Merge pull request #614 from akohlmey/fixes-for-stable

Fixes for stable

lib/colvars/Install.py

@@ -45,12 +45,12 @@ while iarg < nargs:
   if args[iarg] == "-m":
     if iarg+2 > len(args): error()
     machine = args[iarg+1]
-    iarg += 2  
+    iarg += 2
   elif args[iarg] == "-e":
     if iarg+2 > len(args): error()
     extraflag = True
     suffix = args[iarg+1]
-    iarg += 2  
+    iarg += 2
   else: error()
 
 # set lib from working dir

lib/gpu/Install.py

@@ -14,7 +14,7 @@ Syntax from lib dir: python Install.py -m machine -h hdir -a arch -p precision -
 
 specify one or more options, order does not matter
 
-copies an existing Makefile.machine in lib/gpu to Makefile.auto 
+copies an existing Makefile.machine in lib/gpu to Makefile.auto
 optionally edits these variables in Makefile.auto:
   CUDA_HOME, CUDA_ARCH, CUDA_PRECISION, EXTRAMAKE
 optionally uses Makefile.auto to build the GPU library -> libgpu.a
@@ -26,7 +26,7 @@ optionally copies Makefile.auto to a new Makefile.osuffix
   -h = set CUDA_HOME variable in Makefile.auto to hdir
        hdir = path to NVIDIA Cuda software, e.g. /usr/local/cuda
   -a = set CUDA_ARCH variable in Makefile.auto to arch
-       use arch = 20 for Tesla C2050/C2070 (Fermi) (deprecated as of CUDA 8.0) 
+       use arch = 20 for Tesla C2050/C2070 (Fermi) (deprecated as of CUDA 8.0)
                      or GeForce GTX 580 or similar
        use arch = 30 for Tesla K10 (Kepler)
        use arch = 35 for Tesla K40 (Kepler) or GeForce GTX Titan or similar
@@ -108,10 +108,10 @@ if pflag:
   elif precision == "mixed": precstr = "-D_SINGLE_DOUBLE"
   elif precision == "single": precstr = "-D_SINGLE_SINGLE"
   else: error("Invalid precision setting")
-  
+
 # create Makefile.auto
 # reset EXTRAMAKE, CUDA_HOME, CUDA_ARCH, CUDA_PRECISION if requested
-  
+
 if not os.path.exists("Makefile.%s" % isuffix):
   error("lib/gpu/Makefile.%s does not exist" % isuffix)
 

lib/kim/Install.py

@@ -6,6 +6,8 @@
 from __future__ import print_function
 import sys,os,re,subprocess
 
+# help message
+
 help = """
 Syntax from src dir: make lib-kim args="-b -v version  -a kim-name"
                  or: make lib-kim args="-b -a everything"
@@ -23,7 +25,7 @@ specify one or more options, order does not matter
   -b = download and build base KIM API library with example Models
        this will delete any previous installation in the current folder
   -n = do NOT download and build base KIM API library.
-       Use an existing installation 
+       Use an existing installation
   -p = specify location of KIM API installation (implies -n)
   -a = add single KIM model or model driver with kim-name
        to existing KIM API lib (see example below).
@@ -78,13 +80,27 @@ def which(program):
   return None
 
 def geturl(url,fname):
+  success = False
+
   if which('curl') != None:
     cmd = 'curl -L -o "%s" %s' % (fname,url)
-  elif which('wget') != None:
+    try:
+      subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+      success = True
+    except subprocess.CalledProcessError as e:
+      print("Calling curl failed with: %s" % e.output.decode('UTF-8'))
+
+  if not success and which('wget') != None:
     cmd = 'wget -O "%s" %s' % (fname,url)
-  else: error("cannot find 'wget' or 'curl' to download source code")
-  txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
-  return txt
+    try:
+      subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+      success = True
+    except subprocess.CalledProcessError as e:
+      print("Calling wget failed with: %s" % e.output.decode('UTF-8'))
+
+  if not success:
+    error("Failed to download source code with 'curl' or 'wget'")
+  return
 
 # parse args
 

lib/mscg/Install.py

@@ -65,13 +65,27 @@ def which(program):
   return None
 
 def geturl(url,fname):
+  success = False
+
   if which('curl') != None:
     cmd = 'curl -L -o "%s" %s' % (fname,url)
-  elif which('wget') != None:
+    try:
+      subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+      success = True
+    except subprocess.CalledProcessError as e:
+      print("Calling curl failed with: %s" % e.output.decode('UTF-8'))
+
+  if not success and which('wget') != None:
     cmd = 'wget -O "%s" %s' % (fname,url)
-  else: error("cannot find 'wget' or 'curl' to download source code")
-  txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
-  return txt
+    try:
+      subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+      success = True
+    except subprocess.CalledProcessError as e:
+      print("Calling wget failed with: %s" % e.output.decode('UTF-8'))
+
+  if not success:
+    error("Failed to download source code with 'curl' or 'wget'")
+  return
 
