git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14805 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/ASPHERE/pair_line_lj.cpp

@@ -69,11 +69,11 @@ PairLineLJ::~PairLineLJ()
 
 void PairLineLJ::compute(int eflag, int vflag)
 {
-  int i,j,ii,jj,inum,jnum,itype,jtype,tmp;
+  int i,j,ii,jj,inum,jnum,itype,jtype;
   int ni,nj,npi,npj,ifirst,jfirst;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
   double rsq,r2inv,r6inv,term1,term2,sig,sig3,forcelj;
-  double xi[2],xj[2],fi[2],fj[2],dxi,dxj,dyi,dyj;
+  double xi[2],xj[2],fi[2],dxi,dxj,dyi,dyj;
   int *ilist,*jlist,*numneigh,**firstneigh;
 
   evdwl = 0.0;

src/DEPEND/fastdep.c

@@ -33,7 +33,24 @@
 #include <sys/types.h>
 #include <sys/stat.h>
 
-const char version[] = "2.0";
+const char version[] = "2.1";
+
+/* store list of accepted extensions for object targets */
+static const char *extensions[] = { ".cpp", ".c", ".cu" };
+static const int numextensions = sizeof(extensions)/sizeof(const char *);
+
+/* strdup() is not part of ANSI C. provide a replacement for portability */
+static char *my_strdup(const char *src)
+{
+    int len;
+    char *ptr;
+
+    if (src == NULL) return NULL;
+    len = strlen(src);
+    ptr = (char *)malloc(len+1);
+    if (ptr) memcpy(ptr,src,len+1);
+    return ptr;
+}
 
 /************************************************************************
  * utility functions
@@ -198,7 +215,7 @@ static void llist_append(llist_t *ll, const char *key)
     llnode_t *tmp;
     if ((ll == NULL) || (key == NULL)) return;
 
-    ll->tail->key = strdup(key);
+    ll->tail->key = my_strdup(key);
     ll->count ++;
     tmp = (llnode_t *)malloc(sizeof(llnode_t));
     tmp->key = NULL;
@@ -286,7 +303,7 @@ static void set_add(set_t *s, const char *key)
         tmp = tmp->next;
     }
     s->count ++;
-    tmp->key = strdup(key);
+    tmp->key = my_strdup(key);
     tmp->next = (llnode_t *)malloc(sizeof(llnode_t));
     tmp = tmp->next;
     tmp->key = NULL;
@@ -375,7 +392,7 @@ static void map_add(map_t *m, const char *key, const char *val)
     /* add new entry to map */
     if (tmp->next == NULL) {
         m->count ++;
-        tmp->key = strdup(key);
+        tmp->key = my_strdup(key);
         tmp->val = set_init(50); /* XXX: chosen arbitrarily */
         tmp->next = (mapnode_t *)malloc(sizeof(mapnode_t));
         tmp->next->key = NULL;
@@ -547,42 +564,52 @@ static void do_depend(llnode_t *head, map_t *deps)
     set_t *incl;
     const char *source;
     char *target, *ptr;
-    int i,num;
+    int i,num,ext;
 
     tmp = head;
     while (tmp->next != NULL) {
         source = tmp->key;
         target = strrchr(source,'/');
         if (target == NULL) {
-            target = strdup(source);
+            target = my_strdup(source);
         } else {
-            target = strdup(target+1);
+            target = my_strdup(target+1);
         }
 
+        ext = 0;
         ptr = strrchr(target,'.');
         if (ptr != NULL) {
-            ptr[1] = 'o';
+            for (i = 0; i < numextensions; ++i) {
-            ptr[2] = '\0';
+                if (strcmp(ptr,extensions[i]) == 0) ++ext;
-        }
+            }
-        fputs(target,stdout);
+            if (ext > 0) {
-        fputs(" : ",stdout);
+                ptr[1] = 'o';
-        fputs(source,stdout);
+                ptr[2] = '\0';
-        free((void *)target);
-
-        incl = set_init(50);
-        add_depend(source,incl,deps);
-
-        num = incl->nbuckets;
-        for (i = 0; i < num; ++i) {
-            lnk = incl->buckets + i;
-            while (lnk->next != NULL) {
-                fputc(' ',stdout);
-                fputs(lnk->key,stdout);
-                lnk = lnk->next;
             }
         }
-        fputc('\n',stdout);
+
-        set_free(incl);
+        if (ext > 0) {
+            fputs(target,stdout);
+            fputs(" : ",stdout);
+            fputs(source,stdout);
+
+            incl = set_init(50);
+            add_depend(source,incl,deps);
+
+            num = incl->nbuckets;
+            for (i = 0; i < num; ++i) {
+                lnk = incl->buckets + i;
+                while (lnk->next != NULL) {
+                    fputc(' ',stdout);
+                    fputs(lnk->key,stdout);
+                    lnk = lnk->next;
+                }
+            }
+            fputc('\n',stdout);
+            set_free(incl);
+        }
+
+        free((void *)target);
         tmp = tmp->next;
     }
 }
@@ -601,6 +628,8 @@ int main(int argc, char **argv)
         fprintf(stderr,"FastDep v%s for LAMMPS\n"
                 "Usage: %s [-I <path> ...] -- <src1> [<src2> ...]\n",
                 version,argv[0]);
+        fprintf(stderr,"Supported extensions: %d, %s, %s\n",numextensions,
+                extensions[0], extensions[1]);
         return 1;
     }
 
