Merge pull request #1621 from akohlmey/collected-small-fixes

Collected small fixes and updates

src/MANYBODY/pair_tersoff.cpp

@@ -30,9 +30,11 @@
 #include "error.h"
 
 #include "math_const.h"
+#include "math_special.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
+using namespace MathSpecial;
 
 #define MAXLINE 1024
 #define DELTA 4
@@ -604,7 +606,7 @@ double PairTersoff::zeta(Param *param, double rsqij, double rsqik,
   costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
               delrij[2]*delrik[2]) / (rij*rik);
 
-  if (param->powermint == 3) arg = pow(param->lam3 * (rij-rik),3.0);
+  if (param->powermint == 3) arg = cube(param->lam3 * (rij-rik));
   else arg = param->lam3 * (rij-rik);
 
   if (arg > 69.0776) ex_delr = 1.e30;
@@ -744,7 +746,7 @@ void PairTersoff::ters_zetaterm_d(double prefactor,
 
   fc = ters_fc(rik,param);
   dfc = ters_fc_d(rik,param);
-  if (param->powermint == 3) tmp = pow(param->lam3 * (rij-rik),3.0);
+  if (param->powermint == 3) tmp = cube(param->lam3 * (rij-rik));
   else tmp = param->lam3 * (rij-rik);
 
   if (tmp > 69.0776) ex_delr = 1.e30;
@@ -752,7 +754,7 @@ void PairTersoff::ters_zetaterm_d(double prefactor,
   else ex_delr = exp(tmp);
 
   if (param->powermint == 3)
-    ex_delr_d = 3.0*pow(param->lam3,3.0) * pow(rij-rik,2.0)*ex_delr;
+    ex_delr_d = 3.0*cube(param->lam3) * square(rij-rik)*ex_delr;
   else ex_delr_d = param->lam3 * ex_delr;
 
   cos_theta = vec3_dot(rij_hat,rik_hat);

src/MANYBODY/pair_tersoff_mod.cpp

@@ -25,11 +25,13 @@
 #include "force.h"
 #include "comm.h"
 #include "math_const.h"
+#include "math_special.h"
 #include "memory.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
+using namespace MathSpecial;
 
 #define MAXLINE 1024
 #define DELTA 4
@@ -241,7 +243,7 @@ double PairTersoffMOD::zeta(Param *param, double rsqij, double rsqik,
   costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
               delrij[2]*delrik[2]) / (rij*rik);
 
-  if (param->powermint == 3) arg = pow(param->lam3 * (rij-rik),3.0);
+  if (param->powermint == 3) arg = cube(param->lam3 * (rij-rik));
   else arg = param->lam3 * (rij-rik);
 
   if (arg > 69.0776) ex_delr = 1.e30;
@@ -314,7 +316,7 @@ void PairTersoffMOD::ters_zetaterm_d(double prefactor,
 
   fc = ters_fc(rik,param);
   dfc = ters_fc_d(rik,param);
-  if (param->powermint == 3) tmp = pow(param->lam3 * (rij-rik),3.0);
+  if (param->powermint == 3) tmp = cube(param->lam3 * (rij-rik));
   else tmp = param->lam3 * (rij-rik);
 
   if (tmp > 69.0776) ex_delr = 1.e30;
@@ -322,7 +324,7 @@ void PairTersoffMOD::ters_zetaterm_d(double prefactor,
   else ex_delr = exp(tmp);
 
   if (param->powermint == 3)
-    ex_delr_d = 3.0*pow(param->lam3,3.0) * pow(rij-rik,2.0)*ex_delr;
+    ex_delr_d = 3.0*cube(param->lam3) * square(rij-rik)*ex_delr;
   else ex_delr_d = param->lam3 * ex_delr;
 
   cos_theta = vec3_dot(rij_hat,rik_hat);

src/MANYBODY/pair_tersoff_zbl.cpp

@@ -28,9 +28,11 @@
 #include "memory.h"
 #include "error.h"
 #include "math_const.h"
+#include "math_special.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
+using namespace MathSpecial;
 
 #define MAXLINE 1024
 #define DELTA 4
@@ -226,7 +228,7 @@ void PairTersoffZBL::repulsive(Param *param, double rsq, double &fforce,
 
   // ZBL repulsive portion
 
-  double esq = pow(global_e,2.0);
+  double esq = square(global_e);
   double a_ij = (0.8854*global_a_0) /
     (pow(param->Z_i,0.23) + pow(param->Z_j,0.23));
   double premult = (param->Z_i * param->Z_j * esq)/(4.0*MY_PI*global_epsilon_0);
@@ -286,5 +288,5 @@ double PairTersoffZBL::F_fermi(double r, Param *param)
 double PairTersoffZBL::F_fermi_d(double r, Param *param)
 {
   return param->ZBLexpscale*exp(-param->ZBLexpscale*(r-param->ZBLcut)) /
-    pow(1.0 + exp(-param->ZBLexpscale*(r-param->ZBLcut)),2.0);
+    square(1.0 + exp(-param->ZBLexpscale*(r-param->ZBLcut)));
 }

src/comm_tiled.h

@@ -14,7 +14,6 @@
 #ifndef LMP_COMM_TILED_H
 #define LMP_COMM_TILED_H
 
-#include <mpi.h>
 #include "comm.h"
 
 namespace LAMMPS_NS {

src/irregular.h

@@ -14,7 +14,6 @@
 #ifndef LMP_IRREGULAR_H
 #define LMP_IRREGULAR_H
 
-#include <mpi.h>
 #include "pointers.h"
 
 namespace LAMMPS_NS {

src/rcb.h

@@ -14,7 +14,6 @@
 #ifndef LAMMPS_RCB_H
 #define LAMMPS_RCB_H
 
-#include <mpi.h>
 #include "pointers.h"
 
 namespace LAMMPS_NS {

src/read_dump.h

@@ -22,7 +22,6 @@ CommandStyle(read_dump,ReadDump)
 #ifndef LMP_READ_DUMP_H
 #define LMP_READ_DUMP_H
 
