/coul/long/tip4p requires atom IDs");
if (!force->newton_pair)
error->all("Pair style lj/cut/coul/long/tip4p requires newton pair on");
if (atom->charge_allow == 0)
if (atom->q == NULL)
error->all("Must use charged atom style with this pair style");
cut_coulsq = cut_coul * cut_coul;
@ -526,3 +529,16 @@ void PairLJCutCoulLongTIP4P::find_M(int i, int &iH1, int &iH2, double *xM)
xM[1] = x[i][1] + alpha * (dely1 + dely2);
xM[2] = x[i][2] + alpha * (delz1 + delz2);
}
/* ---------------------------------------------------------------------- */
void PairLJCutCoulLongTIP4P::extract_tip4p(double *p_qdist,
int *p_typeO, int *p_typeH,
int *p_typeA, int *p_typeB)
{
*p_qdist = qdist;
*p_typeO = typeO;
*p_typeH = typeH;
*p_typeA = typeA;
*p_typeB = typeB;
}

14
src/KSPACE/pair_lj_cut_coul_long_tip4p.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,17 +16,19 @@
#include "pair_lj_cut_coul_long.h"
class PairLJCutCoulLongTIP4P : public PairLJCutCoulLong {
friend class PPPM;
namespace LAMMPS_NS {
class PairLJCutCoulLongTIP4P : public PairLJCutCoulLong {
public:
PairLJCutCoulLongTIP4P();
PairLJCutCoulLongTIP4P(class LAMMPS *);
void compute(int, int);
void settings(int, char **);
void init_style();
void write_restart_settings(FILE *fp);
void read_restart_settings(FILE *fp);
void extract_tip4p(double *, int *, int *, int *, int *);
private:
int typeH,typeO; // atom types of TIP4P water H and O atoms
int typeA,typeB; // angle and bond types of TIP4P water
@ -38,4 +40,6 @@ class PairLJCutCoulLongTIP4P : public PairLJCutCoulLong {
void find_M(int, int &, int &, double *);
};
}
#endif

