Merge pull request lammps#4051 from akohlmey/collected-small-changes

Collected small changes and fixes

.github/workflows/coverity.yml

@@ -25,7 +25,7 @@ jobs:
 
     - name: Cache Coverity
       id: cache-coverity
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ./download/
         key: ${{ runner.os }}-download-${{ hashFiles('**/coverity_tool.*') }}

.github/workflows/unittest-macos.yml

@@ -32,7 +32,7 @@ jobs:
       run: mkdir build
 
     - name: Set up ccache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ env.CCACHE_DIR }}
         key: macos-ccache-${{ github.sha }}

cmake/Modules/Packages/GPU.cmake

@@ -1,3 +1,10 @@
+
+# Silence CMake warnings about FindCUDA being obsolete.
+# We may need to eventually rewrite this section to use enable_language(CUDA)
+if(POLICY CMP0146)
+  cmake_policy(SET CMP0146 OLD)
+endif()
+
 set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
 set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
                 ${GPU_SOURCES_DIR}/fix_gpu.h

cmake/Modules/Packages/MDI.cmake

@@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
 
 if(DOWNLOAD_MDI)
   message(STATUS "MDI download requested - we will build our own")
-  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.16.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum for MDI tarball")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.26.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_MD5 "3124bb85259471e2a53a891f04bf697a" CACHE STRING "MD5 checksum for MDI tarball")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
   GetFallbackURL(MDI_URL MDI_FALLBACK)

doc/Makefile

@@ -100,6 +100,7 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -182,6 +183,7 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -231,6 +233,7 @@ role_check :
 	@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
 	@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
 	@( env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst && exit 1 || : )
+	@( env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst && exit 1 || : )
 
 link_check : $(VENV) html
 	@(\

doc/src/fix_neb.rst

@@ -109,7 +109,7 @@ Note that in this case the specified *Kspring* is in
 force/distance units.
 
 With a value of *ideal*, the spring force is computed as suggested in
-ref`(WeinanE) <WeinanE>`
+:ref:`(WeinanE) <WeinanE>`
 
 .. math::
 
@@ -120,18 +120,18 @@ and :math:`RD_{ideal}` is the ideal *RD* for which all the images are
 equally spaced.  I.e. :math:`RD_{ideal} = (i-1) \cdot meanDist` when the
 climbing replica is off, where *i* is the replica number).  The
 *meanDist* is the average distance between replicas.  Note that in this
-case the specified *Kspring* is in force units. When the climbing replica
-is on, :math:`RD_{ideal}` and :math:`meanDist` are calculated separately
-each side of the climbing image. Note that the *ideal* form of nudging
-can often be more effective at keeping the replicas equally spaced before
-climbing, then equally spaced either side of the climbing image whilst
-climbing.
-
-With a value of *equal* the spring force is computed as for *ideal*
-when the climbing replica is off, promoting equidistance. When the climbing
+case the specified *Kspring* is in force units. When the climbing
+replica is on, :math:`RD_{ideal}` and :math:`meanDist` are calculated
+separately each side of the climbing image. Note that the *ideal* form
+of nudging can often be more effective at keeping the replicas equally
+spaced before climbing, then equally spaced either side of the climbing
+image whilst climbing.
+
+With a value of *equal* the spring force is computed as for *ideal* when
+the climbing replica is off, promoting equidistance. When the climbing
 replica is on, the spring force is computed to promote equidistant
-absolute differences in energy, rather than distance, each side of
-the climbing image:
+absolute differences in energy, rather than distance, each side of the
+climbing image:
 
 .. math::
 
@@ -143,23 +143,22 @@ where *ED* is the cumulative sum of absolute energy differences:
 
    ED = \sum_{i<N} \left|E(R_{i+1}) - E(R_i)\right|,
 
-*meanEdist* is the average absolute energy difference between
-replicas up to the climbing image or from the climbing image
-to the final image, for images before or after the climbing
-image respectively. :math:`ED_{ideal}` is the corresponding
-cumulative sum of average absolute energy differences in
-each case, in close analogy to *ideal*. This form of nudging
-is to aid schemes which integrate forces along, or near to,
-NEB pathways such as :doc:`fix_pafi <fix_pafi>`.
+*meanEdist* is the average absolute energy difference between replicas
+up to the climbing image or from the climbing image to the final image,
+for images before or after the climbing image
+respectively. :math:`ED_{ideal}` is the corresponding cumulative sum of
+average absolute energy differences in each case, in close analogy to
+*ideal*. This form of nudging is to aid schemes which integrate forces
+along, or near to, NEB pathways such as :doc:`fix_pafi <fix_pafi>`.
 