@@ -631,7 +660,7 @@ int main(int argc, char **argv)
             }
         } else if (strcmp(*argv,"--") == 0) {
             break;
-        } // ignore all unrecognized arguments before '--'.
+        } /* ignore all unrecognized arguments before '--'. */
     }
 
     src = llist_init();

src/GRANULAR/pair_gran_hertz_history.cpp

@@ -87,7 +87,6 @@ void PairGranHertzHistory::compute(int eflag, int vflag)
   double **torque = atom->torque;
   double *radius = atom->radius;
   double *rmass = atom->rmass;
-  int *type = atom->type;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
 
@@ -367,7 +366,6 @@ double PairGranHertzHistory::single(int i, int j, int itype, int jtype,
   // if I or J is frozen, meff is other particle
 
   double *rmass = atom->rmass;
-  int *type = atom->type;
   int *mask = atom->mask;
 
   mi = rmass[i];

src/GRANULAR/pair_gran_hooke.cpp

@@ -81,7 +81,6 @@ void PairGranHooke::compute(int eflag, int vflag)
   double **torque = atom->torque;
   double *radius = atom->radius;
   double *rmass = atom->rmass;
-  int *type = atom->type;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
   int newton_pair = force->newton_pair;
@@ -285,7 +284,6 @@ double PairGranHooke::single(int i, int j, int itype, int jtype, double rsq,
   // if I or J is frozen, meff is other particle
 
   double *rmass = atom->rmass;
-  int *type = atom->type;
   int *mask = atom->mask;
 
   mi = rmass[i];

src/GRANULAR/pair_gran_hooke_history.cpp

@@ -129,7 +129,6 @@ void PairGranHookeHistory::compute(int eflag, int vflag)
   double **torque = atom->torque;
   double *radius = atom->radius;
   double *rmass = atom->rmass;
-  int *type = atom->type;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
 
@@ -670,7 +669,6 @@ double PairGranHookeHistory::single(int i, int j, int itype, int jtype,
   // if I or J is frozen, meff is other particle
 
   double *rmass = atom->rmass;
-  int *type = atom->type;
   int *mask = atom->mask;
 
   mi = rmass[i];

src/KOKKOS/Install.sh

@@ -189,6 +189,14 @@ if (test $1 = 1) then
     sed -i -e '5 i \include ..\/..\/lib\/kokkos\/Makefile.kokkos' ../Makefile.package.settings
   fi
 
+  #  comb/omp triggers a persistent bug in nvcc. deleting it.
+  rm -f ../*_comb_omp.*
+
+elif (test $1 = 2) then
+
+  #  comb/omp triggers a persistent bug in nvcc. deleting it.
+  rm -f ../*_comb_omp.*
+
 elif (test $1 = 0) then
 
   if (test -e ../Makefile.package) then

src/KOKKOS/fix_nh_kokkos.cpp

@@ -291,7 +291,6 @@ void FixNHKokkos<DeviceType>::final_integrate()
 template<class DeviceType>
 void FixNHKokkos<DeviceType>::remap()
 {
-  int i;
   double oldlo,oldhi;
   double expfac;
 

src/MANYBODY/pair_airebo.cpp

@@ -2251,7 +2251,6 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
               ril[1] = rij[1]+rjl[1];
               ril[2] = rij[2]+rjl[2];
               ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
-              rijrjl = 2.0*rijmag*rjlmag;
               rjl2 = rjlmag*rjlmag;
               costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
               tspijl = Sp2(costmp,thmin,thmax,dtsijl);

src/MANYBODY/pair_bop.cpp

@@ -993,7 +993,6 @@ void PairBOP::theta()
   int *ilist;
   int *iilist;
   int **firstneigh;
-  int maxn,maxt;
   double rj2,rk2,rsq,ps;
   double rj1k1,rj2k2;
   double **x = atom->x;
@@ -1015,8 +1014,6 @@ void PairBOP::theta()
     itype = map[type[i]]+1;
 
     iilist=firstneigh[i];
-    maxt=0;
-    maxn=0;
     nlisti=BOP_total[i];
     for(jj=0;jj<nlisti;jj++) {
       temp_ij=BOP_index[i]+jj;
@@ -1038,10 +1035,8 @@ void PairBOP::theta()
           +disij[1][temp_ij]*disij[1][temp_ij]
           +disij[2][temp_ij]*disij[2][temp_ij];
       rij[temp_ij]=sqrt(rsq);
-      if(rij[temp_ij]<=rcut[i12]) {
+      if(rij[temp_ij]<=rcut[i12])
         neigh_flag[temp_ij]=1;
-        maxt++;
-      }
       else
         neigh_flag[temp_ij]=0;
       if(rij[temp_ij]<=rcut3[i12])
@@ -1067,7 +1062,6 @@ void PairBOP::theta()
       dRepul[temp_ij]=(pRepul6[i12][ks-1]*ps+pRepul5[i12][ks-1])*ps
           +pRepul4[i12][ks-1];
     }
-    if(maxt>maxn) maxn=maxt;
   }
   for (ii = 0; ii < nall; ii++) {
     n=0;

