2nd set of updates

doc/src/fix_modify.txt

@@ -23,7 +23,7 @@ keyword = {temp} or {press} or {energy} or {virial} or {respa} or {dynamic/dof}
   {dynamic/dof} value = {yes} or {no}
     yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature
   {bodyforces} value = {early} or {late}
-    early/late = compute per-rigid-body forces and torques at post_force (early) or at final_integrate (late) :pre
+    early/late = compute rigid-body forces/torques early or late in the timestep :pre
 :ule
 
 [Examples:]
@@ -86,9 +86,8 @@ if you want virial contribution of the fix to be part of the
 relaxation criteria, although this seems unlikely.
 
 NOTE: This option is only supported by fixes that explicitly say
-so. For some of these (e.g. the
+so. For some of these (e.g. the "fix shake"_fix_shake.html command)
-"fix shake"_fix_shake.html command) the default setting is
+the default setting is {virial yes}, for others it is {virial no}.
-{virial yes}, for others it is {virial no}.
 
 For fixes that set or modify forces, it may be possible to select at
 which "r-RESPA"_run_style.html level the fix operates via the {respa}
@@ -122,22 +121,27 @@ compute to calculate temperature.  See the "compute_modify
 dynamic/dof"_compute_modify.html command for a similar way to insure
 correct temperature normalization for those thermostats.
 
-The {bodyforces} keyword determines whether the resultant forces and
+The {bodyforces} keyword determines whether the forces and torques
-torques acting on rigid bodies are computed at the post-force stage of
+acting on rigid bodies are computed {early} at the post-force stage of
-a time step (i.e. right after per-atom forces have been computed and
+each timestep (right after per-atom forces have been computed and
-communicated among processors) or at the final-integrate stage (i.e.
+communicated among processors), or {late} at the final-integrate stage
-after all other fixes have finished their post-force tasks). This option
+of each timestep (after any other fixes have finished their post-force
-applies for "fix rigid"_fix_rigid.html and "fix rigid/small"_fix_rigid.html,
+tasks).  Only the rigid-body integration fixes use this option, which
-along with their nve, nvt, npt, and nph versions. It also applies for
+includes "fix rigid"_fix_rigid.html and "fix
-"fix poems"_fix_poems.html. Few fix styles actually do post-force
+rigid/small"_fix_rigid.html, and their variants, and also "fix
-tasks. Some of them cause modifications in the computed per-atoms forces
+poems"_fix_poems.html.
-(e.g. "fix addforce"_fix_addforce.html, "fix setforce"_fix_setforce.html,
+
-"fix spring"_fix_spring.html, "fix shake"_fix_shake.html, and
+The default is {late}.  If there are other fixes that add forces to
-"fix rattle"_fix_shake.html). These tasks are executed sequentially for
+individual atoms, then the rigid-body constraints will include these
-each fix, following the order of their definitions in the input script.
+forces when time-integrating the rigid bodies.  If {early} is
-Therefore, once the {bodyforces} keyword is set as {early} for a given
+specified, then new fixes can be written that use or modify the
-rigid-style fix, per-atom force modifications done by other fixes defined
+per-body force and torque, before time-integration of the rigid bodies
-afterwards will have no effect on the per-body forces/torques it computes.
+occurs.  Note however this has the side effect, that fixes such as
+"fix addforce"_fix_addforce.html, "fix setforce"_fix_setforce.html,
+"fix spring"_fix_spring.html, which add forces to individual atoms
+will have no effect on the motion of the rigid bodies if they are
+specified in the input script after the fix rigid command.  LAMMPS
+will give a warning if that is the case.
 
 [Restrictions:] none
 
@@ -149,4 +153,5 @@ pressure"_compute_pressure.html, "thermo_style"_thermo_style.html
 [Default:]
 
 The option defaults are temp = ID defined by fix, press = ID defined
-by fix, energy = no, virial = varies by fix style, respa = 0, bodyforces = late.
+by fix, energy = no, virial = different for each fix style, respa = 0,
+bodyforce = late.