65
src/KSPACE/pppm.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -25,12 +25,7 @@
#include "comm.h"
#include "neighbor.h"
#include "force.h"
#include "pair_buck_coul_long.h"
#include "pair_lj_cut_coul_long.h"
#include "pair_lj_charmm_coul_long.h"
#include "pair_lj_class2_coul_long.h"
#include "pair_lj_cut_coul_long_tip4p.h"
#include "pair_table.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "domain.h"
@ -39,6 +34,8 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
@ -50,7 +47,7 @@
/* ---------------------------------------------------------------------- */
PPPM::PPPM(int narg, char **arg) : KSpace(narg, arg)
PPPM::PPPM(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
{
if (narg != 1) error->all("Illegal kspace_style pppm command");
@ -128,41 +125,35 @@ void PPPM::init()
deallocate();
// insure use of valid pair_style with long-range Coulombics
// set cutoff to short-range Coulombic cutoff
// insure use of long (or table) pair_style with long-range Coulombics
// set cutoff to Pair's short-range Coulombic cutoff
qqrd2e = force->qqrd2e;
Pair *pair = force->pair_match("long");
if (pair == NULL) pair = force->pair_match("table");
if (pair == NULL) error->all("KSpace style is incompatible with Pair style");
pair->extract_long(&cutoff);
// insure use of TIP4P pair_style with TIP4P long-range Coulombics
// set TIP4P params from Pair's params
qdist = 0.0;
Pair *anypair;
if (force->pair == NULL)
error->all("Pair style is incompatible with KSpace style");
else if (anypair = force->pair_match("buck/coul/long"))
cutoff = ((PairBuckCoulLong *) anypair)->cut_coul;
else if (anypair = force->pair_match("lj/cut/coul/long"))
cutoff = ((PairLJCutCoulLong *) anypair)->cut_coul;
else if (anypair = force->pair_match("lj/charmm/coul/long"))
cutoff = ((PairLJCharmmCoulLong *) anypair)->cut_coul;
else if (anypair = force->pair_match("lj/class2/coul/long"))
cutoff = ((PairLJClass2CoulLong *) anypair)->cut_coul;
else if (anypair = force->pair_match("lj/cut/coul/long/tip4p")) {
if (strcmp(force->kspace_style,"pppm/tip4p") != 0)
error->all("Pair style is incompatible with KSpace style");
cutoff = ((PairLJCutCoulLongTIP4P *) anypair)->cut_coul;
qdist = ((PairLJCutCoulLongTIP4P *) anypair)->qdist;
typeO = ((PairLJCutCoulLongTIP4P *) anypair)->typeO;
typeH = ((PairLJCutCoulLongTIP4P *) anypair)->typeH;
int typeA = ((PairLJCutCoulLongTIP4P *) anypair)->typeA;
int typeB = ((PairLJCutCoulLongTIP4P *) anypair)->typeB;
pair = force->pair_match("tip4p");
if (strcmp(force->kspace_style,"pppm/tip4p") != 0 && pair != NULL)
error->all("KSpace style is incompatible with Pair style");
if (strcmp(force->kspace_style,"pppm/tip4p") == 0 && pair == NULL)
error->all("KSpace style is incompatible with Pair style");
if (pair) {
int typeA,typeB;
pair->extract_tip4p(&qdist,&typeO,&typeH,&typeA,&typeB);
if (force->angle == NULL || force->bond == NULL)
error->all("Bond and angle potentials must be defined for TIP4P");
double theta = force->angle->equilibrium_angle(typeA);
double blen = force->bond->equilibrium_distance(typeB);
alpha = qdist / (2.0 * cos(0.5*theta) * blen);
}
else if (anypair = force->pair_match("table"))
cutoff = ((PairTable *) anypair)->cut_coul();
else error->all("Pair style is incompatible with KSpace style");
// compute qsum & qsqsum and warn if not charge-neutral
@ -698,17 +689,17 @@ void PPPM::allocate()
int tmp;
fft1 = new FFT3d(world,nx_pppm,ny_pppm,nz_pppm,
fft1 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
0,0,&tmp);
fft2 = new FFT3d(world,nx_pppm,ny_pppm,nz_pppm,
fft2 = new FFT3d(lmp,world,nx_pppm,ny_pppm,nz_pppm,
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
0,0,&tmp);
remap = new Remap(world,
remap = new Remap(lmp,world,
nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in,
nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft,
1,0,0,2);

15
src/KSPACE/pppm.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,12 +16,11 @@
#include "kspace.h"
class FFT3d;
class Remap;
namespace LAMMPS_NS {
class PPPM : public KSpace {
public:
PPPM(int, char **);
PPPM(class LAMMPS *, int, char **);
~PPPM();
void init();
void setup();
@ -61,8 +60,8 @@ class PPPM : public KSpace {
double *gf_b;
double **rho1d,**rho_coeff;
FFT3d *fft1,*fft2;
Remap *remap;
class FFT3d *fft1,*fft2;
class Remap *remap;
int **part2grid; // storage for particle -> grid mapping
int nmax;
@ -91,4 +90,6 @@ class PPPM : public KSpace {
void slabcorr(int);
};
}
#endif

9
src/KSPACE/pppm_tip4p.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -22,11 +22,14 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define OFFSET 4096
/* ---------------------------------------------------------------------- */
PPPMTIP4P::PPPMTIP4P(int narg, char **arg) : PPPM(narg, arg) {}
PPPMTIP4P::PPPMTIP4P(LAMMPS *lmp, int narg, char **arg) :
PPPM(lmp, narg, arg) {}
/* ----------------------------------------------------------------------
find center grid pt for each of my particles

10
src/KSPACE/pppm_tip4p.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,9 +16,11 @@
#include "pppm.h"
namespace LAMMPS_NS {
class PPPMTIP4P : public PPPM {
public:
PPPMTIP4P(int, char **);
PPPMTIP4P(class LAMMPS *, int, char **);
private:
void particle_map();
@ -28,4 +30,6 @@ class PPPMTIP4P : public PPPM {
void find_M(int, int &, int &, double *);
};
}
#endif

