git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3568 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/compute_property_atom.cpp

@@ -249,7 +249,7 @@ void ComputePropertyAtom::compute_peratom()
     buf = vector;
     (this->*pack_choice[0])(0);
   } else {
-    buf = array[0];
+    if (array) buf = array[0];
     for (int n = 0; n < nvalues; n++)
       (this->*pack_choice[n])(n);
   }

src/compute_property_local.cpp

@@ -14,15 +14,13 @@
 #include "string.h"
 #include "compute_property_local.h"
 #include "atom.h"
+#include "atom_vec.h"
 #include "update.h"
 #include "force.h"
 #include "domain.h"
 #include "memory.h"
 #include "error.h"
 
-
-#include "comm.h"
-
 using namespace LAMMPS_NS;
 
 // customize by adding keyword
@@ -110,7 +108,7 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) :
 	error->all("Compute property/local cannot use these inputs together");
       kindflag = DIHEDRAL;
     } else if (strcmp(arg[iarg],"datom4") == 0) {
-      pack_choice[i] = &ComputePropertyLocal::pack_datom3;
+      pack_choice[i] = &ComputePropertyLocal::pack_datom4;
       if (kindflag != NONE && kindflag != DIHEDRAL) 
 	error->all("Compute property/local cannot use these inputs together");
       kindflag = DIHEDRAL;
@@ -136,7 +134,7 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) :
 	error->all("Compute property/local cannot use these inputs together");
       kindflag = IMPROPER;
     } else if (strcmp(arg[iarg],"iatom4") == 0) {
-      pack_choice[i] = &ComputePropertyLocal::pack_iatom3;
+      pack_choice[i] = &ComputePropertyLocal::pack_iatom4;
       if (kindflag != NONE && kindflag != IMPROPER) 
 	error->all("Compute property/local cannot use these inputs together");
       kindflag = IMPROPER;
@@ -149,6 +147,17 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) :
     } else error->all("Invalid keyword in compute property/local command");
   }
 
+  // error check
+
+  if (kindflag == BOND && atom->avec->bonds_allow == 0)
+    error->all("Compute property/local for property that isn't allocated");
+  if (kindflag == ANGLE && atom->avec->angles_allow == 0)
+    error->all("Compute property/local for property that isn't allocated");
+  if (kindflag == DIHEDRAL && atom->avec->dihedrals_allow == 0)
+    error->all("Compute property/local for property that isn't allocated");
+  if (kindflag == IMPROPER && atom->avec->impropers_allow == 0)
+    error->all("Compute property/local for property that isn't allocated");
+
   nmax = 0;
   vector = NULL;
   array = NULL;
@@ -207,7 +216,7 @@ void ComputePropertyLocal::compute_local()
     buf = vector;
     (this->*pack_choice[0])(0);
   } else {
-    buf = array[0];
+    if (array) buf = array[0];
     for (int n = 0; n < nvalues; n++)
       (this->*pack_choice[n])(n);
   }

src/dump.cpp

@@ -52,6 +52,7 @@ Dump::Dump(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
   format = NULL;
   format_user = NULL;
 
+  clearstep = 0;
   sort_flag = 0;
   append_flag = 0;
 

src/dump.h

@@ -37,6 +37,7 @@ class Dump : protected Pointers {
   int sort_flag;             // 1 if write in sorted order, 0 if not
   int append_flag;           // 1 if open file in append mode, 0 if not
   int singlefile_opened;     // 1 = one big file, already opened, else 0
+  int clearstep;             // 1 if dump invokes computes, 0 if not
 
   char *format_default;      // default format string
   char *format_user;         // format string set by user

src/dump_custom.cpp

@@ -51,6 +51,8 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg == 5) error->all("No dump custom arguments specified");
 
+  clearstep = 1;
+
   nevery = atoi(arg[3]);
 
   size_one = nfield = narg-5;
@@ -81,7 +83,7 @@ DumpCustom::DumpCustom(LAMMPS *lmp, int narg, char **arg) :
   variable = NULL;
   vbuf = NULL;
 
