git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11643 f3b2605a-c512-4ea7-a41b-209d697bcdaa

tools/msi2lmp/README

@@ -1,5 +1,23 @@
-Stephanie Teich-McGoldrick (Sandai) is the current maintainer
+Axel Kohlmeyer is the current maintainer of the msi2lmp tool.
-of the msi2lmp tool.  She can be contacted at steichm at sandia.gov
+Please send any inquiries about msi2lmp to the lammps-users mailing list.
+
+06 Mar 2014 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Fixed a bug in handling of triclinic cells, where the matrices to
+convert to and from fractional coordinates were incorrectly built.
+
+26 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Implemented writing out force field style hints in generated data
+files for improved consistency checking when reading those files.
+Also added writing out CGCMM style comments to identify atom types.
+
+08 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Fixed a memory access violation with Class 2 force fields.
+Free all allocated memory to better detection of memory errors.
+Print out version number and data with all print levels > 0.
+Added valgrind checks to the regression tests
 
 08 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>
 
@@ -99,6 +117,9 @@ see msi2lmp/TriclinicModification.pdf doc for details
                           geometrical center of the provided geometry but
                           rather around the origin
 
+   -- -oldstyle (or -o)   write out a data file without style hints
+                          (to be compatible with older LAMMPS versions)
+
    -- -shift (or -s)      translate the entire system (box and coordinates)
                           by a vector (default: 0.0 0.0 0.0)
 

tools/msi2lmp/src/WriteDataFile.c

@@ -83,7 +83,14 @@ void WriteDataFile(char *nameroot)
 
   /* COEFFICIENTS */
 
-  fprintf(DatF,"Pair Coeffs\n\n");
+  fputs("Pair Coeffs",DatF);
+  if (hintflag) {
+      if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA))
+          fputs(" # lj/cut/coul/long\n\n",DatF);
+      else if (forcefield & FF_TYPE_CLASS2)
+          fputs(" # lj/class2/coul/long\n\n",DatF);
+  } else fputs("\n\n",DatF);
+
   for (i=0; i < no_atom_types; i++) {
     fprintf(DatF, " %3i ", i+1);
     for ( j = 0; j < 2; j++)
@@ -98,7 +105,14 @@ void WriteDataFile(char *nameroot)
     if (forcefield & FF_TYPE_OPLSAA) m = 2;
     if (forcefield & FF_TYPE_CLASS2) m = 4;
 
-    fprintf(DatF,"Bond Coeffs\n\n");
+    fputs("Bond Coeffs",DatF);
+    if (hintflag) {
+        if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA))
+            fputs(" # harmonic\n\n",DatF);
+        else if (forcefield & FF_TYPE_CLASS2)
+            fputs(" # class2\n\n",DatF);
+    } else fputs("\n\n",DatF);
+
     for (i=0; i < no_bond_types; i++) {
       fprintf(DatF, "%3i ", i+1);
       for ( j = 0; j < m; j++)
@@ -114,7 +128,14 @@ void WriteDataFile(char *nameroot)
     if (forcefield & FF_TYPE_OPLSAA) m = 2;
     if (forcefield & FF_TYPE_CLASS2) m = 4;
 
-    fprintf(DatF,"Angle Coeffs\n\n");
+    fputs("Angle Coeffs",DatF);
+    if (hintflag) {
+        if (forcefield & (FF_TYPE_CLASS1|FF_TYPE_OPLSAA))
+            fputs(" # harmonic\n\n",DatF);
+        else if (forcefield & FF_TYPE_CLASS2)
+            fputs(" # class2\n\n",DatF);
+    } else fputs("\n\n",DatF);
+    
     for (i=0; i < no_angle_types; i++) {
       fprintf(DatF, "%3i ", i+1);
       for ( j = 0; j < m; j++)
@@ -127,81 +148,91 @@ void WriteDataFile(char *nameroot)
 
   if (no_dihedral_types > 0) {
 
-    if (forcefield & FF_TYPE_CLASS1) {
+      fputs("Dihedral Coeffs",DatF);
+      if (forcefield & FF_TYPE_CLASS1) {
 