4
src/KSPACE/remap.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

4
src/KSPACE/remap.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

10
src/KSPACE/remap_wrap.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -15,14 +15,16 @@
#include "remap_wrap.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
Remap::Remap(MPI_Comm comm,
Remap::Remap(LAMMPS *lmp, MPI_Comm comm,
int in_ilo, int in_ihi, int in_jlo, int in_jhi,
int in_klo, int in_khi,
int out_ilo, int out_ihi, int out_jlo, int out_jhi,
int out_klo, int out_khi,
int nqty, int permute, int memory, int precision)
int nqty, int permute, int memory, int precision) : Pointers(lmp)
{
plan = remap_3d_create_plan(comm,
in_ilo,in_ihi,in_jlo,in_jhi,in_klo,in_khi,

14
src/KSPACE/remap_wrap.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -14,12 +14,14 @@
#ifndef REMAP_WRAP_H
#define REMAP_WRAP_H
#include "lammps.h"
#include "pointers.h"
#include "remap.h"
class Remap : public LAMMPS {
namespace LAMMPS_NS {
class Remap : protected Pointers {
public:
Remap(MPI_Comm,int,int,int,int,int,int,
Remap(class LAMMPS *, MPI_Comm,int,int,int,int,int,int,
int,int,int,int,int,int,int,int,int,int);
~Remap();
void perform(double *, double *, double *);
@ -28,4 +30,6 @@ class Remap : public LAMMPS {
struct remap_plan_3d *plan;
};
}
#endif

4
src/KSPACE/style_kspace.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

2
src/MAKE/Makefile.linux
View File

@ -8,6 +8,8 @@ SHELL = /bin/sh
CC = icc
CCFLAGS = -O -I/home/sjplimp/tools/mpich/include \
-I/home/sjplimp/tools/fftw/include -DFFT_FFTW -DGZIP
#CCFLAGS = -O -restrict -I/home/sjplimp/tools/mpich/include \
# -I/home/sjplimp/tools/fftw/include -DFFT_FFTW -DGZIP
DEPFLAGS = -M
LINK = icc
LINKFLAGS = -O -L/home/sjplimp/tools/mpich/lib \

6
src/MANYBODY/Install.csh
View File

@ -1,7 +1,5 @@
# Install/unInstall package classes in LAMMPS
# pair_eam.h must always be in src
if ($1 == 1) then
cp style_manybody.h ..
@ -12,7 +10,7 @@ if ($1 == 1) then
cp pair_sw.cpp ..
cp pair_tersoff.cpp ..
# cp pair_eam.h ..
cp pair_eam.h ..
cp pair_eam_alloy.h ..
cp pair_eam_fs.h ..
cp pair_sw.h ..
@ -29,7 +27,7 @@ else if ($1 == 0) then
rm ../pair_sw.cpp
rm ../pair_tersoff.cpp
# rm ../pair_eam.h
rm ../pair_eam.h
rm ../pair_eam_alloy.h
rm ../pair_eam_fs.h
rm ../pair_sw.h

37
src/MANYBODY/pair_eam.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -28,6 +28,8 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
@ -35,7 +37,7 @@
/* ---------------------------------------------------------------------- */
PairEAM::PairEAM()
PairEAM::PairEAM(LAMMPS *lmp) : Pair(lmp)
{
nmax = 0;
rho = NULL;
@ -54,10 +56,14 @@ PairEAM::PairEAM()
frho_spline = NULL;
rhor_spline = NULL;
z2r_spline = NULL;
// set comm size needed by this Pair
comm_forward = 1;
comm_reverse = 1;
}
/* ----------------------------------------------------------------------
free all arrays
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
@ -410,11 +416,6 @@ double PairEAM::init_one(int i, int j)
void PairEAM::init_style()
{
// set communication sizes in comm class
comm->maxforward_pair = MAX(comm->maxforward_pair,1);
comm->maxreverse_pair = MAX(comm->maxreverse_pair,1);
// convert read-in file(s) to arrays and spline them
file2array();
@ -804,17 +805,16 @@ void PairEAM::single(int i, int j, int itype, int jtype,
/* ---------------------------------------------------------------------- */
void PairEAM::single_embed(int i, int itype, double &fpi,
int eflag, double &phi)
void PairEAM::single_embed(int i, int itype, double &phi)
{
printf("AAA %d\n",i);
double p = rho[i]*rdrho + 1.0;
int m = static_cast<int> (p);
m = MAX(1,MIN(m,nrho-1));
p -= m;
double *coeff = frho_spline[type2frho[itype]][m];
fpi = (coeff[0]*p + coeff[1])*p + coeff[2];
if (eflag) phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
}
/* ---------------------------------------------------------------------- */
@ -876,3 +876,14 @@ int PairEAM::memory_usage()
int bytes = 2 * nmax * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
swap fp array with one passed in by caller
------------------------------------------------------------------------- */
void PairEAM::extract_eam(double *fp_caller, double **fp_caller_hold)
{
double *tmp = fp;
fp = fp_caller;
*fp_caller_hold = tmp;
}

