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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11837 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-04-29 22:21:39 +00:00
parent 08ff12cc49
commit 9c889c3f34
12 changed files with 2370 additions and 1 deletions
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1534
src/RIGID/fix_rigid_nh_small.cpp Normal file
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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifndef LMP_FIX_RIGID_NH_SMALL_H
#define LMP_FIX_RIGID_NH_SMALL_H
#include "fix_rigid_small.h"
namespace LAMMPS_NS {
class FixRigidNHSmall : public FixRigidSmall {
public:
FixRigidNHSmall(class LAMMPS *, int, char **);
virtual ~FixRigidNHSmall();
virtual int setmask();
virtual void init();
virtual void setup(int);
virtual void initial_integrate(int);
virtual void final_integrate();
virtual double compute_scalar();
int modify_param(int, char **);
void write_restart(FILE *);
void restart(char *buf);
void reset_target(double);
protected:
double boltz,nktv2p,mvv2e; // boltzman constant, conversion factors
int dimension; // # of dimensions
int nf_t,nf_r; // trans/rot degrees of freedom
double onednft,onednfr; // factors 1 + dimension/trans(rot) degrees of freedom
double *w,*wdti1,*wdti2,*wdti4; // Yoshida-Suzuki coefficients
double *q_t,*q_r; // trans/rot thermostat masses
double *eta_t,*eta_r; // trans/rot thermostat positions
double *eta_dot_t,*eta_dot_r; // trans/rot thermostat velocities
double *f_eta_t,*f_eta_r; // trans/rot thermostat forces
double epsilon_mass[3], *q_b; // baro/thermo masses
double epsilon[3],*eta_b; // baro/thermo positions
double epsilon_dot[3],*eta_dot_b; // baro/thermo velocities
double *f_eta_b; // thermo forces
double akin_t,akin_r; // translational/rotational kinetic energies
int kspace_flag; // 1 if KSpace invoked, 0 if not
int nrigidfix; // number of rigid fixes
int *rfix; // indicies of rigid fixes
double vol0; // reference volume
double t0; // reference temperature
int pdim,g_f; // number of barostatted dims, total DoFs
double p_hydro; // hydrostatic target pressure
double p_freq_max; // maximum barostat frequency
double mtk_term1,mtk_term2; // Martyna-Tobias-Klein corrections
double t_target,t_current;
double t_freq;
char *id_temp,*id_press;
class Compute *temperature,*pressure;
int tcomputeflag,pcomputeflag;
void couple();
void remap();
void nhc_temp_integrate();
void nhc_press_integrate();
virtual void compute_temp_target();
void compute_press_target();
void nh_epsilon_dot();
void allocate_chain();
void allocate_order();
void deallocate_chain();
void deallocate_order();
void no_squish_rotate(int, double *, double *, double *, double);
inline double maclaurin_series(double);
};
inline double FixRigidNHSmall::maclaurin_series(double x)
{
double x2,x4;
x2 = x * x;
x4 = x2 * x2;
return (1.0 + (1.0/6.0) * x2 + (1.0/120.0) * x4 + (1.0/5040.0) * x2 * x4 +
(1.0/362880.0) * x4 * x4);
}
}
#endif
/* ERROR/WARNING messages:
E: Fix rigid npt/nph period must be > 0.0
Self-explanatory.
E: Invalid fix rigid npt/nph command for a 2d simulation
Cannot control z dimension in a 2d model.
E: Invalid fix rigid npt/nph command pressure settings
If multiple dimensions are coupled, those dimensions must be
specified.
E: Cannot use fix rigid npt/nph on a non-periodic dimension
When specifying a diagonal pressure component, the dimension must be
periodic.
E: Invalid fix rigid npt/nph pressure settings
Settings for coupled dimensions must be the same.
E: Fix rigid nvt/npt/nph damping parameters must be > 0.0
Self-explanatory.
E: Fix rigid npt/nph dilate group ID does not exist
Self-explanatory.
E: Temp ID for fix rigid npt/nph does not exist
Specified compute temperature must be valid.
E: fix rigid npt/nph does not yet allow triclinic box
Self-explanatory.
E: Cannot use fix rigid npt/nph and fix deform on same component of stress tensor
This would be changing the same box dimension twice.
E: Press ID for fix rigid npt/nph does not exist
Specified compute pressure must be valid.
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Could not find fix_modify temperature ID
The compute ID for computing temperature does not exist.
E: Fix_modify temperature ID does not compute temperature
The compute ID assigned to the fix must compute temperature.
W: Temperature for fix modify is not for group all
The temperature compute is being used with a pressure calculation
which does operate on group all, so this may be inconsistent.
E: Pressure ID for fix modify does not exist
Self-explanatory.
E: Could not find fix_modify pressure ID
The compute ID for computing pressure does not exist.
E: Fix_modify pressure ID does not compute pressure
The compute ID assigned to the fix must compute pressure.
U: Target temperature for fix rigid nvt/npt cannot be 0.0
Self-explanatory.
U: Temperature ID for fix rigid npt/nph does not exist
Self-explanatory.
U: Pressure ID for fix rigid npt/nph does not exist
Self-explanatory.
*/

