Merge pull request #199 from akohlmey/small-changes

Collected small changes and bugfixes

examples/USER/quip/in.gap

@@ -18,6 +18,5 @@ thermo		10
 timestep	0.001
 
 dump		1 all custom 10 dump.gap id fx fy fz
-dump_modify     1 format "%d %20.15g  %20.15g %20.15g"
 
 run		40

examples/USER/quip/in.sw

@@ -18,6 +18,5 @@ thermo		10
 timestep	0.001
 
 dump		1 all custom 10 dump.sw id fx fy fz
-dump_modify     1 format "%d %20.15g  %20.15g %20.15g"
 
 run		1

lib/quip/Makefile.lammps

@@ -13,8 +13,10 @@ $(error Environment variable QUIP_ARCH must be set.)
 endif
 
 include ${QUIP_ROOT}/build/${QUIP_ARCH}/Makefile.inc
+include ${QUIP_ROOT}/Makefile.rules
 
 quip_SYSLIB = -lquip
+quip_SYSLIB += ${NETCDF_SYSLIBS}
 quip_SYSLIB += ${MATH_LINKOPTS}
 
 ifeq (${F95},gfortran)
@@ -25,4 +27,4 @@ else
 $(error fortran compiler >>${F95}<< not recognised. Edit lib/quip/Makefile.lammps to specify the fortran library your linker should link to)
 endif
 
-quip_SYSPATH = -L${QUIP_ROOT}/build/${QUIP_ARCH} -L${QUIP_ROOT}/src/FoX-4.0.3/objs.${QUIP_ARCH}/lib
+quip_SYSPATH = -L${QUIP_ROOT}/build/${QUIP_ARCH}

src/KOKKOS/pair_reax_c_kokkos.h

@@ -23,7 +23,7 @@ PairStyle(reax/c/kk/host,PairReaxCKokkos<LMPHostType>)
 #ifndef LMP_PAIR_REAXC_KOKKOS_H
 #define LMP_PAIR_REAXC_KOKKOS_H
 
-#include "stdio.h"
+#include <stdio.h>
 #include "pair_kokkos.h"
 #include "pair_reax_c.h"
 #include "neigh_list_kokkos.h"

src/USER-DPD/atom_vec_dpd.cpp

@@ -589,6 +589,8 @@ int AtomVecDPD::unpack_comm_hybrid(int n, int first, double *buf)
     uCond[i] = buf[m++];
     uMech[i] = buf[m++];
     uChem[i] = buf[m++];
+    uCG[i] = buf[m++];
+    uCGnew[i] = buf[m++];
   }
   return m;
 }

src/USER-DPD/compute_dpd_atom.cpp

@@ -15,7 +15,7 @@
    Contributing author: James Larentzos (U.S. Army Research Laboratory)
 ------------------------------------------------------------------------- */
 
-#include "math.h"
+#include <math.h>
 #include <string.h>
 #include <stdlib.h>
 #include "compute_dpd_atom.h"

src/USER-DPD/pair_exp6_rx.cpp

@@ -26,7 +26,7 @@
 #include "error.h"
 #include "modify.h"
 #include "fix.h"
-#include "float.h"
+#include <float.h>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -128,8 +128,8 @@ void PairExp6rx::compute(int eflag, int vflag)
   double epsilon1_j,alpha1_j,rm1_j;
   double epsilon2_i,alpha2_i,rm2_i;
   double epsilon2_j,alpha2_j,rm2_j;
-  double evdwlOldEXP6_12, evdwlOldEXP6_21;
-  double evdwlEXP6_12, evdwlEXP6_21, fpairEXP6_12, fpairEXP6_21;
+  double evdwlOldEXP6_12, evdwlOldEXP6_21, fpairOldEXP6_12, fpairOldEXP6_21;
+  double evdwlEXP6_12, evdwlEXP6_21;
   double fractionOld1_i, fractionOld1_j;
   double fractionOld2_i, fractionOld2_j;
   double fraction1_i, fraction1_j;
@@ -310,15 +310,20 @@ void PairExp6rx::compute(int eflag, int vflag)
 
             uin1 = buck1*(6.0*rin1exp - alphaOld12_ij*rm6ij*rin6inv) - urc - durc*(rin1-rCut);
 
-            win1 = buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc;
+            win1 = -buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc;
 
             aRep = -1.0*win1*powint(rin1,nRep)/nRep;
 
             uin1rep = aRep/powint(rin1,nRep);
 
