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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6835 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2011-08-27 20:01:42 +00:00
parent 1a4f998b04
commit 3179014485
11 changed files with 141 additions and 12 deletions
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7
src/atom.cpp
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@ -83,6 +83,10 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
eradius = ervel = erforce = NULL;
cs = csforce = vforce = ervelforce = NULL;
etag = NULL;
rho = drho = NULL;
e = de = NULL;
cv = NULL;
vest = NULL;
maxspecial = 1;
nspecial = NULL;
@ -106,12 +110,13 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
// customize by adding new flag
sphere_flag = ellipsoid_flag = peri_flag = electron_flag = 0;
wavepacket_flag = 0;
wavepacket_flag = sph_flag = 0;
molecule_flag = q_flag = mu_flag = 0;
rmass_flag = radius_flag = omega_flag = torque_flag = angmom_flag = 0;
vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
cs_flag = csforce_flag = vforce_flag = ervelforce_flag= etag_flag = 0;
rho_flag = e_flag = cv_flag = vest_flag = 0;
// ntype-length arrays

7
src/atom.h
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@ -56,6 +56,10 @@ class Atom : protected Pointers {
double *eradius,*ervel,*erforce,*ervelforce;
double *cs,*csforce,*vforce;
int *etag;
double *rho, *drho;
double *e, *de;
double **vest;
double *cv;
int **nspecial; // 0,1,2 = cummulative # of 1-2,1-3,1-4 neighs
int **special; // IDs of 1-2,1-3,1-4 neighs of each atom
@ -81,12 +85,13 @@ class Atom : protected Pointers {
// customize by adding new flag
int sphere_flag,ellipsoid_flag,peri_flag,electron_flag;
int wavepacket_flag;
int wavepacket_flag,sph_flag;
int molecule_flag,q_flag,mu_flag;
int rmass_flag,radius_flag,omega_flag,torque_flag,angmom_flag;
int vfrac_flag,spin_flag,eradius_flag,ervel_flag,erforce_flag;
int cs_flag,csforce_flag,vforce_flag,ervelforce_flag,etag_flag;
int rho_flag,e_flag,cv_flag,vest_flag;
// extra peratom info in restart file destined for fix & diag

28
src/fix_gravity.cpp
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@ -34,6 +34,9 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
if (narg < 5) error->all("Illegal fix gravity command");
time_depend = 1;
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
magnitude = atof(arg[3]);
@ -90,6 +93,9 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
}
time_origin = update->ntimestep;
eflag = 0;
egrav = 0.0;
}
/* ---------------------------------------------------------------------- */
@ -98,6 +104,7 @@ int FixGravity::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
return mask;
}
@ -155,6 +162,7 @@ void FixGravity::post_force(int vflag)
zacc = magnitude*zgrav;
}
double **x = atom->x;
double **f = atom->f;
double *rmass = atom->rmass;
double *mass = atom->mass;
@ -163,6 +171,9 @@ void FixGravity::post_force(int vflag)
int nlocal = atom->nlocal;
double massone;
eflag = 0;
egrav = 0.0;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
@ -170,6 +181,7 @@ void FixGravity::post_force(int vflag)
f[i][0] += massone*xacc;
f[i][1] += massone*yacc;
f[i][2] += massone*zacc;
egrav -= massone * (xacc*x[i][0] + yacc*x[i][1] + zacc*x[i][2]);
}
} else {
for (int i = 0; i < nlocal; i++)
@ -178,6 +190,7 @@ void FixGravity::post_force(int vflag)
f[i][0] += massone*xacc;
f[i][1] += massone*yacc;
f[i][2] += massone*zacc;
egrav -= massone * (xacc*x[i][0] + yacc*x[i][1] + zacc*x[i][2]);
}
}
}
@ -188,3 +201,18 @@ void FixGravity::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ----------------------------------------------------------------------
potential energy in gravity field
------------------------------------------------------------------------- */
double FixGravity::compute_scalar()
{
// only sum across procs one time
if (eflag == 0) {
MPI_Allreduce(&egrav,&egrav_all,1,MPI_DOUBLE,MPI_SUM,world);
eflag = 1;
}
return egrav_all;
}