src/MANYBODY/pair_eim.cpp

@@ -921,13 +921,13 @@ int PairEIM::grabsingle(FILE *fptr, int i)
     pch1 = strstr(pch1,"element:");
     if (pch1 != NULL) {
       pch2 = strtok(NULL, " \t\n\r\f");
-      if (pch2 != NULL) data = strtok (NULL, "?");
+      if (pch2 != NULL) {
-      if (strcmp(pch2,elements[i]) == 0) {
+        data = strtok (NULL, "?");
-        sscanf(data,"%d %lg %lg %lg %lg %lg %lg",&setfl->ielement[i],
+        if (strcmp(pch2,elements[i]) == 0) {
-          &setfl->mass[i],&setfl->negativity[i],&setfl->ra[i],
+          sscanf(data,"%d %lg %lg %lg %lg %lg %lg",&setfl->ielement[i],
-          &setfl->ri[i],&setfl->Ec[i],&setfl->q0[i]);
+            &setfl->mass[i],&setfl->negativity[i],&setfl->ra[i],
-      } else {
+            &setfl->ri[i],&setfl->Ec[i],&setfl->q0[i]);
-        pch2 = NULL;
+        } else pch2 = NULL;
       }
     }
   }
@@ -960,25 +960,27 @@ int PairEIM::grabpair(FILE *fptr, int i, int j)
       pch2 = strtok (NULL, " \t\n\r\f");
       if (pch2 != NULL) pch3 = strtok (NULL, " \t\n\r\f");
       if (pch3 != NULL) data = strtok (NULL, "?");
-      if ((strcmp(pch2,elements[i]) == 0 &&
+      if ((pch2 != NULL) && (pch3 != NULL)) {
-        strcmp(pch3,elements[j]) == 0) ||
+        if ((strcmp(pch2,elements[i]) == 0 &&
-        (strcmp(pch2,elements[j]) == 0 &&
+          strcmp(pch3,elements[j]) == 0) ||
-        strcmp(pch3,elements[i]) == 0)) {
+          (strcmp(pch2,elements[j]) == 0 &&
-        sscanf(data,"%lg %lg %lg %lg %lg",
+          strcmp(pch3,elements[i]) == 0)) {
-          &setfl->rcutphiA[ij],&setfl->rcutphiR[ij],
+          sscanf(data,"%lg %lg %lg %lg %lg",
-          &setfl->Eb[ij],&setfl->r0[ij],&setfl->alpha[ij]);
+            &setfl->rcutphiA[ij],&setfl->rcutphiR[ij],
-        fgets(line,MAXLINE,fptr);
+            &setfl->Eb[ij],&setfl->r0[ij],&setfl->alpha[ij]);
-        sscanf(line,"%lg %lg %lg %lg %lg",
+          fgets(line,MAXLINE,fptr);
-          &setfl->beta[ij],&setfl->rcutq[ij],&setfl->Asigma[ij],
+          sscanf(line,"%lg %lg %lg %lg %lg",
-          &setfl->rq[ij],&setfl->rcutsigma[ij]);
+            &setfl->beta[ij],&setfl->rcutq[ij],&setfl->Asigma[ij],
-        fgets(line,MAXLINE,fptr);
+            &setfl->rq[ij],&setfl->rcutsigma[ij]);
-        sscanf(line,"%lg %lg %lg %d",
+          fgets(line,MAXLINE,fptr);
-          &setfl->Ac[ij],&setfl->zeta[ij],&setfl->rs[ij],
+          sscanf(line,"%lg %lg %lg %d",
-          &setfl->tp[ij]);
+            &setfl->Ac[ij],&setfl->zeta[ij],&setfl->rs[ij],
-      } else {
+            &setfl->tp[ij]);
-         pch1 = NULL;
+        } else {
-         pch2 = NULL;
+          pch1 = NULL;
-         pch3 = NULL;
+          pch2 = NULL;
+          pch3 = NULL;
+        }
       }
     }
   }

src/MANYBODY/pair_polymorphic.cpp

@@ -631,6 +631,8 @@ void PairPolymorphic::read_file(char *file)
   if (ptr) maxX = atof(ptr);
   if (ptr == NULL)
     error->all(FLERR,"Potential file incompatible with this pair style version");
+  if ((ng == 0) || (nr == 0) || (nx == 0))
+    error->all(FLERR,"Error reading potential file header");
 
   npair = nelements*(nelements+1)/2;
   ntriple = nelements*nelements*nelements;

src/MEAM/pair_meam.cpp

@@ -555,7 +555,7 @@ void PairMEAM::read_files(char *globalfile, char *userfile)
 
     for (i = 0; i < nelements; i++)
       if (strcmp(words[0],elements[i]) == 0) break;
-    if (i == nelements) continue;
+    if (i >= nelements) continue;
 
     // skip if element already appeared
 

src/Make.py

@@ -15,14 +15,14 @@ import sys,os,commands,re,copy,subprocess
 # setargs = makefile settings
 # actionargs = allowed actions (also lib-dir and machine)
 
