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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2937 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2009-07-01 20:28:37 +00:00
parent b58c43a5ec
commit c318361d2f
15 changed files with 97 additions and 101 deletions
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12
src/ASPHERE/compute_temp_asphere.cpp
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@ -31,6 +31,8 @@
using namespace LAMMPS_NS;
enum{DUMMY0,INVOKED_SCALAR,INVOKED_VECTOR,DUMMMY3,INVOKED_PERATOM};
/* ---------------------------------------------------------------------- */
ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
@ -159,7 +161,10 @@ double ComputeTempAsphere::compute_scalar()
invoked_scalar = update->ntimestep;
if (tempbias) {
if (tbias->invoked_scalar != update->ntimestep) tbias->compute_scalar();
if (!(tbias->invoked_flag & INVOKED_SCALAR)) {
tbias->compute_scalar();
tbias->invoked_flag |= INVOKED_SCALAR;
}
tbias->remove_bias_all();
}
@ -216,7 +221,10 @@ void ComputeTempAsphere::compute_vector()
invoked_vector = update->ntimestep;
if (tempbias) {
if (tbias->invoked_vector != update->ntimestep) tbias->compute_vector();
if (!(tbias->invoked_flag & INVOKED_VECTOR)) {
tbias->compute_vector();
tbias->invoked_flag |= INVOKED_VECTOR;
}
tbias->remove_bias_all();
}

9
src/compute.cpp
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@ -64,7 +64,6 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
pressatomflag = peatomflag = 0;
tempbias = 0;
id_pre = NULL;
timeflag = 0;
comm_forward = comm_reverse = 0;
@ -87,7 +86,6 @@ Compute::~Compute()
{
delete [] id;
delete [] style;
delete [] id_pre;
memory->sfree(tlist);
}
@ -129,6 +127,13 @@ void Compute::reset_extra_dof()
extra_dof = domain->dimension;
}
/* ---------------------------------------------------------------------- */
void Compute::reset_extra_compute(char *)
{
error->all("Compute does not allow an extra compute to be reset");
}
/* ----------------------------------------------------------------------
add ntimestep to list of timesteps the compute will be called on
do not add if already in list

6
src/compute.h
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@ -47,14 +47,12 @@ class Compute : protected Pointers {
int tempbias; // 0/1 if Compute temp includes self/extra bias
char *id_pre; // ID of pre-compute the Compute may store
int timeflag; // 1 if Compute stores list of timesteps it's called on
int ntime; // # of entries in time list
int maxtime; // max # of entries time list can hold
int *tlist; // time list of steps the Compute is called on
int invoked_flag; // 1 if invoked or accessed this step, 0 if not
int invoked_flag; // non-zero if invoked or accessed this step, 0 if not
int invoked_scalar; // last timestep on which compute_scalar() was invoked
int invoked_vector; // ditto for compute_vector()
int invoked_peratom; // ditto for compute_peratom()
@ -86,6 +84,8 @@ class Compute : protected Pointers {
virtual void restore_bias(int, double *) {}
virtual void restore_bias_all() {}
virtual void reset_extra_compute(char *);
void addstep(int);
int matchstep(int);
void clearstep();

32
src/compute_pressure.cpp
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@ -31,6 +31,8 @@
using namespace LAMMPS_NS;
enum{DUMMY0,INVOKED_SCALAR,INVOKED_VECTOR,DUMMMY3,INVOKED_PERATOM};
/* ---------------------------------------------------------------------- */
ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
@ -50,10 +52,10 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
// insure it is valid for temperature computation
int n = strlen(arg[3]) + 1;
id_pre = new char[n];
strcpy(id_pre,arg[3]);
id_temp = new char[n];
strcpy(id_temp,arg[3]);
int icompute = modify->find_compute(id_pre);
int icompute = modify->find_compute(id_temp);
if (icompute < 0) error->all("Could not find compute pressure temp ID");
if (modify->compute[icompute]->tempflag == 0)
error->all("Compute pressure temp ID does not compute temperature");
@ -98,6 +100,7 @@ ComputePressure::ComputePressure(LAMMPS *lmp, int narg, char **arg) :
ComputePressure::~ComputePressure()
{
delete [] id_temp;
delete [] vector;
delete [] vptr;
}
@ -113,7 +116,7 @@ void ComputePressure::init()
// set temperature compute, must be done in init()
// fixes could have changed or compute_modify could have changed it
int icompute = modify->find_compute(id_pre);
int icompute = modify->find_compute(id_temp);
if (icompute < 0) error->all("Could not find compute pressure temp ID");
temperature = modify->compute[icompute];
@ -169,9 +172,10 @@ double ComputePressure::compute_scalar()
double t;
if (keflag) {
if (temperature->invoked_scalar == update->ntimestep)
t = temperature->scalar;
else t = temperature->compute_scalar();
if (!(temperature->invoked_flag & INVOKED_SCALAR)) {
t = temperature->compute_scalar();
temperature->invoked_flag |= INVOKED_SCALAR;
} else t = temperature->scalar;
}
if (dimension == 3) {
@ -210,8 +214,10 @@ void ComputePressure::compute_vector()
double *ke_tensor;
if (keflag) {
if (temperature->invoked_vector != update->ntimestep)
if (!(temperature->invoked_flag & INVOKED_VECTOR)) {
temperature->compute_vector();
temperature->invoked_flag |= INVOKED_VECTOR;
}
ke_tensor = temperature->vector;
}
@ -269,3 +275,13 @@ void ComputePressure::virial_compute(int n, int ndiag)
if (force->pair && force->pair->tail_flag)
for (i = 0; i < ndiag; i++) virial[i] += force->pair->ptail * inv_volume;
}
/* ---------------------------------------------------------------------- */
void ComputePressure::reset_extra_compute(char *id_new)
{
delete [] id_temp;
int n = strlen(id_new) + 1;
id_temp = new char[n];
strcpy(id_temp,id_new);
}