-            evdwlOldEXP6_12 = uin1 - uin1rep + aRep/powint(r,nRep);
+            forceExp6 = -double(nRep)*aRep/powint(r,nRep);
+            fpairOldEXP6_12 = factor_lj*forceExp6*r2inv;
 
+            evdwlOldEXP6_12 = uin1 - uin1rep + aRep/powint(r,nRep);
           } else {
+            forceExp6 = buck1*buck2*(r*rexp*rminv - rm6ij*r6inv) + r*durc;
+            fpairOldEXP6_12 = factor_lj*forceExp6*r2inv;
+
             evdwlOldEXP6_12 = buck1*(6.0*rexp - alphaOld12_ij*rm6ij*r6inv) - urc - durc*(r-rCut);
           }
 
@@ -345,15 +350,20 @@ void PairExp6rx::compute(int eflag, int vflag)
 
             uin1 = buck1*(6.0*rin1exp - alphaOld21_ij*rm6ij*rin6inv) - urc - durc*(rin1-rCut);
 
-            win1 = buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc;
+            win1 = -buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc;
 
             aRep = -1.0*win1*powint(rin1,nRep)/nRep;
 
             uin1rep = aRep/powint(rin1,nRep);
 
-            evdwlOldEXP6_21 = uin1 - uin1rep + aRep/powint(r,nRep);
+            forceExp6 = -double(nRep)*aRep/powint(r,nRep);
+            fpairOldEXP6_21 = factor_lj*forceExp6*r2inv;
 
+            evdwlOldEXP6_21 = uin1 - uin1rep + aRep/powint(r,nRep);
           } else {
+            forceExp6 = buck1*buck2*(r*rexp*rminv - rm6ij*r6inv) + r*durc;
+            fpairOldEXP6_21 = factor_lj*forceExp6*r2inv;
+
             evdwlOldEXP6_21 = buck1*(6.0*rexp - alphaOld21_ij*rm6ij*r6inv) - urc - durc*(r-rCut);
           }
 
@@ -395,22 +405,14 @@ void PairExp6rx::compute(int eflag, int vflag)
 
             uin1 = buck1*(6.0*rin1exp - alpha12_ij*rm6ij*rin6inv) - urc - durc*(rin1-rCut);
 
-            win1 = buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc;
+            win1 = -buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc;
 
             aRep = -1.0*win1*powint(rin1,nRep)/nRep;
 
             uin1rep = aRep/powint(rin1,nRep);
 
             evdwlEXP6_12 = uin1 - uin1rep + aRep/powint(r,nRep);
-
-            forceExp6 = -double(nRep)*aRep/powint(r,nRep);
-            fpairEXP6_12 = factor_lj*forceExp6*r2inv;
-
           } else {
-
-            // A4.  Compute the exp-6 force and energy
-            forceExp6 = buck1*buck2*(r*rexp*rminv - rm6ij*r6inv) + r*durc;
-            fpairEXP6_12 = factor_lj*forceExp6*r2inv;
             evdwlEXP6_12 = buck1*(6.0*rexp - alpha12_ij*rm6ij*r6inv) - urc - durc*(r-rCut);
           }
 
@@ -435,30 +437,22 @@ void PairExp6rx::compute(int eflag, int vflag)
 
             uin1 = buck1*(6.0*rin1exp - alpha21_ij*rm6ij*rin6inv) - urc - durc*(rin1-rCut);
 
-            win1 = buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc;
+            win1 = -buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc;
 
             aRep = -1.0*win1*powint(rin1,nRep)/nRep;
 
             uin1rep = aRep/powint(rin1,nRep);
 
             evdwlEXP6_21 = uin1 - uin1rep + aRep/powint(r,nRep);
-
-            forceExp6 = -double(nRep)*aRep/powint(r,nRep);
-            fpairEXP6_21 = factor_lj*forceExp6*r2inv;
-
           } else {
-
-            // A4.  Compute the exp-6 force and energy
-            forceExp6 = buck1*buck2*(r*rexp*rminv - rm6ij*r6inv) + r*durc;
-            fpairEXP6_21 = factor_lj*forceExp6*r2inv;
             evdwlEXP6_21 = buck1*(6.0*rexp - alpha21_ij*rm6ij*r6inv) - urc - durc*(r-rCut);
           }
 