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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Dac Nguyen (ORNL)
references: Kamberaj et al., J. Chem. Phys. 122, 224114 (2005)
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
#include "string.h"
#include "fix_rigid_nph_small.h"
#include "domain.h"
#include "modify.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixRigidNPHSmall::FixRigidNPHSmall(LAMMPS *lmp, int narg, char **arg) :
FixRigidNHSmall(lmp, narg, arg)
{
// other setting are made by parent
scalar_flag = 1;
restart_global = 1;
box_change_size = 1;
extscalar = 1;
// error checks
if (pstat_flag == 0)
error->all(FLERR,"Pressure control must be used with fix nph");
if (tstat_flag == 1)
error->all(FLERR,"Temperature control must not be used with fix nph");
if (p_start[0] < 0.0 || p_start[1] < 0.0 || p_start[2] < 0.0 ||
p_stop[0] < 0.0 || p_stop[1] < 0.0 || p_stop[2] < 0.0)
error->all(FLERR,"Target pressure for fix rigid/nph cannot be 0.0");
// convert input periods to frequency
p_freq[0] = p_freq[1] = p_freq[2] = 0.0;
if (p_flag[0]) p_freq[0] = 1.0 / p_period[0];
if (p_flag[1]) p_freq[1] = 1.0 / p_period[1];
if (p_flag[2]) p_freq[2] = 1.0 / p_period[2];
// create a new compute temp style
// id = fix-ID + temp
// compute group = all since pressure is always global (group all)
// and thus its KE/temperature contribution should use group all
int n = strlen(id) + 6;
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
delete [] newarg;
tcomputeflag = 1;
// create a new compute pressure style
// id = fix-ID + press, compute group = all
// pass id_temp as 4th arg to pressure constructor
n = strlen(id) + 7;
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = (char *) "all";
newarg[2] = (char *) "pressure";
newarg[3] = id_temp;
modify->add_compute(4,newarg);
delete [] newarg;
pcomputeflag = 1;
}

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/* ----------------------------------------------------------------------
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 FIX_CLASS
FixStyle(rigid/nph/small,FixRigidNPHSmall)
#else
#ifndef LMP_FIX_RIGID_NPH_SMALL_H
#define LMP_FIX_RIGID_NPH_SMALL_H
#include "fix_rigid_nh_small.h"
namespace LAMMPS_NS {
class FixRigidNPHSmall : public FixRigidNHSmall {
public:
FixRigidNPHSmall(class LAMMPS *, int, char **);
~FixRigidNPHSmall() {}
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Pressure control must be used with fix rigid nph/small
UNDOCUMENTED
E: Temperature control must not be used with fix rigid/nph/small
UNDOCUMENTED
E: Target pressure for fix rigid/nph/small cannot be 0.0
UNDOCUMENTED
*/