13
src/MANYBODY/pair_eam_alloy.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -24,8 +24,17 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
/* ---------------------------------------------------------------------- */
PairEAMAlloy::PairEAMAlloy(LAMMPS *lmp) : PairEAM(lmp)
{
one_coeff = 1;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
read DYNAMO setfl file

16
src/MANYBODY/pair_eam_alloy.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,13 +16,21 @@
#include "pair_eam.h"
class PairEAMAlloy : public PairEAM {
namespace LAMMPS_NS {
// use virtual public since this class is parent in multiple inheritance
class PairEAMAlloy : virtual public PairEAM {
public:
PairEAMAlloy(class LAMMPS *);
virtual ~PairEAMAlloy() {}
void coeff(int, char **);
private:
protected:
void read_file(char *);
void file2array();
};
}
#endif

13
src/MANYBODY/pair_eam_fs.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -24,8 +24,17 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
/* ---------------------------------------------------------------------- */
PairEAMFS::PairEAMFS(LAMMPS *lmp) : PairEAM(lmp)
{
one_coeff = 1;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
read EAM Finnis-Sinclair file

16
src/MANYBODY/pair_eam_fs.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,13 +16,21 @@
#include "pair_eam.h"
class PairEAMFS : public PairEAM {
namespace LAMMPS_NS {
// use virtual public since this class is parent in multiple inheritance
class PairEAMFS : virtual public PairEAM {
public:
PairEAMFS(class LAMMPS *);
virtual ~PairEAMFS() {}
void coeff(int, char **);
private:
protected:
void read_file(char *);
void file2array();
};
}
#endif

14
src/MANYBODY/pair_sw.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -29,12 +29,14 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
#define DELTA 4
/* ---------------------------------------------------------------------- */
PairSW::PairSW()
PairSW::PairSW(LAMMPS *lmp) : Pair(lmp)
{
neigh_half_every = 0;
neigh_full_every = 1;
@ -50,7 +52,6 @@ PairSW::PairSW()
}
/* ----------------------------------------------------------------------
free all arrays
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
@ -211,7 +212,7 @@ void PairSW::settings(int narg, char **arg)
void PairSW::coeff(int narg, char **arg)
{
int i,j,m,n;
int i,j,n;
if (!allocated) allocate();
@ -325,7 +326,7 @@ void PairSW::read_file(char *file)
// one set of params can span multiple lines
// store params if all 3 element tags are in element list
int i,n,nwords,ielement,jelement,kelement;
int n,nwords,ielement,jelement,kelement;
char line[MAXLINE],*ptr;
int eof = 0;
@ -491,7 +492,6 @@ void PairSW::twobody(Param *param, double rsq, double &fforce,
int eflag, double &eng)
{
double r,rinvsq,rp,rq,rainv,rainvsq,expsrainv;
double delr[3];
r = sqrt(rsq);
rinvsq = 1.0/rsq;

10
src/MANYBODY/pair_sw.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,9 +16,11 @@
#include "pair.h"
namespace LAMMPS_NS {
class PairSW : public Pair {
public:
PairSW();
PairSW(class LAMMPS *);
~PairSW();
void compute(int, int);
void settings(int, char **);
@ -55,4 +57,6 @@ class PairSW : public Pair {
double *, double *, int, double &);
};
}
#endif