           //
           // Apply Mixing Rule to get the overall force for the CG pair
           //
-          if (isite1 == isite2) fpair = sqrt(fractionOld1_i*fractionOld2_j)*fpairEXP6_12; 
-          else fpair = sqrt(fractionOld1_i*fractionOld2_j)*fpairEXP6_12 + sqrt(fractionOld2_i*fractionOld1_j)*fpairEXP6_21;
+          if (isite1 == isite2) fpair = sqrt(fractionOld1_i*fractionOld2_j)*fpairOldEXP6_12; 
+          else fpair = sqrt(fractionOld1_i*fractionOld2_j)*fpairOldEXP6_12 + sqrt(fractionOld2_i*fractionOld1_j)*fpairOldEXP6_21;
 
           f[i][0] += delx*fpair;
           f[i][1] += dely*fpair;

src/USER-DPD/pair_multi_lucy.cpp

@@ -21,7 +21,7 @@
    The Journal of Chemical Physics, 2016, 144, 104501.
 ------------------------------------------------------------------------------------------- */
 
-#include "mpi.h"
+#include <mpi.h>
 #include <math.h>
 #include "math_const.h"
 #include <stdlib.h>

src/USER-DPD/pair_multi_lucy_rx.cpp

@@ -21,7 +21,7 @@
    The Journal of Chemical Physics, 2016, 144, 104501.
 ------------------------------------------------------------------------------------------- */
 
-#include "mpi.h"
+#include <mpi.h>
 #include <math.h>
 #include "math_const.h"
 #include <stdlib.h>

src/USER-DPD/pair_table_rx.cpp

@@ -15,7 +15,7 @@
    Contributing author: Paul Crozier (SNL)
 ------------------------------------------------------------------------- */
 
-#include "mpi.h"
+#include <mpi.h>
 #include <math.h>
 #include <stdlib.h>
 #include <string.h>

src/USER-INTEL/dihedral_charmm_intel.cpp

@@ -15,8 +15,8 @@
    Contributing author: W. Michael Brown (Intel)
 ------------------------------------------------------------------------- */
 
-#include "mpi.h"
-#include "math.h"
+#include <mpi.h>
+#include <math.h>
 #include "dihedral_charmm_intel.h"
 #include "atom.h"
 #include "comm.h"

src/USER-INTEL/dihedral_harmonic_intel.cpp

@@ -15,8 +15,8 @@
    Contributing author: W. Michael Brown (Intel)
 ------------------------------------------------------------------------- */
 
-#include "mpi.h"
-#include "math.h"
+#include <mpi.h>
+#include <math.h>
 #include "dihedral_harmonic_intel.h"
 #include "atom.h"
 #include "comm.h"

src/USER-INTEL/dihedral_opls_intel.cpp

@@ -15,8 +15,8 @@
    Contributing author: W. Michael Brown (Intel)
 ------------------------------------------------------------------------- */
 
-#include "mpi.h"
-#include "math.h"
+#include <mpi.h>
+#include <math.h>
 #include "dihedral_opls_intel.h"
 #include "atom.h"
 #include "comm.h"

src/USER-INTEL/fix_npt_intel.cpp

@@ -11,7 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "string.h"
+#include <string.h>
 #include "fix_npt_intel.h"
 #include "modify.h"
 #include "error.h"

src/USER-INTEL/fix_nve_asphere_intel.cpp

@@ -15,9 +15,9 @@
    Contributing author: W. Michael Brown (Intel)
 ------------------------------------------------------------------------- */
 
-#include "math.h"
-#include "stdio.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <string.h>
 #include "fix_nve_asphere_intel.h"
 #include "math_extra_intel.h"
 #include "atom.h"

src/USER-INTEL/pair_buck_coul_cut_intel.cpp

@@ -15,10 +15,10 @@
    Contributing author: Rodrigo Canales (RWTH Aachen University)
 ------------------------------------------------------------------------- */
 
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
 #include "pair_buck_coul_cut_intel.h"
 #include "atom.h"
 #include "comm.h"

src/USER-INTEL/pair_buck_coul_long_intel.cpp

@@ -15,10 +15,10 @@
    Contributing author: Rodrigo Canales (RWTH Aachen University)
 ------------------------------------------------------------------------- */
 
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
 #include "pair_buck_coul_long_intel.h"
 #include "atom.h"
 #include "comm.h"

src/USER-INTEL/pair_buck_intel.cpp

@@ -15,7 +15,7 @@
    Contributing author: Rodrigo Canales (RWTH Aachen University)
 ------------------------------------------------------------------------- */
 