doc/src/fix_poems.txt

@@ -105,17 +105,19 @@ off, and there is only a single fix poems defined.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
-The "fix_modify"_fix_modify.html {bodyforces} option is supported by
-this fix style to set whether per-body forces and torques are
-computed early or late in a time step, i.e., at the post-force stage
-or at the final-integrate stage, respectively.
-
 No information about this fix is written to "binary restart
-files"_restart.html. No global or per-atom quantities are stored
+files"_restart.html.  
-by this fix for access by various "output
+
-commands"_Section_howto.html#howto_15.  No parameter of this fix can
+The "fix_modify"_fix_modify.html {bodyforces} option is supported by
-be used with the {start/stop} keywords of the "run"_run.html command.
+this fix style to set whether per-body forces and torques are computed
-This fix is not invoked during "energy minimization"_minimize.html.
+early or late in a timestep, i.e. at the post-force stage or at the
+final-integrate stage, respectively.
+
+No global or per-atom quantities are stored by this fix for access by
+various "output commands"_Section_howto.html#howto_15.  No parameter
+of this fix can be used with the {start/stop} keywords of the
+"run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
 
 [Restrictions:]
 

doc/src/fix_rigid.txt

@@ -223,10 +223,10 @@ via several options.
 
 NOTE: With the {rigid/small} styles, which require that {bodystyle} be
 specified as {molecule} or {custom}, you can define a system that has
-no rigid bodies initially.  This is useful when you are using the {mol}
+no rigid bodies initially.  This is useful when you are using the
-keyword in conjunction with another fix that is adding rigid bodies
+{mol} keyword in conjunction with another fix that is adding rigid
-on-the-fly as molecules, such as "fix deposit"_fix_deposit.html or
+bodies on-the-fly as molecules, such as "fix deposit"_fix_deposit.html
-"fix pour"_fix_pour.html.
+or "fix pour"_fix_pour.html.
 
 For bodystyle {single} the entire fix group of atoms is treated as one
 rigid body.  This option is only allowed for the {rigid} styles.
@@ -744,8 +744,8 @@ instantaneous temperature.
 
 The "fix_modify"_fix_modify.html {bodyforces} option is supported by
 all rigid styles to set whether per-body forces and torques are
-computed early or late in a time step, i.e., at the post-force stage
+computed early or late in a timestep, i.e. at the post-force stage or
-or at the final-integrate stage, respectively.
+at the final-integrate stage or the timestep, respectively.
 
 The 2 NVE rigid fixes compute a global scalar which can be accessed by
 various "output commands"_Section_howto.html#howto_15.  The scalar

src/RIGID/fix_rigid.cpp

@@ -174,7 +174,8 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
         MPI_Allreduce(&vmin,&minval,1,MPI_INT,MPI_MIN,world);
         molecule = new tagint[nlocal];
         for (i = 0; i < nlocal; i++)
-          if (mask[i] & groupbit) molecule[i] = (tagint)((tagint)value[i] - minval + 1);
+          if (mask[i] & groupbit) 
+            molecule[i] = (tagint)((tagint)value[i] - minval + 1);
         delete[] value;
       } else error->all(FLERR,"Unsupported fix rigid custom property");
     } else {
@@ -624,7 +625,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
 
   setupflag = 0;
 
-  // compute per body forces and torques inside final_integrate() by default
+  // compute per body forces and torques at final_integrate() by default
 
   earlyflag = 0;
 
@@ -688,29 +689,12 @@ 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;
   mask |= INITIAL_INTEGRATE;
   mask |= FINAL_INTEGRATE;
-  mask |= POST_FORCE;
+  if (langflag || earlyflag) mask |= POST_FORCE;
   mask |= PRE_NEIGHBOR;
   mask |= INITIAL_INTEGRATE_RESPA;
   mask |= FINAL_INTEGRATE_RESPA;
@@ -732,19 +716,25 @@ void FixRigid::init()
   avec_tri = (AtomVecTri *) atom->style_match("tri");
 
   // warn if more than one rigid fix
+  // if earlyflag, warn if any post-force fixes come after POEMS fix
 
   int count = 0;
-  int myindex, myposition;
   for (i = 0; i < modify->nfix; i++)
-    if (strcmp(modify->fix[i]->style,"rigid") == 0) {
+    if (modify->fix[i]->rigid_flag) count++;
-      count++;
+  if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid");
-      if (strcmp(modify->fix[i]->id,this->id) == 0) {
+
-        myindex = i;
+  if (earlyflag) {
-        myposition = count;
+    int rflag = 0;
+    for (i = 0; i < modify->nfix; i++) {
+      if (modify->fix[i]->rigid_flag) rflag = 1;
+      if (rflag && (modify->fmask[i] & POST_FORCE) && 
+          !modify->fix[i]->rigid_flag) {
+        char str[128];
+        sprintf(str,"Fix %d alters forces after fix rigid",modify->fix[i]->id);
+        error->warning(FLERR,str);
       }
     }
-  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
 