-  // process keywords
+  // process attributes
 
   parse_fields(narg,arg);
 
@@ -974,7 +976,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
       char *ptr = strchr(suffix,'[');
       if (ptr) {
 	if (suffix[strlen(suffix)-1] != ']')
-	  error->all("Invalid keyword in dump custom command");
+	  error->all("Invalid attribute in dump custom command");
 	argindex[i] = atoi(ptr+1);
 	*ptr = '\0';
       } else argindex[i] = 0;
@@ -1008,7 +1010,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
       char *ptr = strchr(suffix,'[');
       if (ptr) {
 	if (suffix[strlen(suffix)-1] != ']')
-	  error->all("Invalid keyword in dump custom command");
+	  error->all("Invalid attribute in dump custom command");
 	argindex[i] = atoi(ptr+1);
 	*ptr = '\0';
       } else argindex[i] = 0;
@@ -1048,7 +1050,7 @@ void DumpCustom::parse_fields(int narg, char **arg)
       field2index[i] = add_variable(suffix);
       delete [] suffix;
 
-    } else error->all("Invalid keyword in dump custom command");
+    } else error->all("Invalid attribute in dump custom command");
   }
 }
 
@@ -1173,7 +1175,7 @@ int DumpCustom::modify_param(int narg, char **arg)
       memory->srealloc(thresh_value,(nthresh+1)*sizeof(double),
 		       "dump:thresh_value");
 
-    // set keyword type of threshhold
+    // set attribute type of threshhold
     // customize by adding to if statement
     
     if (strcmp(arg[1],"id") == 0) thresh_array[nthresh] = ID;
@@ -1258,25 +1260,25 @@ int DumpCustom::modify_param(int narg, char **arg)
       char *ptr = strchr(suffix,'[');
       if (ptr) {
 	if (suffix[strlen(suffix)-1] != ']')
-	  error->all("Invalid keyword in dump custom command");
+	  error->all("Invalid attribute in dump modify command");
 	argindex[nfield+nthresh] = atoi(ptr+1);
 	*ptr = '\0';
       } else argindex[nfield+nthresh] = 0;
       
       n = modify->find_compute(suffix);
-      if (n < 0) error->all("Could not find dump custom compute ID");
+      if (n < 0) error->all("Could not find dump modify compute ID");
 
       if (modify->compute[n]->peratom_flag == 0)
-	error->all("Dump custom compute ID does not compute per-atom info");
+	error->all("Dump modify compute ID does not compute per-atom info");
       if (argindex[nfield+nthresh] == 0 && 
 	  modify->compute[n]->size_peratom_cols > 0)
-	error->all("Dump custom compute ID does not compute per-atom vector");
+	error->all("Dump modify compute ID does not compute per-atom vector");
       if (argindex[nfield+nthresh] > 0 && 
 	  modify->compute[n]->size_peratom_cols == 0)
-	error->all("Dump custom compute ID does not compute per-atom array");
+	error->all("Dump modify compute ID does not compute per-atom array");
       if (argindex[nfield+nthresh] > 0 && 
 	  argindex[nfield+nthresh] > modify->compute[n]->size_peratom_cols)
-	error->all("Dump custom compute ID vector is not large enough");
+	error->all("Dump modify compute ID vector is not large enough");
 
       field2index[nfield+nthresh] = add_compute(suffix);
       delete [] suffix;
@@ -1300,25 +1302,25 @@ int DumpCustom::modify_param(int narg, char **arg)
       char *ptr = strchr(suffix,'[');
       if (ptr) {
 	if (suffix[strlen(suffix)-1] != ']')
-	  error->all("Invalid keyword in dump custom command");
+	  error->all("Invalid attribute in dump modify command");
 	argindex[nfield+nthresh] = atoi(ptr+1);
 	*ptr = '\0';
       } else argindex[nfield+nthresh] = 0;
       
       n = modify->find_fix(suffix);
-      if (n < 0) error->all("Could not find dump custom fix ID");
+      if (n < 0) error->all("Could not find dump modify fix ID");
 
