Collected small changes for the next patch release

cmake/CMakeLists.txt

@@ -613,8 +613,9 @@ if(PKG_USER-PLUMED)
 endif()
 
 if(PKG_USER-MOLFILE)
+  set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
   add_library(molfile INTERFACE)
-  target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile)
+  target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
   target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
   list(APPEND LAMMPS_LINK_LIBS molfile)
 endif()
@@ -626,7 +627,6 @@ if(PKG_USER-NETCDF)
   add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
 endif()
 
-
 if(PKG_USER-SMD)
   option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF)
   if(DOWNLOAD_EIGEN3)

doc/src/Build_extras.txt

@@ -893,7 +893,17 @@ USER-MOLFILE package :h4,link(user-molfile)
 
 [CMake build]:
 
-No additional settings are needed besides "-D PKG_USER-MOLFILE=yes".
+-D MOLFILE_INCLUDE_DIRS=path   # (optional) path where VMD molfile plugin headers are installed
+-D PKG_USER-MOLFILE=yes     :pre
+
+
+Using "-D PKG_USER-MOLFILE=yes" enables the package, and setting
+"-D MOLFILE_INCLUDE DIRS" allows to provide a custom location for
+the molfile plugin header files. These should match the ABI of the
+plugin files used, and thus one typically sets them to include
+folder of the local VMD installation in use. LAMMPS ships with a
+couple of default header files that correspond to a popular VMD
+version, usually the latest release.
 
 [Traditional make]:
 
@@ -902,7 +912,11 @@ loading library libdl.a that is typically present on all systems.  It
 is required for LAMMPS to link with this package.  If the setting is
 not valid for your system, you will need to edit the Makefile.lammps
 file.  See lib/molfile/README and lib/molfile/Makefile.lammps for
-details.
+details. It is also possible to configure a different folder with
+the VMD molfile plugin header files. LAMMPS ships with a couple of
+default headers, but these are not compatible with all VMD versions,
+so it is often best to change this setting to the location of the
+same include files of the local VMD installation in use.
 
 :line
 

lib/gpu/lal_device.cpp

@@ -237,7 +237,7 @@ int DeviceT::set_ocl_params(char *ocl_vendor) {
                         " -DBLOCK_CELL_ID="+params[11]+
                         " -DMAX_BIO_SHARED_TYPES="+params[12];
   }
-  _ocl_compile_string="-cl-fast-relaxed-math -cl-mad-enable "+std::string(OCL_INT_TYPE)+" "+
+  _ocl_compile_string="-cl-std=CL1.2 -cl-fast-relaxed-math -cl-mad-enable "+std::string(OCL_INT_TYPE)+" "+
                       std::string(OCL_PRECISION_COMPILE)+" "+_ocl_vendor_string;
   #endif
   return 0;

src/CLASS2/pair_lj_class2.cpp

@@ -38,20 +38,20 @@ PairLJClass2::PairLJClass2(LAMMPS *lmp) : Pair(lmp)
 
 PairLJClass2::~PairLJClass2()
 {
-  if (!copymode) {
-    if (allocated) {
-      memory->destroy(setflag);
-      memory->destroy(cutsq);
-
-      memory->destroy(cut);
-      memory->destroy(epsilon);
-      memory->destroy(sigma);
-      memory->destroy(lj1);
-      memory->destroy(lj2);
-      memory->destroy(lj3);
-      memory->destroy(lj4);
-      memory->destroy(offset);
-    }
+  if (copymode) return;
+
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+
+    memory->destroy(cut);
+    memory->destroy(epsilon);
+    memory->destroy(sigma);
+    memory->destroy(lj1);
+    memory->destroy(lj2);
+    memory->destroy(lj3);
+    memory->destroy(lj4);
+    memory->destroy(offset);
   }
 }
 

src/CLASS2/pair_lj_class2_coul_cut.cpp

@@ -39,23 +39,23 @@ PairLJClass2CoulCut::PairLJClass2CoulCut(LAMMPS *lmp) : Pair(lmp)
 