@@ -758,29 +748,6 @@ void FixRigid::init()
         error->all(FLERR,"Rigid fix must come before NPT/NPH fix");
   }
 
-  // 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 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);
-          }
-        }
-    }
-  }
-
   // timestep info
 
   dtv = update->dt;
@@ -993,7 +960,7 @@ void FixRigid::initial_integrate(int vflag)
    apply Langevin thermostat to all 6 DOF of rigid bodies
    computed by proc 0, broadcast to other procs
    unlike fix langevin, this stores extra force in extra arrays,
-     which are added in when one calculates a new fcm/torque
+     which are added in when final_integrate() calculates a new fcm/torque
 ------------------------------------------------------------------------- */
 
 void FixRigid::apply_langevin_thermostat()
@@ -1063,6 +1030,7 @@ void FixRigid::enforce2d()
 void FixRigid::compute_forces_and_torques()
 {
   int i,ibody;
+  double dtfm;
 
   // sum over atoms to get force and torque on rigid body
 
@@ -1125,6 +1093,7 @@ void FixRigid::compute_forces_and_torques()
   }
 }
 
+
 /* ---------------------------------------------------------------------- */
 
 void FixRigid::post_force(int vflag)
@@ -2660,6 +2629,21 @@ void FixRigid::zero_rotation()
   set_v();
 }
 
+/* ---------------------------------------------------------------------- */
+
+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;
+}
+
 /* ----------------------------------------------------------------------
    return temperature of collection of rigid bodies
    non-active DOF are removed by fflag/tflag and in tfactor

src/RIGID/fix_rigid.h

@@ -28,7 +28,6 @@ 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);
@@ -55,6 +54,7 @@ class FixRigid : public Fix {
   void reset_dt();
   void zero_momentum();
   void zero_rotation();
+  virtual int modify_param(int, char **);
   virtual void *extract(const char*, int &);
   double extract_ke();
   double extract_erotational();
@@ -70,7 +70,7 @@ 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 earlyflag;            // 1 if forces/torques computed at post_force()
 
   int dimension;            // # of dimensions
   int nbody;                // # of rigid bodies
@@ -146,7 +146,7 @@ class FixRigid : public Fix {
   void setup_bodies_static();
   void setup_bodies_dynamic();
   void apply_langevin_thermostat();
-  virtual void compute_forces_and_torques();
+  void compute_forces_and_torques();
   void readfile(int, double *, double **, double **, double **,
                 imageint *, int *);
 };

src/RIGID/fix_rigid_nh.cpp

@@ -591,9 +591,9 @@ void FixRigidNH::initial_integrate(int vflag)
 
 void FixRigidNH::final_integrate()
 {
-  int ibody;
+  int i,ibody;
   double tmp,scale_t[3],scale_r;
-  double dtfm;
+  double dtfm,xy,xz,yz;
   double mbody[3],tbody[3],fquat[4];
 
   double dtf2 = dtf * 2.0;
@@ -1249,7 +1249,9 @@ int FixRigidNH::modify_param(int narg, char **arg)
     if (pressure->pressflag == 0)
       error->all(FLERR,"Fix_modify pressure ID does not compute pressure");
     return 2;
-  } else return FixRigid::modify_param(narg,arg);
+  }
+
+  return FixRigid::modify_param(narg,arg);
 }
 
 /* ---------------------------------------------------------------------- */

src/RIGID/fix_rigid_nh_small.cpp

@@ -618,7 +618,7 @@ void FixRigidNHSmall::initial_integrate(int vflag)
 
 void FixRigidNHSmall::final_integrate()
 {
-  int ibody;
+  int i,ibody;
   double tmp,scale_t[3],scale_r;
   double dtfm;
   double mbody[3],tbody[3],fquat[4];
@@ -1367,7 +1367,9 @@ 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;
-  } else return FixRigidSmall::modify_param(narg,arg);
+  }
+
+  return FixRigidSmall::modify_param(narg,arg);
 }
 
