Keyword 'bodyforces' added to fix_modify command (6e945f72) · Commits · 郑智淋 / lammps

src/POEMS/fix_poems.cpp

+64 −19

Original line number	Diff line number	Diff line
		@@ -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

		@@ -368,20 +399,25 @@ 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++;
		// 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 = 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);
		}
		}
		}
		}
		@@ -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);

src/POEMS/fix_poems.h

+4 −0

Original line number	Diff line number	Diff line
		@@ -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();

src/RIGID/fix_rigid.cpp

+52 −34

Original line number	Diff line number	Diff line
		@@ -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

		@@ -684,23 +711,24 @@ 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 (earlyflag) {
		if (langflag) apply_langevin_thermostat();
		if (earlyflag) compute_forces_and_torques();
		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;
		}

src/RIGID/fix_rigid.h

+2 −2

Original line number	Diff line number	Diff line
		@@ -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

src/RIGID/fix_rigid_nh_small.cpp

+2 −3

Original line number	Diff line number	Diff line
		@@ -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);
		}

		/* ---------------------------------------------------------------------- */

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