 PairLJClass2CoulCut::~PairLJClass2CoulCut()
 {
-  if (!copymode) {
-    if (allocated) {
-      memory->destroy(setflag);
-      memory->destroy(cutsq);
-
-      memory->destroy(cut_lj);
-      memory->destroy(cut_ljsq);
-      memory->destroy(cut_coul);
-      memory->destroy(cut_coulsq);
-      memory->destroy(epsilon);
-      memory->destroy(sigma);
-      memory->destroy(lj1);
-      memory->destroy(lj2);
-      memory->destroy(lj3);
-      memory->destroy(lj4);
-      memory->destroy(offset);
-    }
+  if (copymode) return;
+
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+
+    memory->destroy(cut_lj);
+    memory->destroy(cut_ljsq);
+    memory->destroy(cut_coul);
+    memory->destroy(cut_coulsq);
+    memory->destroy(epsilon);
+    memory->destroy(sigma);
+    memory->destroy(lj1);
+    memory->destroy(lj2);
+    memory->destroy(lj3);
+    memory->destroy(lj4);
+    memory->destroy(offset);
   }
 }
 

src/CLASS2/pair_lj_class2_coul_long.cpp

@@ -50,21 +50,21 @@ PairLJClass2CoulLong::PairLJClass2CoulLong(LAMMPS *lmp) : Pair(lmp)
 
 PairLJClass2CoulLong::~PairLJClass2CoulLong()
 {
-  if (!copymode) {
-    if (allocated) {
-      memory->destroy(setflag);
-      memory->destroy(cutsq);
-
-      memory->destroy(cut_lj);
-      memory->destroy(cut_ljsq);
-      memory->destroy(epsilon);
-      memory->destroy(sigma);
-      memory->destroy(lj1);
-      memory->destroy(lj2);
-      memory->destroy(lj3);
-      memory->destroy(lj4);
-      memory->destroy(offset);
-    }
+  if (copymode) return;
+
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+
+    memory->destroy(cut_lj);
+    memory->destroy(cut_ljsq);
+    memory->destroy(epsilon);
+    memory->destroy(sigma);
+    memory->destroy(lj1);
+    memory->destroy(lj2);
+    memory->destroy(lj3);
+    memory->destroy(lj4);
+    memory->destroy(offset);
   }
   if (ftable) free_tables();
 }

src/KSPACE/pair_buck_coul_long.cpp

@@ -50,23 +50,23 @@ PairBuckCoulLong::PairBuckCoulLong(LAMMPS *lmp) : Pair(lmp)
 
 PairBuckCoulLong::~PairBuckCoulLong()
 {
-  if (!copymode) {
-    if (allocated) {
-      memory->destroy(setflag);
-      memory->destroy(cutsq);
-
-      memory->destroy(cut_lj);
-      memory->destroy(cut_ljsq);
-      memory->destroy(a);
-      memory->destroy(rho);
-      memory->destroy(c);
-      memory->destroy(rhoinv);
-      memory->destroy(buck1);
-      memory->destroy(buck2);
-      memory->destroy(offset);
-    }
-    if (ftable) free_tables();
+  if (copymode) return;
+
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+
+    memory->destroy(cut_lj);
+    memory->destroy(cut_ljsq);
+    memory->destroy(a);
+    memory->destroy(rho);
+    memory->destroy(c);
+    memory->destroy(rhoinv);
+    memory->destroy(buck1);
+    memory->destroy(buck2);
+    memory->destroy(offset);
   }
+  if (ftable) free_tables();
 }
 
 /* ---------------------------------------------------------------------- */

src/KSPACE/pair_coul_long.cpp

@@ -55,15 +55,15 @@ PairCoulLong::PairCoulLong(LAMMPS *lmp) : Pair(lmp)
 
 PairCoulLong::~PairCoulLong()
 {
-  if (!copymode) {
-    if (allocated) {
-      memory->destroy(setflag);
-      memory->destroy(cutsq);
+  if (copymode) return;
 
-      memory->destroy(scale);
-    }
-    if (ftable) free_tables();
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+
+    memory->destroy(scale);
   }
+  if (ftable) free_tables();
 }
 
 /* ---------------------------------------------------------------------- */

src/KSPACE/pair_lj_charmm_coul_long.cpp

@@ -59,27 +59,27 @@ PairLJCharmmCoulLong::PairLJCharmmCoulLong(LAMMPS *lmp) : Pair(lmp)
 
