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Keyword 'bodyforces' added to fix_modify command

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- Applies to classes FixRigid, FixRigidSmall, and FixPOEMS
This commit is contained in:
Charlles Abreu
2017-09-01 00:16:54 -03:00
parent 251bc882cf
commit 6e945f72f4
7 changed files with 182 additions and 98 deletions
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83
src/POEMS/fix_poems.cpp
View File

@ -280,6 +280,10 @@ FixPOEMS::FixPOEMS(LAMMPS *lmp, int narg, char **arg) :
fprintf(logfile,"%d clusters, %d bodies, %d joints, %d atoms\n",
ncluster,nbody,njoint,nsum);
}
// compute per body forces and torques inside final_integrate() by default
earlyflag = 0;
}
/* ----------------------------------------------------------------------
@ -330,6 +334,25 @@ FixPOEMS::~FixPOEMS()
/* ---------------------------------------------------------------------- */
int FixPOEMS::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"bodyforces") == 0) {
if (narg < 2)
error->all(FLERR,"Illegal fix_modify command");
if (strcmp(arg[1],"early") == 0)
earlyflag = 1;
else if (strcmp(arg[1],"late") == 0)
earlyflag = 0;
else
error->all(FLERR,"Illegal fix_modify command");
return 2;
}
else
return 0;
}
/* ---------------------------------------------------------------------- */
int FixPOEMS::setmask()
{
int mask = 0;
@ -352,9 +375,17 @@ void FixPOEMS::init()
// warn if more than one POEMS fix
int count = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"poems") == 0) count++;
if (count > 1 && comm->me == 0) error->warning(FLERR,"More than one fix poems");
int myindex, myposition;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"poems") == 0) {
count++;
if (strcmp(modify->fix[i]->id,id) != 0) {
myindex = i;
myposition = count;
}
}
if (count > 1 && myposition == 1 && comm->me == 0)
error->warning(FLERR,"More than one fix poems");
// error if npt,nph fix comes before rigid fix
@ -368,21 +399,26 @@ void FixPOEMS::init()
error->all(FLERR,"POEMS fix must come before NPT/NPH fix");
}
// warn if any non-rigid fix with post_force succeeds any fix rigid:
int first_rigid = 0;
while (!modify->fix[first_rigid]->rigid_flag)
first_rigid++;
count = 0;
for (i = first_rigid + 1; i < modify->nfix; i++) {
Fix *ifix = modify->fix[i];
if ( (modify->fmask[i] & POST_FORCE) && (!ifix->rigid_flag) ) {
count++;
if (comm->me == 0) {
if (count == 1)
error->warning(FLERR,"The following fixes must preceed any rigid-body fixes");
if (screen) fprintf(screen,"> fix %s %s\n",ifix->id,ifix->style);
if (logfile) fprintf(logfile,"> fix %s %s\n",ifix->id,ifix->style);
}
// warn if fix poems preceeds non-rigid fixes with post-force tasks
// when computing body forces and torques in post_force() instead of final_integrate()
if (earlyflag) {
int has_post_force[modify->nfix - myindex];
count = 0;
for (i = myindex + 1; i < modify->nfix; i++)
if ( (modify->fmask[i] & POST_FORCE) && (!modify->fix[i]->rigid_flag) )
has_post_force[count++] = i;
if (count) {
FILE *p[2] = {screen, logfile};
for (int j = 0; j < 2; j++)
if (p[j]) {
fprintf(p[j],"WARNING: fix %s %s",id,style);
fprintf(p[j]," will add up forces before they are handled by:\n");
for (int k = 0; k < count; k++) {
Fix *fix = modify->fix[has_post_force[k]];
fprintf(p[j]," => fix %s %s\n",fix->id,fix->style);
}
}
}
}
@ -747,7 +783,7 @@ void FixPOEMS::initial_integrate(int vflag)
only count joint atoms in 1st body
------------------------------------------------------------------------- */
void FixPOEMS::post_force(int vflag)
void FixPOEMS::compute_forces_and_torques()
{
int i,ibody;
int xbox,ybox,zbox;
@ -798,6 +834,13 @@ void FixPOEMS::post_force(int vflag)
}
}
/* ---------------------------------------------------------------------- */
void FixPOEMS::post_force(int vflag)
{
if (earlyflag) compute_forces_and_torques();
}
/* ----------------------------------------------------------------------
update vcm,omega by last 1/2 step
set v of body atoms accordingly
@ -805,6 +848,8 @@ void FixPOEMS::post_force(int vflag)
void FixPOEMS::final_integrate()
{
if (!earlyflag) compute_forces_and_torques();
// perform POEMS integration
poems->LobattoTwo(vcm,omega,torque,fcm);