13
src/MANYBODY/pair_tersoff.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -29,12 +29,14 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
#define DELTA 4
/* ---------------------------------------------------------------------- */
PairTersoff::PairTersoff()
PairTersoff::PairTersoff(LAMMPS *lmp) : Pair(lmp)
{
neigh_half_every = 0;
neigh_full_every = 1;
@ -53,7 +55,6 @@ PairTersoff::PairTersoff()
}
/* ----------------------------------------------------------------------
free all arrays
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
@ -248,7 +249,7 @@ void PairTersoff::settings(int narg, char **arg)
void PairTersoff::coeff(int narg, char **arg)
{
int i,j,m,n;
int i,j,n;
if (!allocated) allocate();
@ -361,7 +362,7 @@ void PairTersoff::read_file(char *file)
// read each line out of file, skipping blank lines or leading '#'
// store line of params if all 3 element tags are in element list
int i,n,nwords,ielement,jelement,kelement;
int n,nwords,ielement,jelement,kelement;
char line[MAXLINE],*ptr;
int eof = 0;

10
src/MANYBODY/pair_tersoff.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,9 +16,11 @@
#include "pair.h"
namespace LAMMPS_NS {
class PairTersoff : public Pair {
public:
PairTersoff();
PairTersoff(class LAMMPS *);
~PairTersoff();
void compute(int, int);
void settings(int, char **);
@ -85,4 +87,6 @@ class PairTersoff : public Pair {
}
};
}
#endif

4
src/MANYBODY/style_manybody.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

28
src/MOLECULE/Install.csh
View File

@ -13,10 +13,9 @@ if ($1 == 1) then
cp angle_cosine_squared.cpp ..
cp angle_harmonic.cpp ..
cp angle_hybrid.cpp ..
cp atom_angle.cpp ..
cp atom_bond.cpp ..
cp atom_full.cpp ..
cp atom_molecular.cpp ..
cp atom_vec_angle.cpp ..
cp atom_vec_bond.cpp ..
cp atom_vec_molecular.cpp ..
cp bond.cpp ..
cp bond_fene.cpp ..
cp bond_fene_expand.cpp ..
@ -46,10 +45,9 @@ if ($1 == 1) then
cp angle_cosine_squared.h ..
cp angle_harmonic.h ..
cp angle_hybrid.h ..
cp atom_angle.h ..
cp atom_bond.h ..
cp atom_full.h ..
cp atom_molecular.h ..
cp atom_vec_angle.h ..
cp atom_vec_bond.h ..
cp atom_vec_molecular.h ..
# cp bond.h ..
cp bond_fene.h ..
cp bond_fene_expand.h ..
@ -84,10 +82,9 @@ else if ($1 == 0) then
rm ../angle_cosine_squared.cpp
rm ../angle_harmonic.cpp
rm ../angle_hybrid.cpp
rm ../atom_angle.cpp
rm ../atom_bond.cpp
rm ../atom_full.cpp
rm ../atom_molecular.cpp
rm ../atom_vec_angle.cpp
rm ../atom_vec_bond.cpp
rm ../atom_vec_molecular.cpp
rm ../bond.cpp
rm ../bond_fene.cpp
rm ../bond_fene_expand.cpp
@ -117,10 +114,9 @@ else if ($1 == 0) then
rm ../angle_cosine_squared.h
rm ../angle_harmonic.h
rm ../angle_hybrid.h
rm ../atom_angle.h
rm ../atom_bond.h
rm ../atom_full.h
rm ../atom_molecular.h
rm ../atom_vec_angle.h
rm ../atom_vec_bond.h
rm ../atom_vec_molecular.h
# rm ../bond.h
rm ../bond_fene.h
rm ../bond_fene_expand.h

8
src/MOLECULE/angle.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,9 +16,11 @@
#include "atom.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
Angle::Angle()
Angle::Angle(LAMMPS *lmp) : Pointers(lmp)
{
allocated = 0;
PI = 4.0*atan(1.0);

14
src/MOLECULE/angle_charmm.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -26,11 +26,15 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define SMALL 0.001
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
AngleCharmm::AngleCharmm(LAMMPS *lmp) : Angle(lmp) {}
/* ---------------------------------------------------------------------- */
AngleCharmm::~AngleCharmm()
{