 # parse args
 

lib/smd/Install.py

@@ -65,13 +65,27 @@ def which(program):
   return None
 
 def geturl(url,fname):
+  success = False
+
   if which('curl') != None:
     cmd = 'curl -L -o "%s" %s' % (fname,url)
-  elif which('wget') != None:
+    try:
+      subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+      success = True
+    except subprocess.CalledProcessError as e:
+      print("Calling curl failed with: %s" % e.output.decode('UTF-8'))
+
+  if not success and which('wget') != None:
     cmd = 'wget -O "%s" %s' % (fname,url)
-  else: error("cannot find 'wget' or 'curl' to download source code")
-  txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
-  return txt
+    try:
+      subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+      success = True
+    except subprocess.CalledProcessError as e:
+      print("Calling wget failed with: %s" % e.output.decode('UTF-8'))
+
+  if not success:
+    error("Failed to download source code with 'curl' or 'wget'")
+  return
 
 # parse args
 

lib/voronoi/Install.py

@@ -64,13 +64,27 @@ def which(program):
   return None
 
 def geturl(url,fname):
+  success = False
+
   if which('curl') != None:
     cmd = 'curl -L -o "%s" %s' % (fname,url)
-  elif which('wget') != None:
+    try:
+      subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+      success = True
+    except subprocess.CalledProcessError as e:
+      print("Calling curl failed with: %s" % e.output.decode('UTF-8'))
+
+  if not success and which('wget') != None:
     cmd = 'wget -O "%s" %s' % (fname,url)
-  else: error("cannot find 'wget' or 'curl' to download source code")
-  txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
-  return txt
+    try:
+      subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+      success = True
+    except subprocess.CalledProcessError as e:
+      print("Calling wget failed with: %s" % e.output.decode('UTF-8'))
+
+  if not success:
+    error("Failed to download source code with 'curl' or 'wget'")
+  return
 
 # parse args
 

src/Makefile

@@ -339,17 +339,18 @@ no-%:
         fi;
 
 # download/build/install a package library
+# update the timestamp on main.cpp to trigger a relink with "make machine"
 
 lib-%:
 	@if [ -e ../lib/$(LIBDIR)/Install.py ]; then \
 	  echo "Installing lib $(@:lib-%=%)"; \
-	  cd ../lib/$(LIBDIR); $(PYTHON) Install.py $(args); \
+	  ( cd ../lib/$(LIBDIR); $(PYTHON) Install.py $(args) ); \
 	elif [ -e ../lib/$(LIBUSERDIR)/Install.py ]; then \
 	  echo "Installing lib $(@:lib-user-%=%)"; \
-	  cd ../lib/$(LIBUSERDIR); $(PYTHON) Install.py $(args); \
+	  ( cd ../lib/$(LIBUSERDIR); $(PYTHON) Install.py $(args) ); \
 	else \
 	  echo "Install script for lib $(@:lib-%=%) does not exist"; \
-	fi;
+	fi; touch main.cpp
 
 # status = list src files that differ from package files
 # update = replace src files with newer package files

src/pair.cpp

@@ -75,7 +75,7 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp)
   ewaldflag = pppmflag = msmflag = dispersionflag = tip4pflag = dipoleflag = 0;
   reinitflag = 1;
 
-  // pair_modify settingsx
+  // pair_modify settings
 
   compute_flag = 1;
   manybody_flag = 0;

src/pair_hybrid.cpp

@@ -36,7 +36,7 @@ PairHybrid::PairHybrid(LAMMPS *lmp) : Pair(lmp),
   map(NULL), special_lj(NULL), special_coul(NULL), compute_tally(NULL)
 {
   nstyles = 0;
-  
+
   outerflag = 0;
   respaflag = 0;
 
@@ -490,7 +490,7 @@ void PairHybrid::init_style()
         if (((force->special_lj[i] == 0.0) || (force->special_lj[i] == 1.0))
             && (force->special_lj[i] != special_lj[istyle][i]))
           error->all(FLERR,"Pair_modify special setting for pair hybrid "
-		     "incompatible with global special_bonds setting");
+                     "incompatible with global special_bonds setting");
       }
     }
 
@@ -500,7 +500,7 @@ void PairHybrid::init_style()
              || (force->special_coul[i] == 1.0))
             && (force->special_coul[i] != special_coul[istyle][i]))
           error->all(FLERR,"Pair_modify special setting for pair hybrid "
-		     "incompatible with global special_bonds setting");
+                     "incompatible with global special_bonds setting");
       }
     }
   }
@@ -832,6 +832,12 @@ void PairHybrid::modify_params(int narg, char **arg)
     Pair::modify_params(narg,arg);
     for (int m = 0; m < nstyles; m++) styles[m]->modify_params(narg,arg);
   }
+
+  // reset global compute_flag since there may have been changes
+  // to any of the substyles
+  compute_flag = 0;
+  for (int m = 0; m < nstyles; m++)
+    if (styles[m]->compute_flag) compute_flag = 1;
 }
 
 /* ----------------------------------------------------------------------