4
src/POEMS/fix_poems.h
View File

@ -28,6 +28,7 @@ class FixPOEMS : public Fix {
public:
FixPOEMS(class LAMMPS *, int narg, char **arg);
~FixPOEMS();
int modify_param(int, char **);
int setmask();
void init();
void setup(int);
@ -56,6 +57,8 @@ class FixPOEMS : public Fix {
int nlevels_respa;
double total_ke;
int earlyflag; // 1 if forces and torques are computed at post_force()
// atom assignment to rigid bodies
// double count joint atoms as being in multiple bodies
@ -96,6 +99,7 @@ class FixPOEMS : public Fix {
// internal class functions
void compute_forces_and_torques();
void readfile(char *);
int readline(FILE *, char **, int *);
void jointbuild();

86
src/RIGID/fix_rigid.cpp
View File

@ -639,6 +639,25 @@ FixRigid::~FixRigid()
/* ---------------------------------------------------------------------- */
int FixRigid::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"bodyforces") == 0) {
if (narg < 2)
error->all(FLERR,"Illegal fix_modify command");
if (strcmp(arg[1],"early") == 0)
earlyflag = 1;
else if (strcmp(arg[1],"late") == 0)
earlyflag = 0;
else
error->all(FLERR,"Illegal fix_modify command");
return 2;
}
else
return 0;
}
/* ---------------------------------------------------------------------- */
int FixRigid::setmask()
{
int mask = 0;
@ -668,9 +687,17 @@ void FixRigid::init()
// warn if more than one rigid fix
int count = 0;
int myindex, myposition;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"rigid") == 0) count++;
if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid");
if (strcmp(modify->fix[i]->style,"rigid") == 0) {
count++;
if (strcmp(modify->fix[i]->id,id) != 0) {
myindex = i;
myposition = count;
}
}
if (count > 1 && myposition == 1 && comm->me == 0)
error->warning(FLERR,"More than one fix rigid");
// error if npt,nph fix comes before rigid fix
@ -684,25 +711,26 @@ void FixRigid::init()
error->all(FLERR,"Rigid fix must come before NPT/NPH fix");
}
// warn if any non-rigid fix with post_force succeeds any fix rigid instance
// warn if fix rigid preceeds non-rigid fixes with post-force tasks
// when computing body forces and torques in post_force() instead of final_integrate()
if (earlyflag) {
int first_rigid = 0;
while (!modify->fix[first_rigid]->rigid_flag)
first_rigid++;
int has_post_force[modify->nfix - myindex];
count = 0;
for (i = first_rigid + 1; i < modify->nfix; i++) {
Fix *ifix = modify->fix[i];
if ( (modify->fmask[i] & POST_FORCE) && (!ifix->rigid_flag) ) {
count++;
if (comm->me == 0) {
if (count == 1)
error->warning(FLERR,"The following fixes must preceed any rigid-body fixes");
if (screen) fprintf(screen,"> fix %s %s\n",ifix->id,ifix->style);
if (logfile) fprintf(logfile,"> fix %s %s\n",ifix->id,ifix->style);
for (i = myindex + 1; i < modify->nfix; i++)
if ( (modify->fmask[i] & POST_FORCE) && (!modify->fix[i]->rigid_flag) )
has_post_force[count++] = i;
if (count) {
FILE *p[2] = {screen, logfile};
for (int j = 0; j < 2; j++)
if (p[j]) {
fprintf(p[j],"WARNING: fix %s %s",id,style);
fprintf(p[j]," will add up forces before they are handled by:\n");
for (int k = 0; k < count; k++) {
Fix *fix = modify->fix[has_post_force[k]];
fprintf(p[j]," => fix %s %s\n",fix->id,fix->style);
}
}
}
}
}
@ -1054,8 +1082,10 @@ void FixRigid::compute_forces_and_torques()
void FixRigid::post_force(int vflag)
{
if (langflag) apply_langevin_thermostat();
if (earlyflag) compute_forces_and_torques();
if (earlyflag) {
if (langflag) apply_langevin_thermostat();
compute_forces_and_torques();
}
}
/* ---------------------------------------------------------------------- */
@ -1065,7 +1095,10 @@ void FixRigid::final_integrate()
int ibody;
double dtfm;
if (!earlyflag) compute_forces_and_torques();
if (!earlyflag) {
if (langflag) apply_langevin_thermostat();
compute_forces_and_torques();
}
// update vcm and angmom
// fflag,tflag = 0 for some dimensions in 2d
@ -2701,18 +2734,3 @@ double FixRigid::compute_array(int i, int j)
if (j == 13) return (imagebody[i] >> IMGBITS & IMGMASK) - IMGMAX;
return (imagebody[i] >> IMG2BITS) - IMGMAX;
}
/* ---------------------------------------------------------------------- */
int FixRigid::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"bodyforces") == 0) {
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
if (strcmp(arg[1],"early") == 0) earlyflag=1;
else if (strcmp(arg[1],"late") == 0) earlyflag=0;
else error->all(FLERR,"Illegal fix_modify command");
return 2;
}
return 0;
}