-      fprintf(DatF,"Dihedral Coeffs\n\n");
+          if (hintflag) fputs(" # harmonic\n\n",DatF);
+          else fputs("\n\n",DatF);
 
-      for (i=0; i < no_dihedral_types; i++)
+          for (i=0; i < no_dihedral_types; i++)
-        fprintf(DatF, "%3i %10.4f %3i %3i\n", i+1,
+              fprintf(DatF, "%3i %10.4f %3i %3i\n", i+1,
-                dihedraltypes[i].params[0],
+                      dihedraltypes[i].params[0],
-                (int) dihedraltypes[i].params[1],
+                      (int) dihedraltypes[i].params[1],
-                (int) dihedraltypes[i].params[2]);
+                      (int) dihedraltypes[i].params[2]);
 
-    } else if (forcefield & FF_TYPE_OPLSAA) {
+      } else if (forcefield & FF_TYPE_OPLSAA) {
 
-      fprintf(DatF,"Dihedral Coeffs\n\n");
+          if (hintflag) fputs(" # opls\n\n",DatF);
+          else fputs("\n\n",DatF);
 
-      for (i=0; i < no_dihedral_types; i++) {
+          for (i=0; i < no_dihedral_types; i++) {
-        fprintf(DatF, "%3i",i+1);
+              fprintf(DatF, "%3i",i+1);
-        for ( j = 0; j < 4; j++)
+              for ( j = 0; j < 4; j++)
-          fprintf(DatF, " %10.4f",dihedraltypes[i].params[j]);
+                  fprintf(DatF, " %10.4f",dihedraltypes[i].params[j]);
 
-        fputs("\n",DatF);
+              fputs("\n",DatF);
+          }
+      } else if (forcefield & FF_TYPE_CLASS2) {
+
+          if (hintflag) fputs(" # class2\n\n",DatF);
+          else fputs("\n\n",DatF);
+
+          for (i=0; i < no_dihedral_types; i++) {
+              fprintf(DatF, "%3i",i+1);
+              for ( j = 0; j < 6; j++)
+                  fprintf(DatF, " %10.4f",dihedraltypes[i].params[j]);
+
+              fputs("\n",DatF);
+          }
       }
-    } else if (forcefield & FF_TYPE_CLASS2) { 
+      fputs("\n",DatF);
-
-      fprintf(DatF,"Dihedral Coeffs\n\n");
-
-      for (i=0; i < no_dihedral_types; i++) {
-        fprintf(DatF, "%3i",i+1);
-        for ( j = 0; j < 6; j++)
-          fprintf(DatF, " %10.4f",dihedraltypes[i].params[j]);
-
-        fputs("\n",DatF);
-      }
-    }
-    fputs("\n",DatF);
   }
 