2
src/compute_pressure.h
View File

@ -25,6 +25,7 @@ class ComputePressure : public Compute {
void init();
double compute_scalar();
void compute_vector();
void reset_extra_compute(char *);
private:
double boltz,nktv2p,inv_volume;
@ -32,6 +33,7 @@ class ComputePressure : public Compute {
double **vptr;
double *kspace_virial;
Compute *temperature;
char *id_temp;
double virial[6];
int keflag,pairflag,bondflag,angleflag,dihedralflag,improperflag;
int fixflag,kspaceflag;

12
src/compute_temp_sphere.cpp
View File

@ -26,6 +26,8 @@
using namespace LAMMPS_NS;
enum{DUMMY0,INVOKED_SCALAR,INVOKED_VECTOR,DUMMMY3,INVOKED_PERATOM};
#define INERTIA 0.4 // moment of inertia for sphere
/* ---------------------------------------------------------------------- */
@ -240,7 +242,10 @@ double ComputeTempSphere::compute_scalar()
invoked_scalar = update->ntimestep;
if (tempbias) {
if (tbias->invoked_scalar != update->ntimestep) tbias->compute_scalar();
if (!(tbias->invoked_flag & INVOKED_SCALAR)) {
tbias->compute_scalar();
tbias->invoked_flag |= INVOKED_SCALAR;
}
tbias->remove_bias_all();
}
@ -324,7 +329,10 @@ void ComputeTempSphere::compute_vector()
invoked_vector = update->ntimestep;
if (tempbias) {
if (tbias->invoked_vector != update->ntimestep) tbias->compute_vector();
if (!(tbias->invoked_flag & INVOKED_VECTOR)) {
tbias->compute_vector();
tbias->invoked_flag |= INVOKED_VECTOR;
}
tbias->remove_bias_all();
}

6
src/fix_box_relax.cpp
View File

@ -466,13 +466,11 @@ int FixBoxRelax::modify_param(int narg, char **arg)
if (temperature->igroup != 0 && comm->me == 0)
error->warning("Temperature for fix modify is not for group all");
// reset id_pre of pressure to new temp ID
// reset id_temp of pressure to new temp ID
icompute = modify->find_compute(id_press);
if (icompute < 0) error->all("Pressure ID for fix modify does not exist");
delete [] modify->compute[icompute]->id_pre;
modify->compute[icompute]->id_pre = new char[n];
strcpy(modify->compute[icompute]->id_pre,id_temp);
modify->compute[icompute]->reset_extra_compute(id_temp);
return 2;

40
src/fix_indent.cpp
View File

@ -30,6 +30,7 @@
using namespace LAMMPS_NS;
enum{NONE,SPHERE,CYLINDER,PLANE};
enum{INSIDE,OUTSIDE};
/* ---------------------------------------------------------------------- */
@ -48,14 +49,6 @@ FixIndent::FixIndent(LAMMPS *lmp, int narg, char **arg) :
k = atof(arg[3]);
// set defaults
istyle = NONE;
vx = vy = vz = 0.0;
radflag = 0;
r0_start = 0.0;
scaleflag = 1;
// read options from end of input line
options(narg-4,&arg[4]);
@ -198,9 +191,14 @@ void FixIndent::post_force(int vflag)
dely = x[i][1] - y1;
delz = x[i][2] - z1;
r = sqrt(delx*delx + dely*dely + delz*delz);
dr = r - r0;
if (side == OUTSIDE) {
dr = r - r0;
fmag = k*dr*dr;
} else {
dr = r0 - r;
fmag = -k*dr*dr;
}
if (dr >= 0.0) continue;
fmag = k*dr*dr;
fx = delx*fmag/r;
fy = dely*fmag/r;
fz = delz*fmag/r;
@ -255,9 +253,14 @@ void FixIndent::post_force(int vflag)
delz = 0;
}
r = sqrt(delx*delx + dely*dely + delz*delz);
dr = r - r0;
if (side == OUTSIDE) {
dr = r - r0;
fmag = k*dr*dr;
} else {
dr = r0 - r;
fmag = -k*dr*dr;
}
if (dr >= 0.0) continue;
fmag = k*dr*dr;
fx = delx*fmag/r;
fy = dely*fmag/r;
fz = delz*fmag/r;
@ -353,6 +356,13 @@ void FixIndent::options(int narg, char **arg)
{
if (narg < 0) error->all("Illegal fix indent command");
istyle = NONE;
vx = vy = vz = 0.0;
radflag = 0;
r0_start = 0.0;
scaleflag = 1;
side = OUTSIDE;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"sphere") == 0) {
@ -403,6 +413,12 @@ void FixIndent::options(int narg, char **arg)
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
else error->all("Illegal fix indent command");
iarg += 2;
} else if (strcmp(arg[iarg],"side") == 0) {
if (iarg+2 > narg) error->all("Illegal fix indent command");
if (strcmp(arg[iarg+1],"in") == 0) side = INSIDE;
else if (strcmp(arg[iarg+1],"out") == 0) side = OUTSIDE;
else error->all("Illegal fix indent command");
iarg += 2;
} else error->all("Illegal fix indent command");
}
}