4
src/RIGID/fix_rigid.h
View File

@ -28,6 +28,7 @@ class FixRigid : public Fix {
public:
FixRigid(class LAMMPS *, int, char **);
virtual ~FixRigid();
int modify_param(int, char **);
virtual int setmask();
virtual void init();
virtual void setup(int);
@ -38,7 +39,6 @@ class FixRigid : public Fix {
void final_integrate_respa(int, int);
void write_restart_file(char *);
virtual double compute_scalar();
virtual int modify_param(int, char **);
double memory_usage();
void grow_arrays(int);
@ -72,6 +72,7 @@ class FixRigid : public Fix {
char *infile; // file to read rigid body attributes from
int rstyle; // SINGLE,MOLECULE,GROUP
int setupflag; // 1 if body properties are setup, else 0
int earlyflag; // 1 if forces and torques are computed at post_force()
int dimension; // # of dimensions
int nbody; // # of rigid bodies
@ -107,7 +108,6 @@ class FixRigid : public Fix {
int orientflag; // 1 if particles store spatial orientation
int dorientflag; // 1 if particles store dipole orientation
int reinitflag; // 1 if re-initialize rigid bodies between runs
int earlyflag; // 1 if compute body forces and torques early, i.e. in post_force()
imageint *xcmimage; // internal image flags for atoms in rigid bodies
// set relative to in-box xcm of each body

5
src/RIGID/fix_rigid_nh_small.cpp
View File

@ -1438,9 +1438,8 @@ int FixRigidNHSmall::modify_param(int narg, char **arg)
if (pressure->pressflag == 0)
error->all(FLERR,"Fix_modify pressure ID does not compute pressure");
return 2;
}
return 0;
} else
return FixRigidSmall::modify_param(narg,arg);
}
/* ---------------------------------------------------------------------- */