       if (modify->fix[n]->peratom_flag == 0)
-	error->all("Dump custom fix ID does not compute per-atom info");
+	error->all("Dump modify fix ID does not compute per-atom info");
       if (argindex[nfield+nthresh] == 0 && 
 	  modify->fix[n]->size_peratom_cols > 0)
-	error->all("Dump custom fix ID does not compute per-atom vector");
+	error->all("Dump modify fix ID does not compute per-atom vector");
       if (argindex[nfield+nthresh] > 0 && 
 	  modify->fix[n]->size_peratom_cols == 0)
-	error->all("Dump custom fix ID does not compute per-atom array");
+	error->all("Dump modify fix ID does not compute per-atom array");
       if (argindex[nfield+nthresh] > 0 && 
 	  argindex[nfield+nthresh] > modify->fix[n]->size_peratom_cols)
-	error->all("Dump custom fix ID vector is not large enough");
+	error->all("Dump modify fix ID vector is not large enough");
 
       field2index[nfield+nthresh] = add_fix(suffix);
       delete [] suffix;
@@ -1341,9 +1343,9 @@ int DumpCustom::modify_param(int narg, char **arg)
       argindex[nfield+nthresh] = 0;
       
       n = input->variable->find(suffix);
-      if (n < 0) error->all("Could not find dump custom variable name");
+      if (n < 0) error->all("Could not find dump modify variable name");
       if (input->variable->atomstyle(n) == 0)
-	error->all("Dump custom variable is not atom-style variable");
+	error->all("Dump modify variable is not atom-style variable");
 
       field2index[nfield+nthresh] = add_variable(suffix);
       delete [] suffix;
@@ -1457,9 +1459,9 @@ void DumpCustom::pack_variable(int n)
 }
 
 /* ----------------------------------------------------------------------
-   one method for every keyword dump custom can output
+   one method for every attribute dump custom can output
    the atom property is packed into buf starting at n with stride size_one
-   customize a new keyword by adding a method
+   customize a new attribute by adding a method
 ------------------------------------------------------------------------- */
 
 /* ---------------------------------------------------------------------- */

src/dump_local.cpp

@@ -24,12 +24,8 @@
 #include "memory.h"
 #include "error.h"
 
-
-#include "comm.h"
-
 using namespace LAMMPS_NS;
 
-enum{INDEX,COMPUTE,FIX};
 enum{INT,DOUBLE};
 
 #define INVOKED_LOCAL 16
@@ -41,6 +37,8 @@ DumpLocal::DumpLocal(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg == 5) error->all("No dump local arguments specified");
 
+  clearstep = 1;
+
   nevery = atoi(arg[3]);
 
   size_one = nfield = narg-5;
@@ -60,7 +58,7 @@ DumpLocal::DumpLocal(LAMMPS *lmp, int narg, char **arg) :
   id_fix = NULL;
   fix = NULL;
 
-  // process keywords
+  // process attributes
 
   parse_fields(narg,arg);
 
@@ -88,7 +86,12 @@ DumpLocal::DumpLocal(LAMMPS *lmp, int narg, char **arg) :
     strcat(columns," ");
   }
 
-  label = "BONDS";
+  // setup default label string
+
+  char *str = "ENTRIES";
+  n = strlen(str) + 1;
+  label = new char[n];
+  strcpy(label,str);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -112,6 +115,7 @@ DumpLocal::~DumpLocal()
   delete [] vformat;
 
   delete [] columns;
+  delete [] label;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -145,17 +149,17 @@ void DumpLocal::init()
   int icompute;
   for (int i = 0; i < ncompute; i++) {
     icompute = modify->find_compute(id_compute[i]);
-    if (icompute < 0) error->all("Could not find dump custom compute ID");
+    if (icompute < 0) error->all("Could not find dump local compute ID");
     compute[i] = modify->compute[icompute];
   }
 
   int ifix;
   for (int i = 0; i < nfix; i++) {
     ifix = modify->find_fix(id_fix[i]);
-    if (ifix < 0) error->all("Could not find dump custom fix ID");
+    if (ifix < 0) error->all("Could not find dump local fix ID");
     fix[i] = modify->fix[ifix];
-    if (nevery % modify->fix[ifix]->peratom_freq)
+    if (nevery % modify->fix[ifix]->local_freq)
-      error->all("Dump custom and fix not computed at compatible times");
+      error->all("Dump local and fix not computed at compatible times");
   }
 