   if (forcefield & FF_TYPE_CLASS1) {
-    if (no_oop_types > 0) {
+      if (no_oop_types > 0) {
-      /* cvff improper coeffs are: type K0 d n */
+          /* cvff improper coeffs are: type K0 d n */
-      fprintf(DatF,"Improper Coeffs\n\n");
+          if (hintflag) fputs("Improper Coeffs # cvff\n\n",DatF);
-      for (i=0; i < no_oop_types; i++) {
+          else fputs("Improper Coeffs\n\n",DatF);
-        fprintf(DatF,"%5i %10.4f %3i %3i\n",i+1,
+
-                ooptypes[i].params[0], (int) ooptypes[i].params[1],
+          for (i=0; i < no_oop_types; i++) {
-                (int) ooptypes[i].params[2]);
+              fprintf(DatF,"%5i %10.4f %3i %3i\n",i+1,
+                      ooptypes[i].params[0], (int) ooptypes[i].params[1],
+                      (int) ooptypes[i].params[2]);
+          }
+          fputs("\n",DatF);
       }
-      fputs("\n",DatF);
-    }
   } else if (forcefield & FF_TYPE_OPLSAA) {
-    if (no_oop_types > 0) {
+      if (no_oop_types > 0) {
-      /* opls improper coeffs are like cvff: type K0 d(=-1) n(=2) */
+          /* opls improper coeffs are like cvff: type K0 d(=-1) n(=2) */
-      fprintf(DatF,"Improper Coeffs\n\n");
+          if (hintflag) fputs("Improper Coeffs # cvff\n\n",DatF);
-      for (i=0; i < no_oop_types; i++) {
+          else fputs("Improper Coeffs\n\n",DatF);
-        fprintf(DatF,"%5i %10.4f %3i %3i\n",i+1,
+
-                ooptypes[i].params[0], (int) ooptypes[i].params[1],
+          for (i=0; i < no_oop_types; i++) {
-                (int) ooptypes[i].params[2]);
+              fprintf(DatF,"%5i %10.4f %3i %3i\n",i+1,
+                      ooptypes[i].params[0], (int) ooptypes[i].params[1],
+                      (int) ooptypes[i].params[2]);
+          }
+          fputs("\n",DatF);
       }
-      fputs("\n",DatF);
-    }
   } else if (forcefield & FF_TYPE_CLASS2) {
-    if ((no_oop_types + no_angleangle_types) > 0) {
+      if ((no_oop_types + no_angleangle_types) > 0) {
-      fprintf(DatF,"Improper Coeffs\n\n");
+          if (hintflag) fputs("Improper Coeffs # class2\n\n",DatF);
-      for (i=0; i < no_oop_types; i++) {
+          else fputs("Improper Coeffs\n\n",DatF);
-        fprintf(DatF, "%3i ", i+1);
+
-        for ( j = 0; j < 2; j++)
+          for (i=0; i < no_oop_types; i++) {
-          fprintf(DatF, "%10.4f ", ooptypes[i].params[j]);
+              fprintf(DatF, "%3i ", i+1);
-        fputs("\n",DatF);
+              for ( j = 0; j < 2; j++)
+                  fprintf(DatF, "%10.4f ", ooptypes[i].params[j]);
+              fputs("\n",DatF);
+          }
+          for (i=0; i < no_angleangle_types; i++) {
+              fprintf(DatF, "%3i ", i+no_oop_types+1);
+              for ( j = 0; j < 2; j++)
+                  fprintf(DatF, "%10.4f ", 0.0);
+              fputs("\n",DatF);
+          }
+          fputs("\n",DatF);
       }
-      for (i=0; i < no_angleangle_types; i++) {
-        fprintf(DatF, "%3i ", i+no_oop_types+1);
-        for ( j = 0; j < 2; j++)
-          fprintf(DatF, "%10.4f ", 0.0);
-        fputs("\n",DatF);
-      }
-      fputs("\n",DatF);
-    }
   }
 
   if (forcefield & FF_TYPE_CLASS2) {
@@ -302,19 +333,23 @@ void WriteDataFile(char *nameroot)
 
   /* ATOMS */
 
-  fprintf(DatF, "Atoms\n\n");
+  if (hintflag) fputs("Atoms # full\n\n",DatF);
+  else fputs("Atoms\n\n",DatF);
+
   for(k=0; k < total_no_atoms; k++) {
-    fprintf(DatF, " %6i %6i %3i %9.6f %15.9f %15.9f %15.9f %3i %3i %3i\n",
+    int typ = atoms[k].type;
+    fprintf(DatF," %6i %6i %3i %9.6f %15.9f %15.9f %15.9f %3i %3i %3i # %s\n",
             k+1,
             atoms[k].molecule,
-            atoms[k].type+1,
+            typ+1,
             atoms[k].q,
             atoms[k].x[0],
             atoms[k].x[1],
             atoms[k].x[2],
             atoms[k].image[0],
             atoms[k].image[1],
-            atoms[k].image[2]);
+            atoms[k].image[2],
+            atomtypes[typ].potential);
   }
   fputs("\n",DatF);
 