-abbrevs = "adhjmoprsv"
+abbrevs = "adhjmoprsvz"
 
 switchclasses = ("actions","dir","help","jmake","makefile",
-                 "output","packages","redo","settings","verbose")
+                 "output","packages","redo","settings","verbose","zoutput")
 libclasses = ("atc","awpmd","colvars","cuda","gpu","h5md",
               "meam","poems","python","qmmm","reax","voronoi")
 buildclasses = ("intel","kokkos")
-makeclasses = ("cc","mpi","fft","jpg","png")
+makeclasses = ("cc","flags","mpi","fft","jpg","png")
 
 setargs = ("gzip","#gzip","ffmpeg","#ffmpeg","smallbig","bigbig","smallsmall")
 actionargs = ("lib-all","file","clean","exe")
@@ -137,27 +137,37 @@ class Actions:
     lib-all builds all auxiliary libs needed by installed packages
     lib-dir builds a specific lib whether package installed or not
       dir is any dir in lib directory (atc, cuda, meam, etc) except linalg
-  (2) file = create src/MAKE/MINE/Makefile.auto
+  (2) file = create a new src/MAKE/MINE/Makefile.auto
-    use -m switch for Makefile.machine to start from,
+    if file not specified, existing Makefile.auto is NOT changed
-      else use existing Makefile.auto
+      except by -m switch, which will copy Makefile.machine to Makefile.auto
-    adds settings needed for installed accelerator packages
+      note that exe action can add an -m switch, as described below
-    existing Makefile.auto is NOT changed unless "file" action is specified
+    if file is specified, new Makefile.auto is created
+      if "-m machine" specified (or added by exe),
+        start with existing Makefile.machine, else existing Makefile.auto
+      if "-m none" specified, start Makefile.auto from scratch
+        must use -cc and -mpi switches to specify compiler and MPI
+      settings for these switches will alter Makefile.auto
+        -s, -intel, -kokkos, -cc, -mpi, -fft, -jpg, -png
+      if these accelerator packages are installed, they induce settings
+        that will alter Makefile.auto: opt, user-omp, user-intel, kokkos
+     use -z switch to copy final Makefile.auto to new filename
   (3) clean = invoke "make clean-auto" to insure clean build on current files
     useful if compiler flags have changed
   (4) exe or machine = build LAMMPS
     machine can be any existing Makefile.machine suffix
-      machine is converted to "exe" action, as well as:
+      machine is converted to "exe" action, and additionally:
         "-m machine" is added if -m switch is not specified
         "-o machine" is added if -o switch is not specified
         if either "-m"  or "-o" are specified, they are not overridden
     does not invoke any lib builds, since libs could be previously built
-    exe always builds using src/MAKE/MINE/Makefile.auto
+    exe ALWAYS builds using src/MAKE/MINE/Makefile.auto
-      if file action also specified, it creates Makefile.auto
+      if file action also specified, it creates a new Makefile.auto
       else if -m switch specified,
         existing Makefile.machine is copied to create Makefile.auto
       else Makefile.auto must already exist and is not changed
-    produces src/lmp_auto, or error message if unsuccessful
+    build produces src/lmp_auto, or error message if unsuccessful
       use -o switch to copy src/lmp_auto to new filename
+      use -z switch to copy src/MAKE/MINE/Makefile.auto to new filename
 """
   
   def check(self):
@@ -177,7 +187,7 @@ class Actions:
         cleans.append(one)
       elif one == "exe":
         exes.append(one)
-      # one action can be unknown in case is a machine (checked in setup)
+      # one action can be unknown, must be a machine (checked in setup)
       else:
         exes.append(one)
     if len(set(libs)) != len(libs) or \
@@ -236,9 +246,9 @@ class Actions:
   
   def file(self,caller):
 
-    # if caller = "file", create from mpi or read from makefile.machine or auto
+    # if caller="file", create from mpi or read from Makefile.machine or auto
-    # if caller = "exe" and "file" action already invoked, read from auto
+    # if caller="exe" and "file" action already invoked, read from auto
-    # if caller = "exe" and no "file" action, read from makefile.machine or auto
+    # if caller="exe" and no "file" action, read from Makefile.machine or auto
     
     if caller == "file":
       if makefile and makefile.machine == "none":
@@ -279,7 +289,7 @@ class Actions:
               make.addvar("CC","-cxx=%s" % wrapper)
               make.addvar("LINK","-cxx=%s" % wrapper)
             elif "-lmpi" in txt:
-              make.addvar("OMPI_CXX",wrapper,"cc")
+              make.addvar("export OMPI_CXX",wrapper,"cc")
               precompiler = "env OMPI_CXX=%s " % wrapper
             else: error("Could not add MPI wrapper compiler, " +
                         "did not recognize OpenMPI or MPICH")
@@ -287,8 +297,20 @@ class Actions:
         make.addvar("CCFLAGS","-O3")
         make.setvar("LINKFLAGS","-g")
         make.addvar("LINKFLAGS","-O")
+        
+      # add CC and LINK flags
 
-# add MPI settings
+      if flags:
+        for flag in flags.CC:
+          flag = "-" + flag
+          if flag[:2] == "-O": make.delvar("CCFLAGS","-O*")
+          make.addvar("CCFLAGS",flag)
+        for flag in flags.LINK:
+          flag = "-" + flag
+          if flag[:2] == "-O": make.delvar("LINKFLAGS","-O*")
+          make.addvar("LINKFLAGS",flag)
+
+      # add MPI settings
 
       if mpi:
         make.delvar("MPI_INC","*")
@@ -397,7 +419,7 @@ class Actions:
           make.addvar("KOKKOS_DEVICES","OpenMP","lmp")
           make.addvar("KOKKOS_ARCH","KNC","lmp")
 
-      # add LMP settings
+      # add LMP_INC ifdef settings
       
       if settings:
         list = settings.inlist
@@ -465,12 +487,13 @@ class Actions:
 
     # set self.stubs if Makefile.auto uses STUBS lib in MPI settings
 
-    if "-lmpi_stubs" in make.getvar("MPI_LIB"): self.stubs = 1
+    if make.getvar("MPI_LIB") and "-lmpi_stubs" in make.getvar("MPI_LIB"):
+      self.stubs = 1
     else: self.stubs = 0
     