-#include "math.h"
+#include <math.h>
 #include "pair_buck_intel.h"
 #include "atom.h"
 #include "comm.h"

src/USER-INTEL/pair_tersoff_intel.cpp

@@ -15,10 +15,10 @@
    Contributing author: Markus H<>hnerbach (RWTH)
 ------------------------------------------------------------------------- */
 
-#include "math.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
 #include "pair_tersoff_intel.h"
 #include "atom.h"
 #include "neighbor.h"

src/USER-MANIFOLD/fix_manifoldforce.cpp

@@ -11,9 +11,9 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "math.h"
-#include "string.h"
-#include "stdlib.h"
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
 #include "atom.h"
 #include "update.h"
 #include "respa.h"

src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp

@@ -32,16 +32,16 @@
 ------------------------------------------------------------------------- */
 
 
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
 #include "respa.h"
 #include "error.h"
 #include "group.h"
-#include "math.h"
+#include <math.h>
 #include "input.h"
 #include "variable.h"
 #include "citeme.h"

src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp

@@ -32,16 +32,16 @@
 ------------------------------------------------------------------------- */
 
 
-#include "stdio.h"
-#include "stdlib.h"
-#include "string.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
 #include "atom.h"
 #include "force.h"
 #include "update.h"
 #include "respa.h"
 #include "error.h"
 #include "group.h"
-#include "math.h"
+#include <math.h>
 #include "input.h"
 #include "variable.h"
 #include "citeme.h"

src/compute_dipole_chunk.cpp

@@ -11,7 +11,7 @@
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
-#include "string.h"
+#include <string.h>
 #include "compute_dipole_chunk.h"
 #include "atom.h"
 #include "update.h"

tools/msi2lmp/README

@@ -1,13 +1,18 @@
 Axel Kohlmeyer is the current maintainer of the msi2lmp tool.
 Please send any inquiries about msi2lmp to the lammps-users mailing list.
 
+06 Oct 2016 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Improved whitespace handling in parsing topology and force field
+files to avoid bogus warnings about type name truncation.
+
 24 Oct 2015 Axel Kohlmeyer <akohlmey@gmail.com>
 
 Added check to make certain that force field files
 are consistent with the notation of non-bonded parameters
 that the msi2lmp code expects. For Class 1 and OPLS-AA
 the A-B notation with geometric mixing is expected and for
-Class 2 the r-eps notation with sixthpower mixing.(
+Class 2 the r-eps notation with sixthpower mixing.
 
 11 Sep 2014 Axel Kohlmeyer <akohlmey@gmail.com>
 

tools/msi2lmp/src/ReadMdfFile.c

@@ -74,9 +74,9 @@ void ReadMdfFile(void)
         at_end = 1;
       } else if (strncmp(line,"@column",7) == 0) {
 
-        temp_string = strtok(line," ");
-        col_no = strtok(NULL," ");
-        col_name = strtok(NULL," ");
+        temp_string = strtok(line,WHITESPACE);
+        col_no = strtok(NULL,WHITESPACE);
+        col_name = strtok(NULL,WHITESPACE);
         if (strncmp(col_name,"charge",6) == 0) {
           if (strlen(col_name) < 8) {
             q_col_no = atoi(col_no);
@@ -285,7 +285,7 @@ int get_molecule(char *line, int connect_col_no, int q_col_no,
     /* Get atom name */
     cur_field = strtok(line,":");
     sscanf(cur_field, "%s", atoms[*counter].residue_string);
-    cur_field = strtok(NULL," ");
+    cur_field = strtok(NULL,WHITESPACE);
     /* Compare atom name with that in .car file */
     if (strcmp(atoms[*counter].name, cur_field)) {
       printf("Names %s from .car file and %s from .mdf file do not match\n",
@@ -297,18 +297,18 @@ int get_molecule(char *line, int connect_col_no, int q_col_no,
 
     /* Skip unwanted fields until charge column, then update charge */
 
-    for (i=1; i < q_col_no; i++) strtok(NULL," ");
-    cur_field = strtok(NULL, " ");
+    for (i=1; i < q_col_no; i++) strtok(NULL,WHITESPACE);
+    cur_field = strtok(NULL, WHITESPACE);
     atoms[*counter].q = atof(cur_field);
 