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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Dac Nguyen (ORNL)
references: Kamberaj et al., J. Chem. Phys. 122, 224114 (2005)
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
#include "string.h"
#include "fix_rigid_npt_small.h"
#include "domain.h"
#include "modify.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixRigidNPTSmall::FixRigidNPTSmall(LAMMPS *lmp, int narg, char **arg) :
FixRigidNHSmall(lmp, narg, arg)
{
// other setting are made by parent
scalar_flag = 1;
restart_global = 1;
box_change_size = 1;
extscalar = 1;
// error checks
if (tstat_flag == 0 || pstat_flag == 0)
error->all(FLERR,"Did not set temp or press for fix rigid/npt/small");
if (t_start <= 0.0 || t_stop <= 0.0)
error->all(FLERR,"Target temperature for fix rigid/npt/small cannot be 0.0");
if (p_start[0] < 0.0 || p_start[1] < 0.0 || p_start[2] < 0.0 ||
p_stop[0] < 0.0 || p_stop[1] < 0.0 || p_stop[2] < 0.0)
error->all(FLERR,"Target pressure for fix rigid/npt/small cannot be 0.0");
if (t_period <= 0.0) error->all(FLERR,"Fix rigid/npt/small period must be > 0.0");
// thermostat chain parameters
if (t_chain < 1) error->all(FLERR,"Illegal fix_modify command");
if (t_iter < 1) error->all(FLERR,"Illegal fix_modify command");
if (t_order != 3 && t_order != 5)
error->all(FLERR,"Fix_modify order must be 3 or 5");
// convert input periods to frequency
t_freq = 0.0;
p_freq[0] = p_freq[1] = p_freq[2] = 0.0;
t_freq = 1.0 / t_period;
if (p_flag[0]) p_freq[0] = 1.0 / p_period[0];
if (p_flag[1]) p_freq[1] = 1.0 / p_period[1];
if (p_flag[2]) p_freq[2] = 1.0 / p_period[2];
// create a new compute temp style
// id = fix-ID + temp
// compute group = all since pressure is always global (group all)
// and thus its KE/temperature contribution should use group all
int n = strlen(id) + 6;
id_temp = new char[n];
strcpy(id_temp,id);
strcat(id_temp,"_temp");
char **newarg = new char*[3];
newarg[0] = id_temp;
newarg[1] = (char *) "all";
newarg[2] = (char *) "temp";
modify->add_compute(3,newarg);
delete [] newarg;
tcomputeflag = 1;
// create a new compute pressure style
// id = fix-ID + press, compute group = all
// pass id_temp as 4th arg to pressure constructor
n = strlen(id) + 7;
id_press = new char[n];
strcpy(id_press,id);
strcat(id_press,"_press");
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = (char *) "all";
newarg[2] = (char *) "pressure";
newarg[3] = id_temp;
modify->add_compute(4,newarg);
delete [] newarg;
pcomputeflag = 1;
}

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/* ----------------------------------------------------------------------
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 FIX_CLASS
FixStyle(rigid/npt/small,FixRigidNPTSmall)
#else
#ifndef LMP_FIX_RIGID_NPT_SMALL_H
#define LMP_FIX_RIGID_NPT_SMALL_H
#include "fix_rigid_nh_small.h"
namespace LAMMPS_NS {
class FixRigidNPTSmall : public FixRigidNHSmall {
public:
FixRigidNPTSmall(class LAMMPS *, int, char **);
~FixRigidNPTSmall() {}
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Did not set temp or press for fix rigid/npt/small
UNDOCUMENTED
E: Target temperature for fix rigid/npt/small cannot be 0.0
UNDOCUMENTED
E: Target pressure for fix rigid/npt/small cannot be 0.0
UNDOCUMENTED
E: Fix rigid/npt/small period must be > 0.0
UNDOCUMENTED
E: Illegal ... command
UNDOCUMENTED
E: Fix_modify order must be 3 or 5
UNDOCUMENTED
*/

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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Dac Nguyen (ORNL)
references: Kamberaj et al., J. Chem. Phys. 122, 224114 (2005)
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
#include "fix_rigid_nve_small.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixRigidNVESmall::FixRigidNVESmall(LAMMPS *lmp, int narg, char **arg) :
FixRigidNHSmall(lmp, narg, arg) {}

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/* ----------------------------------------------------------------------
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 FIX_CLASS
FixStyle(rigid/nve/small,FixRigidNVESmall)
#else
#ifndef LMP_FIX_RIGID_NVE_SMALL_H
#define LMP_FIX_RIGID_NVE_SMALL_H
#include "fix_rigid_nh_small.h"
namespace LAMMPS_NS {
class FixRigidNVESmall : public FixRigidNHSmall {
public:
FixRigidNVESmall(class LAMMPS *, int, char **);
~FixRigidNVESmall() {}
};
}
#endif
#endif