     # write out Makefile.auto
     # unless caller = "exe" and "file" action already invoked
-
+    
     if caller == "file" or "file" not in self.alist:
       make.write("%s/MAKE/MINE/Makefile.auto" % dir.src,1)
       print "Created src/MAKE/MINE/Makefile.auto"
@@ -510,13 +533,23 @@ class Actions:
         print txt
         error('Unsuccessful "make stubs"')
       print "Created src/STUBS/libmpi_stubs.a"
-    if jmake: str = "cd %s; make -j %d auto" % (dir.src,jmake.n)
+
-    else: str = "cd %s; make auto" % dir.src
+    # special hack for shannon GPU cluster
+    # must use "srun make" if on it and building w/ GPU package, else just make
+    # this is b/c Cuda libs are not all available on host
+
+    make = "make"
+    if "shannon" in os.environ.get("HOST") and packages.final["gpu"]:
+      make = "srun make"
+      
+    if jmake: str = "cd %s; %s -j %d auto" % (dir.src,make,jmake.n)
+    else: str = "cd %s; %s auto" % (dir.src,make)
     
     # if verbose, print output as build proceeds, else only print if fails
 
     if verbose: subprocess.call(str,shell=True)
     else:
+      print str
       try: subprocess.check_output(str,stderr=subprocess.STDOUT,shell=True)
       except Exception as e: print e.output
 
@@ -574,8 +607,8 @@ Syntax: Make.py switch args ...
     list one or more actions, in any order
     machine is a Makefile.machine suffix
   one-letter switches:
-    -d (dir), -j (jmake), -m (makefile), -o (output),
+    -d (dir), -j (jmake), -m (makefile), -o (output), -p (packages),
-    -p (packages), -r (redo), -s (settings), -v (verbose)
+    -r (redo), -s (settings), -v (verbose), -z (makefile output)
   switches for libs:
     -atc, -awpmd, -colvars, -cuda, -gpu, -h5md,
     -meam, -poems, -python, -qmmm, -reax, -voronoi
@@ -898,9 +931,13 @@ class Settings:
   def help(self):
     return """
 -s set1 set2 ...
-  possible settings = gzip smallbig bigbig smallsmall
+  possible settings = gzip #gzip ffmpeg #ffmpeg smallbig bigbig smallsmall
-  add each setting as LAMMPS setting to created Makefile.auto
+  alter LAMMPS ifdef settings in Makefile.auto
-  if -s not specified, no settings are changed in Makefile.auto
+    only happens if new Makefile.auto is created by use of "file" action
+  gzip and #gzip turn on/off LAMMPS_GZIP setting
+  ffmpeg and #ffmpeg turn on/off LAMMPS_FFMPEG setting
+  smallbig, bigbig, smallsmall turn on LAMMPS_SMALLBIG, etc
+    and turn off other two
 """
   
   def check(self):
@@ -924,6 +961,23 @@ class Verbose:
   def check(self):
     if len(self.inlist): error("-v args are invalid")
 
+# zoutput switch for making copy of final Makefile.auto
+
+class Zoutput:
+  def __init__(self,list):
+    self.inlist = copy.copy(list)
+
+  def help(self):
+    return """
+-z machine
+  copy created/used src/MAKE/MINE/Makefile.auto to Makefile.machine in same dir
+  this can be used to preserve the machine makefile
+"""
+
+  def check(self):
+    if len(self.inlist) != 1: error("-z args are invalid")
+    self.machine = self.inlist[0]
+
 # ----------------------------------------------------------------
 # lib classes, one per LAMMPS auxiliary lib
 # ----------------------------------------------------------------
@@ -1087,15 +1141,15 @@ class CUDA:
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.mode = "double"
-    self.arch = "31"
+    self.arch = "35"
 
   def help(self):
     return """
--cuda mode=double arch=31
+-cuda mode=double arch=35
   all args are optional and can be in any order
   mode = double or mixed or single (def = double)
-  arch = M (def = 31)
+  arch = M (def = 35)
-    M = 31 for Kepler
+    M = 31,35,37,etc for Kepler
     M = 20 for CC2.0 (GF100/110, e.g. C2050,GTX580,GTX470)
     M = 21 for CC2.1 (GF104/114,  e.g. GTX560, GTX460, GTX450)
     M = 13 for CC1.3 (GF200, e.g. C1060, GTX285)
@@ -1144,16 +1198,18 @@ class GPU:
   def __init__(self,list):
     self.inlist = copy.copy(list)
     self.make = "linux.double"
-    self.lammpsflag = self.modeflag = self.archflag = 0
+    self.lammpsflag = self.modeflag = self.archflag = self.homeflag = 0
 
   def help(self):
     return """
--gpu make=suffix lammps=suffix2 mode=double arch=N
+-gpu make=suffix lammps=suffix2 mode=double arch=N home=path
   all args are optional and can be in any order
   make = use Makefile.suffix (def = linux.double)
   lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
   mode = double or mixed or single (def = CUDA_PREC in makefile)
-  arch = 31 (Kepler) or 21 (Fermi) (def = CUDA_ARCH in makefile)
+  arch = 3x (x = digit for Kepler) or 2x (x = digit for Fermi)
+         (def = CUDA_ARCH in makefile)
+  home = path to Cuda, e.g. /usr/local/cuda (def = CUDA_HOME in makefile)
 """
 