 /* ---------------------------------------------------------------------- */

src/RIGID/fix_rigid_small.cpp

@@ -535,29 +535,12 @@ 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;
   mask |= INITIAL_INTEGRATE;
   mask |= FINAL_INTEGRATE;
-  mask |= POST_FORCE;
+  if (langflag || earlyflag) mask |= POST_FORCE;
   mask |= PRE_NEIGHBOR;
   mask |= INITIAL_INTEGRATE_RESPA;
   mask |= FINAL_INTEGRATE_RESPA;
@@ -575,17 +558,22 @@ 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) {
+    if (modify->fix[i]->rigid_flag) count++;
-      count++;
+  if (count > 1 && me == 0) error->warning(FLERR,"More than one fix rigid");
-      if (strcmp(modify->fix[i]->id,this->id) == 0) {
+
-        myindex = i;
+  if (earlyflag) {
-        myposition = count;
+    int rflag = 0;
+    for (i = 0; i < modify->nfix; i++) {
+      if (modify->fix[i]->rigid_flag) rflag = 1;
+      if (rflag && (modify->fmask[i] & POST_FORCE) && 
+          !modify->fix[i]->rigid_flag) {
+        char str[128];
+        sprintf(str,"Fix %d alters forces after fix rigid",modify->fix[i]->id);
+        error->warning(FLERR,str);
       }
     }
-  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
 
@@ -599,29 +587,6 @@ void FixRigidSmall::init()
         error->all(FLERR,"Rigid fix must come before NPT/NPH fix");
   }
 
-  // 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 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);
-          }
-        }
-    }
-  }
-
   // timestep info
 
   dtv = update->dt;
@@ -822,10 +787,10 @@ void FixRigidSmall::initial_integrate(int vflag)
 /* ----------------------------------------------------------------------
    apply Langevin thermostat to all 6 DOF of rigid bodies I own
    unlike fix langevin, this stores extra force in extra arrays,
-     which are added in when one calculates a new fcm/torque
+     which are added in when a new fcm/torque are calculated
 ------------------------------------------------------------------------- */
 
-void FixRigidSmall::apply_langevin_thermostat()
+void FixRigidSmall::apply_langevin_thermostat(int vflag)
 {
   double gamma1,gamma2;
 
@@ -984,13 +949,6 @@ void FixRigidSmall::compute_forces_and_torques()
   }
 }
 
-/* ---------------------------------------------------------------------- */
-
-void FixRigidSmall::post_force(int vflag)
-{
-  if (langflag) apply_langevin_thermostat();
-  if (earlyflag) compute_forces_and_torques();
-}
 
 /* ---------------------------------------------------------------------- */
 
@@ -3454,6 +3412,21 @@ void FixRigidSmall::zero_rotation()
 
 /* ---------------------------------------------------------------------- */
 
+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;
+}
+
+/* ---------------------------------------------------------------------- */
+
 void *FixRigidSmall::extract(const char *str, int &dim)
 {
   if (strcmp(str,"body") == 0) {

src/RIGID/fix_rigid_small.h

@@ -33,7 +33,6 @@ 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);
@@ -64,6 +63,7 @@ class FixRigidSmall : public Fix {
   void reset_dt();
   void zero_momentum();
   void zero_rotation();
+  int modify_param(int, char **);
   void *extract(const char*, int &);
   double extract_ke();
   double extract_erotational();
@@ -79,7 +79,7 @@ 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 earlyflag;            // 1 if forces/torques are computed at post_force()
   int commflag;             // various modes of forward/reverse comm
   int customflag;           // 1 if custom property/variable define bodies
   int nbody;                // total # of rigid bodies
@@ -194,7 +194,7 @@ class FixRigidSmall : public Fix {
   void setup_bodies_static();
   void setup_bodies_dynamic();
   void apply_langevin_thermostat();
-  virtual void compute_forces_and_torques();
+  void compute_forces_and_torques();
   void readfile(int, double **, int *);
   void grow_body();
   void reset_atom2body();

src/USER-OMP/fix_rigid_omp.h

@@ -45,4 +45,3 @@ class FixRigidOMP : public FixRigid {
 
 #endif
 #endif
-

src/USER-OMP/fix_rigid_small_omp.cpp

@@ -618,3 +618,4 @@ void FixRigidSmallOMP::set_v_thr()
     }
   }
 }
+