10
src/MOLECULE/angle_charmm.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -17,9 +17,11 @@
#include "stdio.h"
#include "angle.h"
namespace LAMMPS_NS {
class AngleCharmm : public Angle {
public:
AngleCharmm() {}
AngleCharmm(class LAMMPS *);
~AngleCharmm();
void compute(int, int);
void coeff(int, int, char **);
@ -34,4 +36,6 @@ class AngleCharmm : public Angle {
void allocate();
};
}
#endif

14
src/MOLECULE/angle_cosine.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -22,11 +22,15 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define SMALL 0.001
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
AngleCosine::AngleCosine(LAMMPS *lmp) : Angle(lmp) {}
/* ---------------------------------------------------------------------- */
AngleCosine::~AngleCosine()
{

10
src/MOLECULE/angle_cosine.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -17,9 +17,11 @@
#include "stdio.h"
#include "angle.h"
namespace LAMMPS_NS {
class AngleCosine : public Angle {
public:
AngleCosine() {}
AngleCosine(class LAMMPS *);
~AngleCosine();
void compute(int, int);
void coeff(int, int, char **);
@ -34,4 +36,6 @@ class AngleCosine : public Angle {
void allocate();
};
}
#endif

14
src/MOLECULE/angle_cosine_squared.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -26,11 +26,15 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define SMALL 0.001
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
AngleCosineSquared::AngleCosineSquared(LAMMPS *lmp) : Angle(lmp) {}
/* ---------------------------------------------------------------------- */
AngleCosineSquared::~AngleCosineSquared()
{

10
src/MOLECULE/angle_cosine_squared.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -17,9 +17,11 @@
#include "stdio.h"
#include "angle.h"
namespace LAMMPS_NS {
class AngleCosineSquared : public Angle {
public:
AngleCosineSquared() {}
AngleCosineSquared(class LAMMPS *);
~AngleCosineSquared();
void compute(int, int);
void coeff(int, int, char **);
@ -34,4 +36,6 @@ class AngleCosineSquared : public Angle {
void allocate();
};
}
#endif

14
src/MOLECULE/angle_harmonic.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -22,11 +22,15 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define SMALL 0.001
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
AngleHarmonic::AngleHarmonic(LAMMPS *lmp) : Angle(lmp) {}
/* ---------------------------------------------------------------------- */
AngleHarmonic::~AngleHarmonic()
{

10
src/MOLECULE/angle_harmonic.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -17,9 +17,11 @@
#include "stdio.h"
#include "angle.h"
namespace LAMMPS_NS {
class AngleHarmonic : public Angle {
public:
AngleHarmonic() {}
AngleHarmonic(class LAMMPS *);
~AngleHarmonic();
void compute(int, int);
void coeff(int, int, char **);
@ -34,4 +36,6 @@ class AngleHarmonic : public Angle {
void allocate();
};
}
#endif

16
src/MOLECULE/angle_hybrid.cpp
View File

@ -1,7 +1,7 @@
/* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -22,20 +22,18 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define EXTRA 1000
/* ----------------------------------------------------------------------
set all global defaults
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
AngleHybrid::AngleHybrid()
AngleHybrid::AngleHybrid(LAMMPS *lmp) : Angle(lmp)
{
nstyles = 0;
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
AngleHybrid::~AngleHybrid()
{

10
src/MOLECULE/angle_hybrid.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -17,9 +17,11 @@
#include "stdio.h"
#include "angle.h"
namespace LAMMPS_NS {
class AngleHybrid : public Angle {
public:
AngleHybrid();
AngleHybrid(class LAMMPS *);
~AngleHybrid();
void compute(int, int);
void settings(int, char **);
@ -43,4 +45,6 @@ class AngleHybrid : public Angle {
void allocate();
};
}
#endif

8
src/MOLECULE/bond.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -16,12 +16,14 @@
#include "atom.h"
#include "error.h"
using namespace LAMMPS_NS;
/* -----------------------------------------------------------------------
set bond contribution to Vdwl energy to 0.0
a particular bond style can override this
------------------------------------------------------------------------- */
Bond::Bond()
Bond::Bond(LAMMPS *lmp) : Pointers(lmp)
{
allocated = 0;
eng_vdwl = 0.0;