   def check(self):
@@ -1172,6 +1228,9 @@ class GPU:
       elif words[0] == "arch":
         self.arch = words[1]
         self.archflag = 1
+      elif words[0] == "home":
+        self.home = words[1]
+        self.homeflag = 1
       else: error("-gpu args are invalid")
       if self.modeflag and (self.mode != "double" and
                             self.mode != "mixed" and
@@ -1192,13 +1251,22 @@ class GPU:
         make.setvar("CUDA_PRECISION","-D_SINGLE_SINGLE")
     if self.archflag:
       make.setvar("CUDA_ARCH","-arch=sm_%s" % self.arch)
+    if self.homeflag:
+      make.setvar("CUDA_HOME",self.home)
     if self.lammpsflag:
       make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)
     make.write("%s/Makefile.auto" % libdir)
 
-    commands.getoutput("cd %s; make -f Makefile.auto clean" % libdir)
+    # special hack for shannon GPU cluster
-    if jmake: str = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)
+    # must use "srun make" if on it, else just make
-    else: str = "cd %s; make -f Makefile.auto" % libdir
+    # this is b/c Cuda libs are not all available on host
+
+    make = "make"
+    if "shannon" in os.environ.get("HOST"): make = "srun make"
+    
+    commands.getoutput("cd %s; %s -f Makefile.auto clean" % (libdir,make))
+    if jmake: str = "cd %s; %s -j %d -f Makefile.auto" % (libdir,make,jmake.n)
+    else: str = "cd %s; %s -f Makefile.auto" % (libdir,make)
 
     # if verbose, print output as build proceeds, else only print if fails
 
@@ -1574,14 +1642,16 @@ class Kokkos:
   mode is not optional, arch is optional
   mode = omp or cuda or phi (def = KOKKOS_DEVICES setting in Makefile )
     build Kokkos package for omp or cuda or phi
-    set KOKKOS_DEVICES to "OpenMP" (omp, phi) or "Cuda, OpenMP" (cuda)
+    sets KOKKOS_DEVICES to "OpenMP" (omp, phi) or "Cuda, OpenMP" (cuda)
-  arch = 31 (Kepler) or 21 (Fermi) (def = -arch setting in Makefile)
+  arch = number like 35 (Kepler) or 21 (Fermi)
+    sets KOKKOS_ARCH to appropriate value
 """
 
   def check(self):
+    print self.inlist
     if self.inlist != None and len(self.inlist) == 0:
       error("-kokkos args are invalid")
-
+      
     if self.inlist == None: return
     if len(self.inlist) < 1: error("-kokkos args are invalid")
     self.mode = self.inlist[0]
@@ -1596,7 +1666,7 @@ class Kokkos:
       else: error("-kokkos args are invalid")
       
 # ----------------------------------------------------------------
-# makefile classes for CC, MPI, JPG, PNG, FFT settings
+# makefile classes for CC, FLAGS, MPI, JPG, PNG, FFT settings
 # ----------------------------------------------------------------
 
 # Cc class
@@ -1610,7 +1680,8 @@ class Cc:
   def help(self):
     return """
 -cc compiler wrap=wcompiler
-  change CC setting in makefile
+  alter CC setting in Makefile.auto
+    only happens if new Makefile.auto is created by use of "file" action
   compiler is required, all other args are optional
   compiler = any string with g++ or icc or icpc
              or mpi (or mpicxx, mpiCC, mpiicpc, etc)
@@ -1644,6 +1715,41 @@ class Cc:
         self.wrap = words[1]
       else: error("-cc args are invalid")
 
+# Flags class
+
+class Flags:
+  def __init__(self,list):
+    self.inlist = copy.copy(list)
+    self.CC = []
+    self.LINK = []
+    
+  def help(self):
+    return """
+-flags flag f1 f2 ... flag f1 f2 ... 
+  alter CCFLAGS or LINKFLAGS settings in Makefile.auto
+    only happens if new Makefile.auto is created by use of "file" action
+  flag = CC or LINK
+    one or both can be specified
+  f1,f2,etc = flag to add or replace
+    "-" char will be prepended to each
+    for example: g, O3, xHost, "fp-model fast=2"
+    will become: -g, -O3, -xHost, -fp-model fast=2
+    for -O,-O2,-O3,etc: existing -O* will first be removed
+"""
+
+  def check(self):
+    if len(self.inlist) < 1: error("-flags args are invalid")
+    self.CC = []     # necessary?
+    self.LINK = []
+    mode = ""
+    for one in self.inlist:
+      if one == "CC": mode = "CC"
+      elif one == "LINK": mode = "LINK"
+      else:
+        if not mode: error("-flags args are invalid")
+        if mode == "CC": self.CC.append(one)
+        elif mode == "LINK": self.LINK.append(one)
+    
 # Mpi class
 