3
src/fix_gravity.h
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@ -34,6 +34,7 @@ class FixGravity : public Fix {
void setup(int);
void post_force(int);
void post_force_respa(int, int, int);
double compute_scalar();
private:
int style;
@ -44,6 +45,8 @@ class FixGravity : public Fix {
double degree2rad;
int nlevels_respa;
int time_origin;
int eflag;
double egrav,egrav_all;
};
}

16
src/min.cpp
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@ -137,12 +137,16 @@ void Min::init()
ev_setup();
// set flags for what arrays to clear in force_clear()
// need to clear torques,erforce if arrays exists
// need to clear additionals arrays if they exist
torqueflag = 0;
if (atom->torque_flag) torqueflag = 1;
erforceflag = 0;
if (atom->erforce_flag) erforceflag = 1;
e_flag = 0;
if (atom->e_flag) e_flag = 1;
rho_flag = 0;
if (atom->rho_flag) rho_flag = 1;
// orthogonal vs triclinic simulation box
@ -537,6 +541,16 @@ void Min::force_clear()
double *erforce = atom->erforce;
for (i = 0; i < nall; i++) erforce[i] = 0.0;
}
if (e_flag) {
double *de = atom->de;
for (i = 0; i < nall; i++) de[i] = 0.0;
}
if (rho_flag) {
double *drho = atom->drho;
for (i = 0; i < nall; i++) drho[i] = 0.0;
}
}
/* ----------------------------------------------------------------------

3
src/min.h
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@ -60,9 +60,10 @@ class Min : protected Pointers {
class Compute **vlist_global;
class Compute **vlist_atom;
int triclinic; // 0 if domain is orthog, 1 if triclinic
int pairflag;
int torqueflag,erforceflag;
int triclinic; // 0 if domain is orthog, 1 if triclinic
int e_flag,rho_flag;
int narray; // # of arrays stored by fix_minimize
class FixMinimize *fix_minimize; // fix that stores auxiliary data

16
src/respa.cpp
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@ -278,12 +278,16 @@ void Respa::init()
ev_setup();
// set flags for what arrays to clear in force_clear()
// need to clear torques,erforce if arrays exists
// need to clear additionals arrays if they exist
torqueflag = 0;
if (atom->torque_flag) torqueflag = 1;
erforceflag = 0;
if (atom->erforce_flag) erforceflag = 1;
e_flag = 0;
if (atom->e_flag) e_flag = 1;
rho_flag = 0;
if (atom->rho_flag) rho_flag = 1;
// step[] = timestep for each level
@ -623,6 +627,16 @@ void Respa::force_clear(int newtonflag)
double *erforce = atom->erforce;
for (i = 0; i < nall; i++) erforce[i] = 0.0;
}
if (e_flag) {
double *de = atom->de;
for (i = 0; i < nall; i++) de[i] = 0.0;
}
if (rho_flag) {
double *drho = atom->drho;
for (i = 0; i < nall; i++) drho[i] = 0.0;
}
}
/* ----------------------------------------------------------------------

4
src/respa.h
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@ -53,8 +53,8 @@ class Respa : public Integrate {
private:
int triclinic; // 0 if domain is orthog, 1 if triclinic
int torqueflag; // zero out arrays every step
int erforceflag;
int torqueflag,erforceflag;
int e_flag,rho_flag;
int *newton; // newton flag at each level
class FixRespa *fix_respa; // Fix to store the force level array

