git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5591 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/KSPACE/pppm.cpp

@@ -144,6 +144,7 @@ void PPPM::init()
   cutoff = *p_cutoff;
 
   // if kspace is TIP4P, extract TIP4P params from pair style
+  // bond/angle are not yet init(), so insure equilibrium request is valid
 
   qdist = 0.0;
 
@@ -165,6 +166,12 @@ void PPPM::init()
 
     if (force->angle == NULL || force->bond == NULL)
       error->all("Bond and angle potentials must be defined for TIP4P");
+    if (typeA < 1 || typeA > atom->nangletypes || 
+	force->angle->setflag[typeA] == 0)
+      error->all("Bad TIP4P angle type for PPPM/TIP4P");
+    if (typeB < 1 || typeA > atom->nbondtypes || 
+	force->bond->setflag[typeB] == 0)
+      error->all("Bad TIP4P bond type for PPPM/TIP4P");
     double theta = force->angle->equilibrium_angle(typeA);
     double blen = force->bond->equilibrium_distance(typeB);
     alpha = qdist / (2.0 * cos(0.5*theta) * blen);

src/error.h

@@ -28,6 +28,7 @@ class Error : protected Pointers {
   void all(const char *);
   void one(const char *);
   void warning(const char *, int = 1);
+  void message(char *, int = 1);
 };
 
 }

src/input.cpp

@@ -16,6 +16,8 @@
 #include "stdlib.h"
 #include "string.h"
 #include "ctype.h"
+#include "unistd.h"
+#include "sys/stat.h"
 #include "input.h"
 #include "style_command.h"
 #include "universe.h"
@@ -81,10 +83,13 @@ Input::Input(LAMMPS *lmp, int argc, char **argv) : Pointers(lmp)
 
   int iarg = 0;
   while (iarg < argc) {
-    if (strcmp(argv[iarg],"-var") == 0) {
+    if (strcmp(argv[iarg],"-var") == 0 || strcmp(argv[iarg],"-v") == 0) {
-      variable->set(argv[iarg+1],argv[iarg+2]);
+      int jarg = iarg+2;
-      iarg += 3;
+      while (jarg < argc && argv[jarg][0] != '-') jarg++;
-    } else if (strcmp(argv[iarg],"-echo") == 0) {
+      variable->set(argv[iarg+1],jarg-iarg-2,&argv[iarg+2]);
+      iarg = jarg;
+    } else if (strcmp(argv[iarg],"-echo") == 0 || 
+	       strcmp(argv[iarg],"-e") == 0) {
       narg = 1;
       char **tmp = arg;        // trick echo() into using argv instead of arg
       arg = &argv[iarg+1];
@@ -409,6 +414,7 @@ int Input::execute_command()
   else if (!strcmp(command,"log")) log();
   else if (!strcmp(command,"next")) next_command();
   else if (!strcmp(command,"print")) print();
+  else if (!strcmp(command,"shell")) shell();
   else if (!strcmp(command,"variable")) variable_command();
 
   else if (!strcmp(command,"angle_coeff")) angle_coeff();
@@ -752,6 +758,43 @@ void Input::print()
 
 /* ---------------------------------------------------------------------- */
 
+void Input::shell()
+{
+  if (narg < 1) error->all("Illegal shell command");
+
+  if (strcmp(arg[0],"cd") == 0) {
+    if (narg != 2) error->all("Illegal shell command");
+    chdir(arg[1]);
+
+  } else if (strcmp(arg[0],"mkdir") == 0) {
+    if (narg < 2) error->all("Illegal shell command");
+#if !defined(WINDOWS) && !defined(__MINGW32_VERSION) 
+    if (me == 0)
+      for (int i = 1; i < narg; i++)
+	mkdir(arg[i], S_IRWXU | S_IRGRP | S_IXGRP);
+#endif
+
+  } else if (strcmp(arg[0],"mv") == 0) {
+    if (narg != 3) error->all("Illegal shell command");
+    if (me == 0) rename(arg[1],arg[2]);
+
+  } else if (strcmp(arg[0],"rm") == 0) {
+    if (narg < 2) error->all("Illegal shell command");
+    if (me == 0)
+      for (int i = 1; i < narg; i++)
+	unlink(arg[i]);
+
+  } else if (strcmp(arg[0],"rmdir") == 0) {
+    if (narg < 2) error->all("Illegal shell command");
+    if (me == 0)
+      for (int i = 1; i < narg; i++)
+	rmdir(arg[i]);
+
+  } else error->all("Illegal shell command");
+}
+
+/* ---------------------------------------------------------------------- */
+
 void Input::variable_command()
 {
   variable->set(narg,arg);

src/input.h

@@ -58,6 +58,7 @@ class Input : protected Pointers {
   void log();
   void next_command();
   void print();
+  void shell();
   void variable_command();
 
   void angle_coeff();          // LAMMPS commands

src/lammps.cpp

@@ -57,7 +57,8 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
   int iarg = 1;
 