 class Mpi:
@@ -1654,7 +1760,8 @@ class Mpi:
   def help(self):
     return """
 -mpi style dir=path
-  change MPI settings in makefile
+  alter MPI settings in Makefile.auto
+    only happens if new Makefile.auto is created by use of "file" action
   style is required, all other args are optional
   style = mpi or mpich or ompi or serial
     mpi = no MPI settings (assume compiler is MPI wrapper)
@@ -1687,9 +1794,10 @@ class Fft:
   def help(self):
     return """
 -fft mode lib=libname dir=homedir idir=incdir ldir=libdir
-  change FFT settings in makefile
+  alter FFT settings in Makefile.auto
+    only happens if new Makefile.auto is created by use of "file" action
   mode is required, all other args are optional
-  removes all current FFT variable settings
+  first removes all current FFT variable settings
   mode = none or fftw or fftw3 or ...
     adds -DFFT_MODE setting
   lib = name of FFT library to link with (def is libname = mode)
@@ -1727,6 +1835,8 @@ class Jpg:
   def help(self):
     return """
 -jpg flag dir=homedir idir=incdir ldir=libdir
+  alter JPG settings in Makefile.auto
+    only happens if new Makefile.auto is created by use of "file" action
   change JPG settings in makefile
   all args are optional, flag must come first if specified
   flag = yes or no (def = yes)
@@ -1764,7 +1874,8 @@ class Png:
   def help(self):
     return """
 -png flag dir=homedir idir=incdir ldir=libdir
-  change PNG settings in makefile
+  alter PNG settings in Makefile.auto
+    only happens if new Makefile.auto is created by use of "file" action
   all args are optional, flag must come first if specified
   flag = yes or no (def = yes)
     include or exclude PNG support
@@ -2143,13 +2254,22 @@ while 1:
 
   packages.uninstall()
   
-  # create output file if requested and exe action performed
+  # create copy of executable if requested, and exe action performed
 
   if output and actions and "exe" in actions.alist:
     txt = "cp %s/lmp_auto %s/lmp_%s" % (dir.src,dir.cwd,output.machine)
     commands.getoutput(txt)
     print "Created lmp_%s in %s" % (output.machine,dir.cwd)
 
+  # create copy of Makefile.auto if requested, and file or exe action performed
+
+  if zoutput and actions and \
+        ("file" in actions.alist or "exe" in actions.alist):
+    txt = "cp %s/MAKE/MINE/Makefile.auto %s/MAKE/MINE/Makefile.%s" % \
+        (dir.src,dir.src,zoutput.machine)
+    commands.getoutput(txt)
+    print "Created Makefile.%s in %s/MAKE/MINE" % (zoutput.machine,dir.src)
+
   # write current Make.py command to src/Make.py.last
 
   fp = open("%s/Make.py.last" % dir.src,'w')

src/Makefile

@@ -205,8 +205,8 @@ install-python:
 tar:
 	@cd STUBS; $(MAKE) clean
 	@cd ..; tar cvzf src/$(ROOT)_src.tar.gz \
-	  src/Make* src/Package.sh src/Depend.sh \
+	  src/Make* src/Package.sh src/Depend.sh src/Install.sh \
-	  src/MAKE src/*.cpp src/*.h src/STUBS \
+	  src/MAKE src/DEPEND src/*.cpp src/*.h src/STUBS \
 	  $(patsubst %,src/%,$(PACKAGEUC)) $(patsubst %,src/%,$(PACKUSERUC)) \
           --exclude=*/.svn
 	@cd STUBS; $(MAKE)

src/QEQ/fix_qeq_fire.cpp

@@ -107,17 +107,16 @@ void FixQEqFire::init()
 void FixQEqFire::pre_force(int vflag)
 {
   int inum, *ilist;
-  int i,ii,iloop,loopmax;
+  int i,ii,iloop;
-  int *mask = atom->mask;
 
   double *q = atom->q;
   double vmax,vdotf,vdotfall,vdotv,vdotvall,fdotf,fdotfall;
   double scale1,scale2;
   double dtvone,dtv;
-  double enegtot,enegchk,enegmax;
+  double enegtot,enegchk;
   double alpha = qdamp;
   double dt, dtmax;
-  double enegchkall,enegmaxall;
+  double enegchkall;
   bigint ntimestep = update->ntimestep;
   bigint last_negative = 0;
 
@@ -225,7 +224,7 @@ void FixQEqFire::pre_force(int vflag)
   if (comm->me == 0) {
     if (iloop == maxiter) {
       char str[128];
-      sprintf(str,"Charges did not converge at step "BIGINT_FORMAT
+      sprintf(str,"Charges did not converge at step " BIGINT_FORMAT
 		  ": %lg",update->ntimestep,enegchk);
       error->warning(FLERR,str);
     }

src/REPLICA/temper.cpp

@@ -93,13 +93,38 @@ void Temper::command(int narg, char **arg)
   if (nswaps*nevery != nsteps)
     error->universe_all(FLERR,"Non integer # of swaps in temper command");
 
-  // fix style must be appropriate for temperature control
+  // fix style must be appropriate for temperature control, i.e. it needs
+  // to provide a working Fix::reset_target() and must not change the volume.
 
   if ((strcmp(modify->fix[whichfix]->style,"nvt") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/asphere") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/asphere/omp") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/body") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/eff") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/intel") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/kk") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/kk/host") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/kk/device") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/omp") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/sphere") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"nvt/sphere/omp") != 0) &&
       (strcmp(modify->fix[whichfix]->style,"langevin") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"langevin/drude") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"langevin/eff") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"gld") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"gle") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"rigid/nvt") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"rigid/nvt/small") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"rigid/nvt/omp") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"rigid/nvt/small/omp") != 0) &&
       (strcmp(modify->fix[whichfix]->style,"temp/berendsen") != 0) &&
-      (strcmp(modify->fix[whichfix]->style,"temp/rescale") != 0))
+      (strcmp(modify->fix[whichfix]->style,"temp/berendsen/cuda") != 0) &&
-    error->universe_all(FLERR,"Tempering temperature fix is not valid");
+      (strcmp(modify->fix[whichfix]->style,"temp/csvr") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"temp/csld") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"temp/rescale") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"temp/rescale/cuda") != 0) &&
+      (strcmp(modify->fix[whichfix]->style,"temp/rescale/eff") != 0))
+    error->universe_all(FLERR,"Tempering temperature fix is not supported");
 