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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Trung Dac Nguyen (ORNL)
references: Kamberaj et al., J. Chem. Phys. 122, 224114 (2005)
Miller et al., J Chem Phys. 116, 8649-8659 (2002)
------------------------------------------------------------------------- */
#include "fix_rigid_nvt_small.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixRigidNVTSmall::FixRigidNVTSmall(LAMMPS *lmp, int narg, char **arg) :
FixRigidNHSmall(lmp, narg, arg)
{
// other settings are made by parent
scalar_flag = 1;
restart_global = 1;
extscalar = 1;
// error checking
// convert input period to frequency
if (tstat_flag == 0)
error->all(FLERR,"Did not set temp for fix rigid/nvt/small");
if (t_start < 0.0 || t_stop <= 0.0)
error->all(FLERR,"Target temperature for fix rigid/nvt/small cannot be 0.0");
if (t_period <= 0.0) error->all(FLERR,"Fix rigid/nvt/small period must be > 0.0");
t_freq = 1.0 / t_period;
if (t_chain < 1) error->all(FLERR,"Fix rigid nvt/small t_chain should not be less than 1");
if (t_iter < 1) error->all(FLERR,"Fix rigid nvt/small t_iter should not be less than 1");
if (t_order != 3 && t_order != 5)
error->all(FLERR,"Fix rigid nvt/small t_order must be 3 or 5");
}

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/* ----------------------------------------------------------------------
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 FIX_CLASS
FixStyle(rigid/nvt/small,FixRigidNVTSmall)
#else
#ifndef LMP_FIX_RIGID_NVT_SMALL_H
#define LMP_FIX_RIGID_NVT_SMALL_H
#include "fix_rigid_nh_small.h"
namespace LAMMPS_NS {
class FixRigidNVTSmall : public FixRigidNHSmall {
public:
FixRigidNVTSmall(class LAMMPS *, int, char **);
~FixRigidNVTSmall() {}
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Did not set temp for fix rigid/nvt/small
UNDOCUMENTED
E: Target temperature for fix rigid/nvt/small cannot be 0.0
UNDOCUMENTED
E: Fix rigid/nvt/small period must be > 0.0
UNDOCUMENTED
E: Illegal ... command
UNDOCUMENTED
E: Fix_modify order must be 3 or 5
UNDOCUMENTED
*/