   // open single file, one time only
@@ -165,6 +169,21 @@ void DumpLocal::init()
 
 /* ---------------------------------------------------------------------- */
 
+int DumpLocal::modify_param(int narg, char **arg)
+{
+  if (strcmp(arg[0],"label") == 0) {
+    if (narg < 2) error->all("Illegal dump_modify command");
+    delete [] label;
+    int n = strlen(arg[1]) + 1;
+    label = new char[n];
+    strcpy(label,arg[1]);
+    return 2;
+  }
+  return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
 void DumpLocal::write_header(int ndump)
 {
   if (me == 0) {
@@ -172,7 +191,7 @@ void DumpLocal::write_header(int ndump)
     fprintf(fp,"%d\n",update->ntimestep);
     fprintf(fp,"ITEM: NUMBER OF %s\n",label);
     fprintf(fp,"%d\n",ndump);
-    fprintf(fp,"ITEM: %s\n",label);
+    fprintf(fp,"ITEM: %s %s\n",label,columns);
   }
 }
 
@@ -190,11 +209,29 @@ int DumpLocal::count()
       if (!(compute[i]->invoked_flag & INVOKED_LOCAL)) {
 	compute[i]->compute_local();
 	compute[i]->invoked_flag |= INVOKED_LOCAL;
-	nmine = compute[i]->size_local_rows;
       }
     }
   }
 
+  // nmine = # of local values I contribute
+  // must be consistent for all input fields
+
+  nmine = -1;
+
+  int icompute;
+  for (int i = 0; i < ncompute; i++) {
+    if (nmine < 0) nmine = compute[i]->size_local_rows;
+    else if (nmine != compute[i]->size_local_rows)
+      error->one("Dump local count is not consistent across input fields");
+  }
+
+  int ifix;
+  for (int i = 0; i < nfix; i++) {
+    if (nmine < 0) nmine = fix[i]->size_local_rows;
+    else if (nmine != fix[i]->size_local_rows)
+      error->one("Dump local count is not consistent across input fields");
+  }
+
   return nmine;
 }
 
@@ -227,6 +264,8 @@ void DumpLocal::write_data(int n, double *buf)
 
 void DumpLocal::parse_fields(int narg, char **arg)
 {
+  int computefixflag = 0;
+
   // customize by adding to if statement
 
   int i;
@@ -241,6 +280,7 @@ void DumpLocal::parse_fields(int narg, char **arg)
     // if no trailing [], then arg is set to 0, else arg is int between []
 
     } else if (strncmp(arg[iarg],"c_",2) == 0) {
+      computefixflag = 1;
       pack_choice[i] = &DumpLocal::pack_compute;
       vtype[i] = DOUBLE;
 
@@ -251,7 +291,7 @@ void DumpLocal::parse_fields(int narg, char **arg)
       char *ptr = strchr(suffix,'[');
       if (ptr) {
 	if (suffix[strlen(suffix)-1] != ']')
-	  error->all("Invalid keyword in dump local command");
+	  error->all("Invalid attribute in dump local command");
 	argindex[i] = atoi(ptr+1);
 	*ptr = '\0';
       } else argindex[i] = 0;
@@ -275,6 +315,7 @@ void DumpLocal::parse_fields(int narg, char **arg)
     // if no trailing [], then arg is set to 0, else arg is between []
 
     } else if (strncmp(arg[iarg],"f_",2) == 0) {
+      computefixflag = 1;
       pack_choice[i] = &DumpLocal::pack_fix;
       vtype[i] = DOUBLE;
 