   while (iarg < narg) {
-    if (strcmp(arg[iarg],"-partition") == 0) {
+    if (strcmp(arg[iarg],"-partition") == 0 || 
+	strcmp(arg[iarg],"-p") == 0) {
       universe->existflag = 1;
       if (iarg+2 > narg) 
 	error->universe_all("Invalid command-line argument");
@@ -66,26 +67,32 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
 	universe->add_world(arg[iarg]);
 	iarg++;
       }
-    } else if (strcmp(arg[iarg],"-in") == 0) {
+    } else if (strcmp(arg[iarg],"-in") == 0 || 
+	       strcmp(arg[iarg],"-i") == 0) {
       if (iarg+2 > narg) 
 	error->universe_all("Invalid command-line argument");
       inflag = iarg + 1;
       iarg += 2;
-    } else if (strcmp(arg[iarg],"-screen") == 0) {
+    } else if (strcmp(arg[iarg],"-screen") == 0 || 
+	       strcmp(arg[iarg],"-s") == 0) {
       if (iarg+2 > narg) 
 	error->universe_all("Invalid command-line argument");
       screenflag = iarg + 1;
       iarg += 2;
-    } else if (strcmp(arg[iarg],"-log") == 0) {
+    } else if (strcmp(arg[iarg],"-log") == 0 || 
+	       strcmp(arg[iarg],"-l") == 0) {
       if (iarg+2 > narg) 
 	error->universe_all("Invalid command-line argument");
       logflag = iarg + 1;
       iarg += 2;
-    } else if (strcmp(arg[iarg],"-var") == 0) {
+    } else if (strcmp(arg[iarg],"-var") == 0 || 
+	       strcmp(arg[iarg],"-v") == 0) {
       if (iarg+3 > narg) 
 	error->universe_all("Invalid command-line argument");
-      iarg += 3;
+      iarg += 2;
-    } else if (strcmp(arg[iarg],"-echo") == 0) {
+      while (iarg < narg && arg[iarg][0] != '-') iarg++;
+    } else if (strcmp(arg[iarg],"-echo") == 0 || 
+	       strcmp(arg[iarg],"-e") == 0) {
       if (iarg+2 > narg) 
 	error->universe_all("Invalid command-line argument");
       iarg += 2;

src/shell.cpp

@@ -1,65 +0,0 @@
-/* ----------------------------------------------------------------------
-   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
-
-   Copyright (2003) Sandia Corporation.  Under the terms of Contract
-   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-   certain rights in this software.  This software is distributed under 
-   the GNU General Public License.
-
-   See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#include "mpi.h"
-#include "string.h"
-#include "unistd.h"
-#include "sys/stat.h"
-#include "shell.h"
-#include "error.h"
-
-using namespace LAMMPS_NS;
-
-/* ---------------------------------------------------------------------- */
-
-Shell::Shell(LAMMPS *lmp) : Pointers(lmp)
-{
-  MPI_Comm_rank(world,&me);
-}
-
-/* ---------------------------------------------------------------------- */
-
-void Shell::command(int narg, char **arg)
-{
-  if (narg < 1) error->all("Illegal shell command");
-
-  if (strcmp(arg[0],"cd") == 0) {
-    if (narg != 2) error->all("Illegal shell command");
-    chdir(arg[1]);
-
-  } else if (strcmp(arg[0],"mkdir") == 0) {
-    if (narg < 2) error->all("Illegal shell command");
-#if !defined(WINDOWS) && !defined(__MINGW32_VERSION) 
-    if (me == 0)
-      for (int i = 1; i < narg; i++)
-	mkdir(arg[i], S_IRWXU | S_IRGRP | S_IXGRP);
-#endif
-
-  } else if (strcmp(arg[0],"mv") == 0) {
-    if (narg != 3) error->all("Illegal shell command");
-    if (me == 0) rename(arg[1],arg[2]);
-
-  } else if (strcmp(arg[0],"rm") == 0) {
-    if (narg < 2) error->all("Illegal shell command");
-    if (me == 0)
-      for (int i = 1; i < narg; i++)
-	unlink(arg[i]);
-
-  } else if (strcmp(arg[0],"rmdir") == 0) {
-    if (narg < 2) error->all("Illegal shell command");
-    if (me == 0)
-      for (int i = 1; i < narg; i++)
-	rmdir(arg[i]);
-
-  } else error->all("Illegal shell command");
-}

src/shell.h

@@ -1,39 +0,0 @@
-/* ----------------------------------------------------------------------
-   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   http://lammps.sandia.gov, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov
-
-   Copyright (2003) Sandia Corporation.  Under the terms of Contract
-   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
-   certain rights in this software.  This software is distributed under 
-   the GNU General Public License.
-
-   See the README file in the top-level LAMMPS directory.
-------------------------------------------------------------------------- */
-
-#ifdef COMMAND_CLASS
-
-CommandStyle(shell,Shell)
-
-#else
-
-#ifndef LMP_SHELL_H
-#define LMP_SHELL_H
-
-#include "pointers.h"
-
-namespace LAMMPS_NS {
-
-class Shell : protected Pointers {
- public:
-  Shell(class LAMMPS *);
-  void command(int, char **);
-
- private:
-  int me;
-};
-
-}
-
-#endif
-#endif

src/variable.cpp

@@ -322,17 +322,17 @@ void Variable::set(int narg, char **arg)
 }
 
 /* ----------------------------------------------------------------------
-   single-value INDEX variable created by command-line argument
+   INDEX variable created by command-line argument
    make it INDEX rather than STRING so cannot be re-defined in input script
 ------------------------------------------------------------------------- */
 
-void Variable::set(char *name, char *value)
+void Variable::set(char *name, int narg, char **arg)
 {
-  char **newarg = new char*[3];
+  char **newarg = new char*[2+narg];
   newarg[0] = name;
   newarg[1] = (char *) "index";
-  newarg[2] = value;
+  for (int i = 0; i < narg; i++) newarg[2+i] = arg[i];
-  set(3,newarg);
+  set(2+narg,newarg);
   delete [] newarg;
 }
 

src/variable.h

@@ -23,7 +23,7 @@ class Variable : protected Pointers {
   Variable(class LAMMPS *);
   ~Variable();
   void set(int, char **);
-  void set(char *, char *);
+  void set(char *, int, char **);
   int next(int, char **);
   int find(char *);
   int equalstyle(int);