135
src/RIGID/fix_rigid_small.cpp
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@ -59,6 +59,9 @@ FixRigidSmall *FixRigidSmall::frsptr;
#define DELTA_BODY 10000 #define DELTA_BODY 10000
enum{NONE,XYZ,XY,YZ,XZ}; // same as in FixRigid
enum{ISO,ANISO,TRICLINIC}; // same as in FixRigid
enum{FULL_BODY,INITIAL,FINAL,FORCE_TORQUE,VCM_ANGMOM,XCM_MASS,ITENSOR,DOF}; enum{FULL_BODY,INITIAL,FINAL,FORCE_TORQUE,VCM_ANGMOM,XCM_MASS,ITENSOR,DOF};
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -125,6 +128,23 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
infile = NULL; infile = NULL;
onemol = NULL; onemol = NULL;
tstat_flag = 0;
pstat_flag = 0;
allremap = 1;
id_dilate = NULL;
t_chain = 10;
t_iter = 1;
t_order = 3;
p_chain = 10;
pcouple = NONE;
pstyle = ANISO;
for (int i = 0; i < 3; i++) {
p_start[i] = p_stop[i] = p_period[i] = 0.0;
p_flag[i] = 0;
}
int iarg = 4; int iarg = 4;
while (iarg < narg) { while (iarg < narg) {
if (strcmp(arg[iarg],"langevin") == 0) { if (strcmp(arg[iarg],"langevin") == 0) {
@ -159,6 +179,121 @@ FixRigidSmall::FixRigidSmall(LAMMPS *lmp, int narg, char **arg) :
"fix rigid/small has multiple molecules"); "fix rigid/small has multiple molecules");
onemol = atom->molecules[imol]; onemol = atom->molecules[imol];
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg],"temp") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(style,"rigid/nvt/small") != 0 &&
strcmp(style,"rigid/npt/small") != 0)
error->all(FLERR,"Illegal fix rigid command");
tstat_flag = 1;
t_start = force->numeric(FLERR,arg[iarg+1]);
t_stop = force->numeric(FLERR,arg[iarg+2]);
t_period = force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"iso") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(style,"rigid/npt/small") != 0 &&
strcmp(style,"rigid/nph/small") != 0)
error->all(FLERR,"Illegal fix rigid/small command");
pcouple = XYZ;
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
p_period[0] = p_period[1] = p_period[2] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (domain->dimension == 2) {
p_start[2] = p_stop[2] = p_period[2] = 0.0;
p_flag[2] = 0;
}
iarg += 4;
} else if (strcmp(arg[iarg],"aniso") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(style,"rigid/npt/small") != 0 &&
strcmp(style,"rigid/nph/small") != 0)
error->all(FLERR,"Illegal fix rigid/small command");
p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
p_period[0] = p_period[1] = p_period[2] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
if (domain->dimension == 2) {
p_start[2] = p_stop[2] = p_period[2] = 0.0;
p_flag[2] = 0;
}
iarg += 4;
} else if (strcmp(arg[iarg],"x") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
p_start[0] = force->numeric(FLERR,arg[iarg+1]);
p_stop[0] = force->numeric(FLERR,arg[iarg+2]);
p_period[0] = force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"y") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
p_start[1] = force->numeric(FLERR,arg[iarg+1]);
p_stop[1] = force->numeric(FLERR,arg[iarg+2]);
p_period[1] = force->numeric(FLERR,arg[iarg+3]);
p_flag[1] = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"z") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
p_start[2] = force->numeric(FLERR,arg[iarg+1]);
p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
p_period[2] = force->numeric(FLERR,arg[iarg+3]);
p_flag[2] = 1;
iarg += 4;
} else if (strcmp(arg[iarg],"couple") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(arg[iarg+1],"xyz") == 0) pcouple = XYZ;
else if (strcmp(arg[iarg+1],"xy") == 0) pcouple = XY;
else if (strcmp(arg[iarg+1],"yz") == 0) pcouple = YZ;
else if (strcmp(arg[iarg+1],"xz") == 0) pcouple = XZ;
else if (strcmp(arg[iarg+1],"none") == 0) pcouple = NONE;
else error->all(FLERR,"Illegal fix rigid/small command");
iarg += 2;
} else if (strcmp(arg[iarg],"dilate") == 0) {
if (iarg+2 > narg)
error->all(FLERR,"Illegal fix rigid/small nvt/npt/nph command");
if (strcmp(arg[iarg+1],"all") == 0) allremap = 1;
else {
allremap = 0;
delete [] id_dilate;
int n = strlen(arg[iarg+1]) + 1;
id_dilate = new char[n];
strcpy(id_dilate,arg[iarg+1]);
int idilate = group->find(id_dilate);
if (idilate == -1)
error->all(FLERR,"Fix rigid/small nvt/npt/nph dilate group ID "
"does not exist");
}
iarg += 2;
} else if (strcmp(arg[iarg],"tparam") == 0) {
if (iarg+4 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(style,"rigid/nvt/small") != 0 &&
strcmp(style,"rigid/npt/small") != 0)
error->all(FLERR,"Illegal fix rigid/small command");
t_chain = force->numeric(FLERR,arg[iarg+1]);
t_iter = force->numeric(FLERR,arg[iarg+2]);
t_order = force->numeric(FLERR,arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"pchain") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix rigid/small command");
if (strcmp(style,"rigid/npt/small") != 0 &&
strcmp(style,"rigid/nph/small") != 0)
error->all(FLERR,"Illegal fix rigid/small command");
p_chain = force->numeric(FLERR,arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix rigid/small command"); } else error->all(FLERR,"Illegal fix rigid/small command");
} }

17
src/RIGID/fix_rigid_small.h
View File

@ -97,6 +97,7 @@ class FixRigidSmall : public Fix {
double ez_space[3]; double ez_space[3];
double angmom[3]; // space-frame angular momentum of body double angmom[3]; // space-frame angular momentum of body
double omega[3]; // space-frame omega of body double omega[3]; // space-frame omega of body
double conjqm[4]; // conjugate quaternion momentum
imageint image; // image flags of xcm imageint image; // image flags of xcm
int remapflag[4]; // PBC remap flags int remapflag[4]; // PBC remap flags
int ilocal; // index of owning atom int ilocal; // index of owning atom
@ -151,6 +152,22 @@ class FixRigidSmall : public Fix {
int maxlang; // max size of langextra int maxlang; // max size of langextra
class RanMars *random; // RNG class RanMars *random; // RNG
int tstat_flag,pstat_flag; // 0/1 = no/yes thermostat/barostat
int t_chain,t_iter,t_order;
double p_start[3],p_stop[3];
double p_period[3],p_freq[3];
int p_flag[3];
int pcouple,pstyle;
int p_chain;
int allremap; // remap all atoms
int dilate_group_bit; // mask for dilation group
char *id_dilate; // group name to dilate
double p_current[3],p_target[3];
// molecules added on-the-fly as rigid bodies // molecules added on-the-fly as rigid bodies
class Molecule *onemol; class Molecule *onemol;