-#include <mpi.h>
 #include "pointers.h"
 
 namespace LAMMPS_NS {

src/variable.cpp

@@ -18,6 +18,7 @@
 #include <cstring>
 #include <cctype>
 #include <unistd.h>
+#include <string>
 #include "universe.h"
 #include "atom.h"
 #include "update.h"
@@ -1302,8 +1303,12 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
         if (word[0] == 'C') lowercase = 0;
 
         int icompute = modify->find_compute(word+2);
-        if (icompute < 0)
+        if (icompute < 0) {
-          print_var_error(FLERR,"Invalid compute ID in variable formula",ivar);
+          std::string mesg = "Invalid compute ID '";
+          mesg += (word+2);
+          mesg += "' in variable formula";
+          print_var_error(FLERR,mesg.c_str(),ivar);
+        }
         Compute *compute = modify->compute[icompute];
 
         // parse zero or one or two trailing brackets
@@ -1604,9 +1609,10 @@ double Variable::evaluate(char *str, Tree **tree, int ivar)
 
         int ifix = modify->find_fix(word+2);
         if (ifix < 0) {
-          char msg[128];
+          std::string mesg = "Invalid fix ID '";
-          snprintf(msg,128,"Invalid fix ID '%s' in variable formula",word+2);
+          mesg += (word+2);
-          print_var_error(FLERR,msg,ivar);
+          mesg += "' in variable formula";
+          print_var_error(FLERR,mesg.c_str(),ivar);
         }
         Fix *fix = modify->fix[ifix];
 
@@ -3792,8 +3798,12 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
   // group to operate on
 
   int igroup = group->find(args[0]);
-  if (igroup == -1)
+  if (igroup == -1) {
-    print_var_error(FLERR,"Group ID in variable formula does not exist",ivar);
+    std::string mesg = "Group ID '";
+    mesg += args[0];
+    mesg += "' in variable formula does not exist";
+    print_var_error(FLERR,mesg.c_str(),ivar);
+  }
 
   // match word to group function
 
@@ -4001,8 +4011,12 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
 int Variable::region_function(char *id, int ivar)
 {
   int iregion = domain->find_region(id);
-  if (iregion == -1)
+  if (iregion == -1) {
-    print_var_error(FLERR,"Region ID in variable formula does not exist",ivar);
+    std::string mesg = "Region ID '";
+    mesg += id;
+    mesg += "' in variable formula does not exist";
+    print_var_error(FLERR,mesg.c_str(),ivar);
+  }
 
   // init region in case sub-regions have been deleted
 
@@ -4080,9 +4094,10 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
 
       int icompute = modify->find_compute(&args[0][2]);
       if (icompute < 0) {
-        char msg[128];
+        std::string mesg = "Invalid compute ID '";
-        snprintf(msg,128,"Invalid compute ID '%s' in variable formula",word+2);
+        mesg += (args[0]+2);
-        print_var_error(FLERR,msg,ivar);
+        mesg += "' in variable formula";
+        print_var_error(FLERR,mesg.c_str(),ivar);
       }
       compute = modify->compute[icompute];
       if (index == 0 && compute->vector_flag) {
@@ -4123,13 +4138,20 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
       } else index = 0;
 
       int ifix = modify->find_fix(&args[0][2]);
-      if (ifix < 0)
+      if (ifix < 0) {
-        print_var_error(FLERR,"Invalid fix ID in variable formula",ivar);
+        std::string mesg = "Invalid fix ID '";
+        mesg += (args[0]+2);
+        mesg += "' in variable formula";
+        print_var_error(FLERR,mesg.c_str(),ivar);
+      }
       fix = modify->fix[ifix];
       if (index == 0 && fix->vector_flag) {
-        if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
+        if (update->whichflag > 0 && update->ntimestep % fix->global_freq) {
-          print_var_error(FLERR,"Fix in variable not computed at "
+          std::string mesg = "Fix with ID '";
-                          "compatible time",ivar);
+          mesg += (args[0]+2);
+          mesg += "' in variable formula not computed at compatible time";
+          print_var_error(FLERR,mesg.c_str(),ivar);
+        }
         nvec = fix->size_vector;
         nstride = 1;
       } else if (index && fix->array_flag) {
@@ -4336,9 +4358,12 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
       print_var_error(FLERR,"Invalid special function in variable formula",ivar);
 
     int ivar = find(args[0]);
-    if (ivar < 0)
+    if (ivar < 0) {
-      print_var_error(FLERR,"Variable ID in "
+      std::string mesg = "Variable ID '";
-                      "variable formula does not exist",ivar);
+      mesg += args[0];
+      mesg += "' in variable formula does not exist";
+      print_var_error(FLERR,mesg.c_str(),ivar);
+    }
 
     // SCALARFILE has single current value, read next one
     // save value in tree or on argstack