 PairLJCharmmCoulLong::~PairLJCharmmCoulLong()
 {
-  if (!copymode) {
-    if (allocated) {
-      memory->destroy(setflag);
-      memory->destroy(cutsq);
-
-      memory->destroy(epsilon);
-      memory->destroy(sigma);
-      memory->destroy(eps14);
-      memory->destroy(sigma14);
-      memory->destroy(lj1);
-      memory->destroy(lj2);
-      memory->destroy(lj3);
-      memory->destroy(lj4);
-      memory->destroy(lj14_1);
-      memory->destroy(lj14_2);
-      memory->destroy(lj14_3);
-      memory->destroy(lj14_4);
-      memory->destroy(offset);
-    }
-    if (ftable) free_tables();
+  if (copymode) return;
+
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+
+    memory->destroy(epsilon);
+    memory->destroy(sigma);
+    memory->destroy(eps14);
+    memory->destroy(sigma14);
+    memory->destroy(lj1);
+    memory->destroy(lj2);
+    memory->destroy(lj3);
+    memory->destroy(lj4);
+    memory->destroy(lj14_1);
+    memory->destroy(lj14_2);
+    memory->destroy(lj14_3);
+    memory->destroy(lj14_4);
+    memory->destroy(offset);
   }
+  if (ftable) free_tables();
 }
 
 /* ---------------------------------------------------------------------- */

src/KSPACE/pair_lj_charmmfsw_coul_long.cpp

@@ -77,27 +77,6 @@ PairLJCharmmfswCoulLong::PairLJCharmmfswCoulLong(LAMMPS *lmp) : Pair(lmp)
 
 PairLJCharmmfswCoulLong::~PairLJCharmmfswCoulLong()
 {
-  if (!copymode) {
-    if (allocated) {
-      memory->destroy(setflag);
-      memory->destroy(cutsq);
-
-      memory->destroy(epsilon);
-      memory->destroy(sigma);
-      memory->destroy(eps14);
-      memory->destroy(sigma14);
-      memory->destroy(lj1);
-      memory->destroy(lj2);
-      memory->destroy(lj3);
-      memory->destroy(lj4);
-      memory->destroy(lj14_1);
-      memory->destroy(lj14_2);
-      memory->destroy(lj14_3);
-      memory->destroy(lj14_4);
-    }
-    if (ftable) free_tables();
-  }
-
   // switch qqr2e back from CHARMM value to LAMMPS value
 
   if (update && strcmp(update->unit_style,"real") == 0) {
@@ -106,6 +85,27 @@ PairLJCharmmfswCoulLong::~PairLJCharmmfswCoulLong()
                      " conversion constant");
     force->qqr2e = force->qqr2e_lammps_real;
   }
+
+  if (copymode) return;
+
+  if (allocated) {
+    memory->destroy(setflag);
+    memory->destroy(cutsq);
+
+    memory->destroy(epsilon);
+    memory->destroy(sigma);
+    memory->destroy(eps14);
+    memory->destroy(sigma14);
+    memory->destroy(lj1);
+    memory->destroy(lj2);
+    memory->destroy(lj3);
+    memory->destroy(lj4);
+    memory->destroy(lj14_1);
+    memory->destroy(lj14_2);
+    memory->destroy(lj14_3);
+    memory->destroy(lj14_4);
+  }
+  if (ftable) free_tables();
 }
 
 /* ---------------------------------------------------------------------- */

src/MOLECULE/pair_lj_charmm_coul_charmm.cpp

@@ -43,8 +43,9 @@ PairLJCharmmCoulCharmm::PairLJCharmmCoulCharmm(LAMMPS *lmp) : Pair(lmp)
 
 PairLJCharmmCoulCharmm::~PairLJCharmmCoulCharmm()
 {
-  if (!copymode) {
-   if (allocated) {
+  if (copymode) return;
+
+  if (allocated) {
     memory->destroy(setflag);
     memory->destroy(cutsq);
 
@@ -60,7 +61,6 @@ PairLJCharmmCoulCharmm::~PairLJCharmmCoulCharmm()
     memory->destroy(lj14_2);
     memory->destroy(lj14_3);
     memory->destroy(lj14_4);
-   }
   }
 }