@@ -285,7 +326,7 @@ void DumpLocal::parse_fields(int narg, char **arg)
       char *ptr = strchr(suffix,'[');
       if (ptr) {
 	if (suffix[strlen(suffix)-1] != ']')
-	  error->all("Invalid keyword in dump local command");
+	  error->all("Invalid attribute in dump local command");
 	argindex[i] = atoi(ptr+1);
 	*ptr = '\0';
       } else argindex[i] = 0;
@@ -305,8 +346,11 @@ void DumpLocal::parse_fields(int narg, char **arg)
       field2index[i] = add_fix(suffix);
       delete [] suffix;
 
-    } else error->all("Invalid keyword in dump local command");
+    } else error->all("Invalid attribute in dump local command");
   }
+
+  if (computefixflag == 0)
+    error->all("Dump local attributes contain no compute or fix");
 }
 
 /* ----------------------------------------------------------------------
@@ -407,9 +451,9 @@ void DumpLocal::pack_fix(int n)
 }
 
 /* ----------------------------------------------------------------------
-   one method for every keyword dump local can output
+   one method for every attribute dump local can output
    the local value is packed into buf starting at n with stride size_one
-   customize a new keyword by adding a method
+   customize a new attribute by adding a method
 ------------------------------------------------------------------------- */
 
 /* ---------------------------------------------------------------------- */

src/dump_local.h

@@ -48,8 +48,7 @@ class DumpLocal : public Dump {
   char **id_fix;             // their IDs
   class Fix **fix;           // list of ptrs to the Fix objects
 
-  // private methods
+  int modify_param(int, char **);
-
   void write_header(int);
   int count();
   int pack();

src/output.cpp

@@ -137,10 +137,7 @@ void Output::setup(int flag)
 
   if (ndump && update->restrict_output == 0) {
     for (int idump = 0; idump < ndump; idump++) {
-      if (strcmp(dump[idump]->style,"custom") == 0 ||
+      if (dump[idump]->clearstep) modify->clearstep_compute();
-	  strcmp(dump[idump]->style,"cfg") == 0 ||
-	  strcmp(dump[idump]->style,"local") == 0)
-	modify->clearstep_compute();
       if ((ntimestep % dump_every[idump] == 0 && 
 	  last_dump[idump] != ntimestep) || last_dump[idump] < 0) {
 	dump[idump]->write();
@@ -148,10 +145,7 @@ void Output::setup(int flag)
       }
       next_dump[idump] = 
 	(ntimestep/dump_every[idump])*dump_every[idump] + dump_every[idump];
-      if (strcmp(dump[idump]->style,"custom") == 0 ||
+      if (dump[idump]->clearstep) modify->addstep_compute(next_dump[idump]);
-	  strcmp(dump[idump]->style,"cfg") == 0 ||
-	  strcmp(dump[idump]->style,"local") == 0)
-	modify->addstep_compute(next_dump[idump]);
       if (idump) next_dump_any = MYMIN(next_dump_any,next_dump[idump]);
       else next_dump_any = next_dump[0];
     }
@@ -208,17 +202,11 @@ void Output::write(int ntimestep)
   if (next_dump_any == ntimestep) {
     for (int idump = 0; idump < ndump; idump++) {
       if (next_dump[idump] == ntimestep && last_dump[idump] != ntimestep) {
-        if (strcmp(dump[idump]->style,"custom") == 0 ||
+        if (dump[idump]->clearstep) modify->clearstep_compute();
-	    strcmp(dump[idump]->style,"cfg") == 0 ||
-	    strcmp(dump[idump]->style,"local") == 0)
-          modify->clearstep_compute();
 	dump[idump]->write();
 	last_dump[idump] = ntimestep;
 	next_dump[idump] += dump_every[idump];
-        if (strcmp(dump[idump]->style,"custom") == 0 ||
+        if (dump[idump]->clearstep) modify->addstep_compute(next_dump[idump]);
-	    strcmp(dump[idump]->style,"cfg") == 0 ||
-	    strcmp(dump[idump]->style,"local") == 0)
-	  modify->addstep_compute(next_dump[idump]);
       }
       if (idump) next_dump_any = MYMIN(next_dump_any,next_dump[idump]);
       else next_dump_any = next_dump[0];