12
src/MOLECULE/bond_fene.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -23,16 +23,16 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondFENE::BondFENE()
BondFENE::BondFENE(LAMMPS *lmp) : Bond(lmp)
{
TWO_1_3 = pow(2.0,(1.0/3.0));
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
BondFENE::~BondFENE()
{

10
src/MOLECULE/bond_fene.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -17,9 +17,11 @@
#include "stdio.h"
#include "bond.h"
namespace LAMMPS_NS {
class BondFENE : public Bond {
public:
BondFENE();
BondFENE(class LAMMPS *);
~BondFENE();
void compute(int, int);
void coeff(int, char **);
@ -35,4 +37,6 @@ class BondFENE : public Bond {
void allocate();
};
}
#endif

18
src/MOLECULE/bond_fene_expand.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -11,8 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
// FENE bond potential, with repulsive LJ, with shift
#include "math.h"
#include "stdlib.h"
#include "bond_fene_expand.h"
@ -25,18 +23,16 @@
#include "memory.h"
#include "error.h"
/* ----------------------------------------------------------------------
set all global defaults
------------------------------------------------------------------------- */
using namespace LAMMPS_NS;
BondFENEExpand::BondFENEExpand()
/* ---------------------------------------------------------------------- */
BondFENEExpand::BondFENEExpand(LAMMPS *lmp) : Bond(lmp)
{
TWO_1_3 = pow(2.0,(1.0/3.0));
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
BondFENEExpand::~BondFENEExpand()
{

10
src/MOLECULE/bond_fene_expand.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -17,9 +17,11 @@
#include "stdio.h"
#include "bond.h"
namespace LAMMPS_NS {
class BondFENEExpand : public Bond {
public:
BondFENEExpand();
BondFENEExpand(class LAMMPS *);
~BondFENEExpand();
void compute(int, int);
void coeff(int, char **);
@ -35,4 +37,6 @@ class BondFENEExpand : public Bond {
void allocate();
};
}
#endif

14
src/MOLECULE/bond_harmonic.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -22,9 +22,13 @@
#include "memory.h"
#include "error.h"
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondHarmonic::BondHarmonic(LAMMPS *lmp) : Bond(lmp) {}
/* ---------------------------------------------------------------------- */
BondHarmonic::~BondHarmonic()
{

10
src/MOLECULE/bond_harmonic.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -17,9 +17,11 @@
#include "stdio.h"
#include "bond.h"
namespace LAMMPS_NS {
class BondHarmonic : public Bond {
public:
BondHarmonic() {}
BondHarmonic(class LAMMPS *);
~BondHarmonic();
void compute(int, int);
void coeff(int, char **);
@ -34,4 +36,6 @@ class BondHarmonic : public Bond {
void allocate();
};
}
#endif

16
src/MOLECULE/bond_hybrid.cpp
View File

@ -1,7 +1,7 @@
/* -----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -22,20 +22,18 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define EXTRA 1000
/* ----------------------------------------------------------------------
set all global defaults
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
BondHybrid::BondHybrid()
BondHybrid::BondHybrid(LAMMPS *lmp) : Bond(lmp)
{
nstyles = 0;
}
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
/* ---------------------------------------------------------------------- */
BondHybrid::~BondHybrid()
{

14
src/MOLECULE/bond_morse.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -26,9 +26,13 @@
#include "memory.h"
#include "error.h"
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondMorse::BondMorse(LAMMPS *lmp) : Bond(lmp) {}
/* ---------------------------------------------------------------------- */
BondMorse::~BondMorse()
{

10
src/MOLECULE/bond_morse.h
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -17,9 +17,11 @@
#include "stdio.h"
#include "bond.h"
namespace LAMMPS_NS {
class BondMorse : public Bond {
public:
BondMorse() {}
BondMorse(class LAMMPS *);
~BondMorse();
void compute(int, int);
void coeff(int, char **);
@ -34,4 +36,6 @@ class BondMorse : public Bond {
void allocate();
};
}
#endif

14
src/MOLECULE/bond_nonlinear.cpp
View File

@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -22,9 +22,13 @@
#include "memory.h"
#include "error.h"
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
BondNonlinear::BondNonlinear(LAMMPS *lmp) : Bond(lmp) {}
/* ---------------------------------------------------------------------- */
BondNonlinear::~BondNonlinear()
{

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