     /* Continue skipping unwanted fields until connectivity records begin */
 
-    for ( i = (q_col_no + 1); i < connect_col_no; i++) strtok(NULL," ");
+    for ( i = (q_col_no + 1); i < connect_col_no; i++) strtok(NULL,WHITESPACE);
 
     /* Process connections */
 
     connect_no = 0; /* reset connections counter */
-    while ((cur_field = strtok(NULL," ")) && (connect_no < MAX_CONNECTIONS)) {
+    while ((cur_field = strtok(NULL,WHITESPACE)) && (connect_no < MAX_CONNECTIONS)) {
       sscanf(cur_field, "%s", atoms[*counter].connections[connect_no++]);
     }
     atoms[*counter].no_connect = connect_no;

tools/msi2lmp/src/SearchAndFill.c

@@ -45,9 +45,9 @@ const char *SearchAndCheck(const char *keyword)
       exit(1);
     }
     if (line[0] == '@') {
-      if (string_match(strtok(line+1," '\t\n'("),keyword)) {
+      if (string_match(strtok(line+1," '\t\n\r\f("),keyword)) {
         got_it = 1;
-        status = strtok(NULL," '\t\n(");
+        status = strtok(NULL," '\t\n\r\f(");
         if (status != NULL)
           return strdup(status);
       }
@@ -79,7 +79,7 @@ void SearchAndFill(struct FrcFieldItem *item)
       exit(1);
     }
     if (line[0] == '#') {
-      if (string_match(strtok(line," '\t'("),item->keyword)) got_it = 1;
+      if (string_match(strtok(line," '\t\r\n("),item->keyword)) got_it = 1;
     }
     /*     if (strncmp(line, item->keyword,strlen(item->keyword))==0) got_it = 1; */
   }
@@ -132,13 +132,13 @@ void SearchAndFill(struct FrcFieldItem *item)
 
     /* version number and reference number */
 
-    version = atof(strtok(line, " "));
-    reference = atoi(strtok(NULL, " "));
+    version = atof(strtok(line, WHITESPACE));
+    reference = atoi(strtok(NULL, WHITESPACE));
 
     /* equivalences */
 
     for(i = 0; i < item->number_of_members; i++ ) {
-      charptr = strtok(NULL, " ");
+      charptr = strtok(NULL, WHITESPACE);
       if (strlen(charptr) > 4) {
         fprintf(stderr,"Warning: type name overflow for '%s'. "
                 "Truncating to 4 characters.\n",charptr);
@@ -150,7 +150,7 @@ void SearchAndFill(struct FrcFieldItem *item)
        endbontor have to be treated carefully */
 
     for( i = 0; i < item->number_of_parameters; i++ ) {
-      charptr = strtok(NULL, " ");
+      charptr = strtok(NULL, WHITESPACE);
       if(charptr == NULL) {
         for ( j = i; j < item->number_of_parameters; j++ )
           parameters[j] = parameters[j-i];

tools/msi2lmp/src/msi2lmp.c

@@ -2,6 +2,9 @@
 *
 *  msi2lmp.exe
 *
+*   v3.9.8 AK- Improved whitespace handling in parsing topology and force
+*              field files to avoid bogus warnings about type name truncation
+*
 *   v3.9.7 AK- Add check to enforce that Class1/OPLS-AA use A-B parameter
 *              conventions in force field file and Class2 us r-eps conventions
 *

tools/msi2lmp/src/msi2lmp.h

@@ -36,7 +36,7 @@
 
 # include <stdio.h>
 
-#define MSI2LMP_VERSION "v3.9.7 / 24 Oct 2015"
+#define MSI2LMP_VERSION "v3.9.8 / 06 Oct 2016"
 
 #define PI_180  0.01745329251994329576
 
@@ -45,6 +45,8 @@
 #define MAX_STRING        64
 #define MAX_NAME          16
 
+#define WHITESPACE " \t\r\n\f"
+
 #define MAX_ATOM_TYPES         100
 #define MAX_BOND_TYPES         200
 #define MAX_ANGLE_TYPES        300

tools/msi2lmp/test/reference/PyAC_bulk-clayff.data

@@ -1,4 +1,4 @@
-LAMMPS data file. msi2lmp v3.9.7 / 24 Oct 2015 / CGCMM for PyAC_bulk-clayff
+LAMMPS data file. msi2lmp v3.9.8 / 06 Oct 2016 / CGCMM for PyAC_bulk-clayff
 
    1280 atoms
     128 bonds