   // setup for long tempering run
 

src/STUBS/Makefile.mingw32-cross

@@ -16,7 +16,7 @@ OBJ = 		$(SRC:%.c=%_mingw32.o)
 # System-specific settings
 
 CC =	        i686-w64-mingw32-gcc
-CCFLAGS =	-O2 -Wall -march=i686 -mtune=generic -mfpmath=387 -mpc64
+CCFLAGS =	-O2 -Wall -march=i686 -mtune=generic -mfpmath=387 -mpc64 -I.
 ARCHIVE =	i686-w64-mingw32-ar
 ARCHFLAG =	rs
 

src/STUBS/Makefile.mingw64-cross

@@ -16,7 +16,7 @@ OBJ = 		$(SRC:%.c=%_mingw64.o)
 # System-specific settings
 
 CC =	        x86_64-w64-mingw32-gcc
-CCFLAGS =	-O2 -Wall -march=core2 -mtune=core2 -msse2 -mpc64
+CCFLAGS =	-O2 -Wall -march=core2 -mtune=core2 -msse2 -mpc64 -I.
 ARCHIVE =	x86_64-w64-mingw32-ar
 ARCHFLAG =	rs
 

src/USER-OMP/pair_airebo_omp.cpp

@@ -1097,7 +1097,6 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
               ril[1] = rij[1]+rjl[1];
               ril[2] = rij[2]+rjl[2];
               ril2 = (ril[0]*ril[0])+(ril[1]*ril[1])+(ril[2]*ril[2]);
-              rijrjl = 2.0*rijmag*rjlmag;
               rjl2 = rjlmag*rjlmag;
               costmp = 0.5*(rij2+rjl2-ril2)/rijmag/rjlmag;
               tspijl = Sp2(costmp,thmin,thmax,dtsijl);

src/compute_chunk_atom.cpp

@@ -398,7 +398,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
     double scale;
     if (which == BIN1D || which == BIN2D || which == BIN3D || 
         which == BINCYLINDER) {
-      if (which == BIN1D || BINCYLINDER) ndim = 1;
+      if (which == BIN1D || which == BINCYLINDER) ndim = 1;
       if (which == BIN2D) ndim = 2;
       if (which == BIN3D) ndim = 3;
       for (int idim = 0; idim < ndim; idim++) {

src/domain.cpp

@@ -503,13 +503,12 @@ void Domain::pbc()
 
   double *coord;
   int n3 = 3*nlocal;
-  if (x) {
+  coord = &x[0][0];  // note: x is always initialzed to at least one element.
-    coord = &x[0][0];
+  int flag = 0;
-    int flag = 0;
+  for (i = 0; i < n3; i++)
-    for (i = 0; i < n3; i++)
+    if (!ISFINITE(*coord++)) flag = 1;
-      if (!ISFINITE(*coord++)) flag = 1;
+  if (flag) error->one(FLERR,"Non-numeric atom coords - simulation unstable");
-    if (flag) error->one(FLERR,"Non-numeric atom coords - simulation unstable");
+
-  }
   // setup for PBC checks
 
   if (triclinic == 0) {

src/dump_image.cpp

@@ -850,7 +850,6 @@ void DumpImage::create_image()
 
   if (bodyflag) {
     Body *bptr = avec_body->bptr;
-    double **x = atom->x;
     int *body = atom->body;
 
     m = 0;

src/fix_ave_time.cpp

@@ -23,7 +23,6 @@
 #include "force.h"
 #include "modify.h"
 #include "compute.h"
-#include "group.h"
 #include "input.h"
 #include "variable.h"
 #include "memory.h"
@@ -55,6 +54,8 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
 
   global_freq = nfreq;
 
+  dynamic_group_allow = 1;
+
   // scan values to count them
   // then read options so know mode = SCALAR/VECTOR before re-reading values
 

src/math_const.h

@@ -25,6 +25,7 @@ namespace MathConst {
   static const double MY_PI2 = 1.57079632679489661923; // pi/2
   static const double MY_PI4 = 0.78539816339744830962; // pi/4
   static const double MY_PIS = 1.77245385090551602729; // sqrt(pi)
+  static const double MY_ISPI4 = 1.12837916709551257389; // 1/sqrt(pi/4)
   static const double MY_SQRT2 = 1.41421356237309504880; // sqrt(2)
   static const double MY_CBRT2 = 1.25992104989487316476; // 2*(1/3)
 }

src/read_data.cpp

@@ -1468,7 +1468,7 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
 
 void ReadData::bodies(int firstpass)
 {
-  int i,m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody,tmp;
+  int m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody,tmp;
   char *eof;
 
   int mapflag = 0;

src/set.cpp

@@ -917,7 +917,6 @@ void Set::setrandom(int keyword)
 
   } else if (keyword == THETA_RANDOM) {
     int nlocal = atom->nlocal;
-    double theta;
     for (i = 0; i < nlocal; i++) {
       if (select[i]) {
 	if (atom->line[i] < 0)