2
src/fix_indent.h
View File

@ -32,7 +32,7 @@ class FixIndent : public Fix {
double compute_vector(int);
private:
int istyle,scaleflag,radflag,thermo_flag,eflag_enable;
int istyle,scaleflag,radflag,thermo_flag,eflag_enable,side;
double k,k3;
double x0,y0,z0,r0_stop,r0_start,planepos;
int indenter_flag,planeside;

6
src/fix_nph.cpp
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@ -816,13 +816,11 @@ int FixNPH::modify_param(int narg, char **arg)
if (temperature->igroup != 0 && comm->me == 0)
error->warning("Temperature for NPH is not for group all");
// reset id_pre of pressure to new temp ID
// reset id_temp of pressure to new temp ID
icompute = modify->find_compute(id_press);
if (icompute < 0) error->all("Press ID for fix npt does not exist");
delete [] modify->compute[icompute]->id_pre;
modify->compute[icompute]->id_pre = new char[n];
strcpy(modify->compute[icompute]->id_pre,id_temp);
modify->compute[icompute]->reset_extra_compute(id_temp);
return 2;

6
src/fix_npt.cpp
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@ -957,13 +957,11 @@ int FixNPT::modify_param(int narg, char **arg)
if (temperature->igroup != 0 && comm->me == 0)
error->warning("Temperature for fix modify is not for group all");
// reset id_pre of pressure to new temp ID
// reset id_temp of pressure to new temp ID
icompute = modify->find_compute(id_press);
if (icompute < 0) error->all("Pressure ID for fix modify does not exist");
delete [] modify->compute[icompute]->id_pre;
modify->compute[icompute]->id_pre = new char[n];
strcpy(modify->compute[icompute]->id_pre,id_temp);
modify->compute[icompute]->reset_extra_compute(id_temp);
return 2;

9
src/fix_press_berendsen.cpp
View File

@ -438,13 +438,12 @@ int FixPressBerendsen::modify_param(int narg, char **arg)
if (temperature->igroup != 0 && comm->me == 0)
error->warning("Temperature for NPT is not for group all");
// reset id_pre of pressure to new temp ID
// reset id_temp of pressure to new temp ID
icompute = modify->find_compute(id_press);
if (icompute < 0) error->all("Press ID for fix press/berendsen does not exist");
delete [] modify->compute[icompute]->id_pre;
modify->compute[icompute]->id_pre = new char[n];
strcpy(modify->compute[icompute]->id_pre,id_temp);
if (icompute < 0)
error->all("Press ID for fix press/berendsen does not exist");
modify->compute[icompute]->reset_extra_compute(id_temp);
return 2;

20
src/style_user_ackland.h
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@ -1,20 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef ComputeInclude
#include "compute_ackland_atom.h"
#endif
#ifdef ComputeClass
ComputeStyle(ackland/atom,ComputeAcklandAtom)
#endif

30
src/style_user_ewaldn.h
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@ -1,30 +0,0 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef KSpaceInclude
#include "ewald_n.h"
#endif
#ifdef KSpaceClass
KSpaceStyle(ewald/n,EwaldN)
#endif
#ifdef PairInclude
#include "pair_buck_coul.h"
#include "pair_lj_coul.h"
#endif
#ifdef PairClass
PairStyle(buck/coul,PairBuckCoul)
PairStyle(lj/coul,PairLJCoul)
#endif

6
src/thermo.cpp
View File

@ -380,7 +380,7 @@ void Thermo::modify_params(int narg, char **arg)
if (temperature->igroup != 0 && comm->me == 0)
error->warning("Temperature for thermo pressure is not for group all");
// reset id_pre of pressure to new temp ID
// reset id_temp of pressure to new temp ID
// either pressure currently being used by thermo or "thermo_press"
if (index_press_scalar >= 0) {
@ -391,9 +391,7 @@ void Thermo::modify_params(int narg, char **arg)
if (icompute < 0) error->all("Press ID for thermo does not exist");
} else icompute = modify->find_compute((char *) "thermo_press");
delete [] modify->compute[icompute]->id_pre;
modify->compute[icompute]->id_pre = new char[n];
strcpy(modify->compute[icompute]->id_pre,arg[iarg+1]);
modify->compute[icompute]->reset_extra_compute(arg[iarg+1]);
iarg += 2;