29
src/set.cpp
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@ -35,7 +35,8 @@ using namespace LAMMPS_NS;
enum{ATOM_SELECT,MOL_SELECT,TYPE_SELECT,GROUP_SELECT,REGION_SELECT};
enum{TYPE,TYPE_FRACTION,MOLECULE,X,Y,Z,CHARGE,MASS,SHAPE,
DIPOLE,DIPOLE_RANDOM,QUAT,QUAT_RANDOM,
DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER};
DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER,
MESO_E,MESO_CV,MESO_RHO};
#define BIG INT_MAX
@ -271,6 +272,27 @@ void Set::command(int narg, char **arg)
error->all("Invalid value in set command");
topology(IMPROPER);
iarg += 2;
} else if (strcmp(arg[iarg],"meso_e") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->e_flag)
error->all("Cannot set this attribute for this atom style");
set(MESO_E);
iarg += 2;
} else if (strcmp(arg[iarg],"meso_cv") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->cv_flag)
error->all("Cannot set this attribute for this atom style");
set(MESO_CV);
iarg += 2;
} else if (strcmp(arg[iarg],"meso_rho") == 0) {
if (iarg+2 > narg) error->all("Illegal set command");
dvalue = atof(arg[iarg+1]);
if (!atom->rho_flag)
error->all("Cannot set meso_rho for this atom style");
set(MESO_RHO);
iarg += 2;
} else error->all("Illegal set command");
// statistics
@ -377,7 +399,10 @@ void Set::set(int keyword)
else if (keyword == MASS) atom->rmass[i] = dvalue;
else if (keyword == DIAMETER) atom->radius[i] = 0.5 * dvalue;
else if (keyword == VOLUME) atom->vfrac[i] = dvalue;
else if (keyword == MESO_E) atom->e[i] = dvalue;
else if (keyword == MESO_CV) atom->cv[i] = dvalue;
else if (keyword == MESO_RHO) atom->rho[i] = dvalue;
// set shape
else if (keyword == SHAPE)

36
src/verlet.cpp
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@ -63,12 +63,16 @@ void Verlet::init()
ev_setup();
// set flags for what arrays to clear in force_clear()
// need to clear torques,erforce if arrays exists
// need to clear additionals arrays if they exist
torqueflag = 0;
if (atom->torque_flag) torqueflag = 1;
erforceflag = 0;
if (atom->erforce_flag) erforceflag = 1;
e_flag = 0;
if (atom->e_flag) e_flag = 1;
rho_flag = 0;
if (atom->rho_flag) rho_flag = 1;
// orthogonal vs triclinic simulation box
@ -334,6 +338,16 @@ void Verlet::force_clear()
for (i = 0; i < nall; i++) erforce[i] = 0.0;
}
if (e_flag) {
double *de = atom->de;
for (i = 0; i < nall; i++) de[i] = 0.0;
}
if (rho_flag) {
double *drho = atom->drho;
for (i = 0; i < nall; i++) drho[i] = 0.0;
}
// neighbor includegroup flag is set
// clear force only on initial nfirst particles
// if either newton flag is set, also include ghosts
@ -362,6 +376,16 @@ void Verlet::force_clear()
for (i = 0; i < nall; i++) erforce[i] = 0.0;
}
if (e_flag) {
double *de = atom->de;
for (i = 0; i < nall; i++) de[i] = 0.0;
}
if (rho_flag) {
double *drho = atom->drho;
for (i = 0; i < nall; i++) drho[i] = 0.0;
}
if (force->newton) {
nall = atom->nlocal + atom->nghost;
@ -384,6 +408,16 @@ void Verlet::force_clear()
double *erforce = atom->erforce;
for (i = atom->nlocal; i < nall; i++) erforce[i] = 0.0;
}
if (e_flag) {
double *de = atom->de;
for (i = 0; i < nall; i++) de[i] = 0.0;
}
if (rho_flag) {
double *drho = atom->drho;
for (i = 0; i < nall; i++) drho[i] = 0.0;
}
}
}
}

4
src/verlet.h
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@ -36,8 +36,8 @@ class Verlet : public Integrate {
protected:
int triclinic; // 0 if domain is orthog, 1 if triclinic
int torqueflag; // zero out arrays every step
int erforceflag;
int torqueflag,erforceflag;
int e_flag,rho_flag;
void force_clear();
};