tools/msi2lmp/src/msi2lmp.c

@@ -2,6 +2,8 @@
 *
 *  msi2lmp.exe
 *
+*   v3.9.4 AK- Make force field style hints optional with a flag
+*
 *   v3.9.3 AK- Bugfix for triclinic cells.
 *
 *   v3.9.2 AK- Support for writing out force field style hints
@@ -51,7 +53,7 @@
 *  The program is started by supplying information at the command prompt
 * according to the usage described below.
 *
-*  USAGE: msi2lmp3 ROOTNAME {-print #} {-class #} {-frc FRC_FILE} {-ignore} {-nocenter}
+*  USAGE: msi2lmp3 ROOTNAME {-print #} {-class #} {-frc FRC_FILE} {-ignore} {-nocenter} {-oldstyle}
 *
 *  -- msi2lmp3 is the name of the executable
 *  -- ROOTNAME is the base name of the .car and .mdf files
@@ -73,6 +75,9 @@
 *  -- -nocenter - tells msi2lmp to not center the box around the (geometrical)
 *                 center of the atoms, but around the origin
 *
+*  -- -oldstyle - tells msi2lmp to write out a data file without style hints
+*                 (to be compatible with older LAMMPS versions)
+*
 *  -- -shift    - tells msi2lmp to shift the entire system (box and coordinates)
 *                 by a vector (default: 0.0 0.0 0.0)
 *
@@ -148,6 +153,7 @@ int    periodic = 1;
 int    TriclinicFlag = 0;
 int    forcefield = 0;
 int    centerflag = 1;
+int    hintflag = 1;
 
 int    pflag;
 int    iflag;
@@ -219,7 +225,7 @@ int main (int argc, char *argv[])
   frc_dir_name = getenv("MSI2LMP_LIBRARY");
 
   if (argc < 2) {
-    printf("usage: %s <rootname> [-class <I|1|II|2>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter]\n",argv[0]);
+    printf("usage: %s <rootname> [-class <I|1|II|2>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle]\n",argv[0]);
     return 1;
   } else { /* rootname was supplied as first argument, copy to rootname */
     int len = strlen(argv[1]) + 1;
@@ -258,8 +264,10 @@ int main (int argc, char *argv[])
       shift[2] = atof(argv[++n]);
     } else if (strncmp(argv[n],"-i",2) == 0 ) {
       iflag = 1;
-    } else if (strncmp(argv[n],"-n",2) == 0 ) {
+    } else if (strncmp(argv[n],"-n",4) == 0 ) {
       centerflag = 0;
+    } else if (strncmp(argv[n],"-o",4) == 0 ) {
+      hintflag = 0;
     } else if (strncmp(argv[n],"-p",2) == 0) {
       n++;
       if (check_arg(argv,"-print",n,argc))
@@ -333,6 +341,10 @@ int main (int argc, char *argv[])
     if (forcefield & FF_TYPE_CLASS2) puts(" Forcefield: Class II");
     if (forcefield & FF_TYPE_OPLSAA) puts(" Forcefield: OPLS-AA");
     printf(" Forcefield file name: %s\n",FrcFileName);
+    if (centerflag) puts(" Output is recentered around geometrical center");
+    if (hintflag) puts(" Output contains style flag hints");
+    else puts(" Style flag hints disabled");
+    printf(" System translated by: %g %g %g\n",shift[0],shift[1],shift[2]); 
   }
 
   n = 0;

tools/msi2lmp/src/msi2lmp.h

@@ -36,7 +36,7 @@
 
 # include <stdio.h>
 
-#define MSI2LMP_VERSION "v3.9.3 / 07 Mar 2014"
+#define MSI2LMP_VERSION "v3.9.4 / 11 Mar 2014"
 
 #define PI_180  0.01745329251994329576
 
@@ -171,6 +171,7 @@ extern int    TriclinicFlag; /* 0= Orthogonal  1= Triclinic */
 extern int    forcefield;    /* BitMask: the value FF_TYPE_COMMON is set for common components of the options below,
                               * FF_TYPE_CLASS1 = ClassI,  FF_TYPE_CLASS2 = ClassII, FF_TYPE_OPLSAA = OPLS-AA*/
 extern int    centerflag;    /* 1= center box  0= keep box */
+extern int    hintflag;      /* 1= print style hint comments  0= no hints */
 extern int    pflag;         /* print level: 0, 1, 2, 3 */
 extern int    iflag;         /* 0 stop at errors   1 = ignore errors */
 extern int    *no_atoms;