92
src/RIGID/fix_rigid_small.cpp
View File

@ -481,6 +481,25 @@ FixRigidSmall::~FixRigidSmall()
/* ---------------------------------------------------------------------- */
int FixRigidSmall::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"bodyforces") == 0) {
if (narg < 2)
error->all(FLERR,"Illegal fix_modify command");
if (strcmp(arg[1],"early") == 0)
earlyflag = 1;
else if (strcmp(arg[1],"late") == 0)
earlyflag = 0;
else
error->all(FLERR,"Illegal fix_modify command");
return 2;
}
else
return 0;
}
/* ---------------------------------------------------------------------- */
int FixRigidSmall::setmask()
{
int mask = 0;
@ -504,9 +523,17 @@ void FixRigidSmall::init()
// warn if more than one rigid fix
int count = 0;
int myindex, myposition;
for (i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"rigid") == 0) count++;
if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid");
if (strcmp(modify->fix[i]->style,"rigid") == 0) {
count++;
if (strcmp(modify->fix[i]->id,id) != 0) {
myindex = i;
myposition = count;
}
}
if (count > 1 && myposition == 1 && comm->me == 0)
error->warning(FLERR,"More than one fix rigid");
// error if npt,nph fix comes before rigid fix
@ -520,27 +547,28 @@ void FixRigidSmall::init()
error->all(FLERR,"Rigid fix must come before NPT/NPH fix");
}
// warn if any non-rigid fix with post_force succeeds any fix rigid instance
// warn if fix rigid preceeds non-rigid fixes with post-force tasks
// when computing body forces and torques in post_force() instead of final_integrate()
if (earlyflag) {
int first_rigid = 0;
while (!modify->fix[first_rigid]->rigid_flag)
first_rigid++;
int has_post_force[modify->nfix - myindex];
count = 0;
for (i = first_rigid + 1; i < modify->nfix; i++) {
Fix *ifix = modify->fix[i];
if ( (modify->fmask[i] & POST_FORCE) && (!ifix->rigid_flag) ) {
count++;
if (comm->me == 0) {
if (count == 1)
error->warning(FLERR,"The following fixes must preceed any rigid-body fixes");
if (screen) fprintf(screen,"> fix %s %s\n",ifix->id,ifix->style);
if (logfile) fprintf(logfile,"> fix %s %s\n",ifix->id,ifix->style);
for (i = myindex + 1; i < modify->nfix; i++)
if ( (modify->fmask[i] & POST_FORCE) && (!modify->fix[i]->rigid_flag) )
has_post_force[count++] = i;
if (count) {
FILE *p[2] = {screen, logfile};
for (int j = 0; j < 2; j++)
if (p[j]) {
fprintf(p[j],"WARNING: fix %s %s",id,style);
fprintf(p[j]," will add up forces before they are handled by:\n");
for (int k = 0; k < count; k++) {
Fix *fix = modify->fix[has_post_force[k]];
fprintf(p[j]," => fix %s %s\n",fix->id,fix->style);
}
}
}
}
}
}
}
// timestep info
@ -908,8 +936,10 @@ void FixRigidSmall::compute_forces_and_torques()
void FixRigidSmall::post_force(int vflag)
{
if (langflag) apply_langevin_thermostat();
if (earlyflag) compute_forces_and_torques();
if (earlyflag) {
if (langflag) apply_langevin_thermostat();
compute_forces_and_torques();
}
}
/* ---------------------------------------------------------------------- */
@ -918,9 +948,12 @@ void FixRigidSmall::final_integrate()
{
double dtfm;
//check(3)
//check(3);
if (!earlyflag) compute_forces_and_torques();
if (!earlyflag) {
if (langflag) apply_langevin_thermostat();
compute_forces_and_torques();
}
// update vcm and angmom, recompute omega
@ -3510,21 +3543,6 @@ double FixRigidSmall::compute_scalar()
return tall;
}
/* ---------------------------------------------------------------------- */
int FixRigidSmall::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"bodyforces") == 0) {
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
if (strcmp(arg[1],"early") == 0) earlyflag=1;
else if (strcmp(arg[1],"late") == 0) earlyflag=0;
else error->all(FLERR,"Illegal fix_modify command");
return 2;
}
return 0;
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */

6
src/RIGID/fix_rigid_small.h
View File

@ -33,11 +33,12 @@ class FixRigidSmall : public Fix {
public:
FixRigidSmall(class LAMMPS *, int, char **);
virtual ~FixRigidSmall();
int modify_param(int, char **);
virtual int setmask();
virtual void init();
virtual void setup(int);
virtual void initial_integrate(int);
virtual void post_force(int);
void post_force(int);
virtual void final_integrate();
void initial_integrate_respa(int, int, int);
void final_integrate_respa(int, int);
@ -69,7 +70,6 @@ class FixRigidSmall : public Fix {
double extract_ke();
double extract_erotational();
double compute_scalar();
virtual int modify_param(int, char **);
double memory_usage();
protected:
@ -81,6 +81,7 @@ class FixRigidSmall : public Fix {
char *infile; // file to read rigid body attributes from
int setupflag; // 1 if body properties are setup, else 0
int earlyflag; // 1 if forces and torques are computed at post_force()
int commflag; // various modes of forward/reverse comm
int nbody; // total # of rigid bodies
int nlinear; // total # of linear rigid bodies
@ -131,7 +132,6 @@ class FixRigidSmall : public Fix {
int orientflag; // 1 if particles store spatial orientation
int dorientflag; // 1 if particles store dipole orientation
int reinitflag; // 1 if re-initialize rigid bodies between runs
int earlyflag; // 1 if compute body forces and torques early, i.e. in post_force()
int POINT,SPHERE,ELLIPSOID,LINE,TRIANGLE,DIPOLE; // bitmasks for eflags
int OMEGA,ANGMOM,TORQUE;