 ----------
 
-The keyword *perp* specifies if and how a perpendicular nudging force
-is computed.  It adds a spring force perpendicular to the path in
-order to prevent the path from becoming too strongly kinked.  It can
+The keyword *perp* specifies if and how a perpendicular nudging force is
+computed.  It adds a spring force perpendicular to the path in order to
+prevent the path from becoming too strongly kinked.  It can
 significantly improve the convergence of the NEB calculation when the
-resolution is poor.  I.e. when few replicas are used; see
-:ref:`(Maras) <Maras1>` for details.
+resolution is poor.  I.e. when few replicas are used; see :ref:`(Maras)
+<Maras1>` for details.
 
 The perpendicular spring force is given by
 
@@ -181,10 +180,10 @@ force is added.
 
 By default, no additional forces act on the first and last replicas
 during the NEB relaxation, so these replicas simply relax toward their
-respective local minima.  By using the key word *end*, additional
-forces can be applied to the first and/or last replicas, to enable
-them to relax toward a MEP while constraining their energy E to the
-target energy ETarget.
+respective local minima.  By using the key word *end*, additional forces
+can be applied to the first and/or last replicas, to enable them to
+relax toward a MEP while constraining their energy E to the target
+energy ETarget.
 
 If :math:`E_{Target} > E`, the interatomic force :math:`F_i` for the
 specified replica becomes:
@@ -197,33 +196,33 @@ specified replica becomes:
 The "spring" constant on the difference in energies is the specified
 *Kspring3* value.
 
-When *estyle* is specified as *first*, the force is applied to the
-first replica.  When *estyle* is specified as *last*, the force is
-applied to the last replica.  Note that the *end* keyword can be used
-twice to add forces to both the first and last replicas.
+When *estyle* is specified as *first*, the force is applied to the first
+replica.  When *estyle* is specified as *last*, the force is applied to
+the last replica.  Note that the *end* keyword can be used twice to add
+forces to both the first and last replicas.
 
 For both these *estyle* settings, the target energy *ETarget* is set
 to the initial energy of the replica (at the start of the NEB
 calculation).
 
 If the *estyle* is specified as *last/efirst* or *last/efirst/middle*,
-force is applied to the last replica, but the target energy *ETarget*
-is continuously set to the energy of the first replica, as it evolves
+force is applied to the last replica, but the target energy *ETarget* is
+continuously set to the energy of the first replica, as it evolves
 during the NEB relaxation.
 
 The difference between these two *estyle* options is as follows.  When
 *estyle* is specified as *last/efirst*, no change is made to the
-inter-replica force applied to the intermediate replicas (neither
-first or last).  If the initial path is too far from the MEP, an
-intermediate replica may relax "faster" and reach a lower energy than
-the last replica.  In this case the intermediate replica will be
-relaxing toward its own local minima.  This behavior can be prevented
-by specifying *estyle* as *last/efirst/middle* which will alter the
-inter-replica force applied to intermediate replicas by removing the
-contribution of the gradient to the inter-replica force.  This will
-only be done if a particular intermediate replica has a lower energy
-than the first replica.  This should effectively prevent the
-intermediate replicas from over-relaxing.
+inter-replica force applied to the intermediate replicas (neither first
+or last).  If the initial path is too far from the MEP, an intermediate
+replica may relax "faster" and reach a lower energy than the last
+replica.  In this case the intermediate replica will be relaxing toward
+its own local minima.  This behavior can be prevented by specifying
+*estyle* as *last/efirst/middle* which will alter the inter-replica
+force applied to intermediate replicas by removing the contribution of
+the gradient to the inter-replica force.  This will only be done if a
+particular intermediate replica has a lower energy than the first
+replica.  This should effectively prevent the intermediate replicas from
+over-relaxing.
 
 After converging a NEB calculation using an *estyle* of
 *last/efirst/middle*, you should check that all intermediate replicas
@@ -237,9 +236,10 @@ target energy.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
-are relevant to this fix.  No global or per-atom quantities are stored
-by this fix for access by various :doc:`output commands <Howto_output>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
+relevant to this fix.  No global or per-atom quantities are stored by
+this fix for access by various :doc:`output commands <Howto_output>`.
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.
 

doc/src/neb.rst

@@ -10,7 +10,7 @@ Syntax
 
    neb etol ftol N1 N2 Nevery file-style arg keyword values
 
-* etol = stopping tolerance for energy (energy units)
+* etol = stopping tolerance for energy (dimensionless)
 * ftol = stopping tolerance for force (force units)
 * N1 = max # of iterations (timesteps) to run initial NEB
 * N2 = max # of iterations (timesteps) to run barrier-climbing NEB
@@ -89,10 +89,11 @@ potentials, and the starting configuration when the neb command is
 issued should be the same for every replica.
 
 In a NEB calculation each replica is connected to other replicas by
-inter-replica nudging forces.  These forces are imposed by the :doc:`fix neb <fix_neb>` command, which must be used in conjunction with the
-neb command.  The group used to define the fix neb command defines the
-NEB atoms which are the only ones that inter-replica springs are
-applied to.  If the group does not include all atoms, then non-NEB
+inter-replica nudging forces.  These forces are imposed by the
+:doc:`fix neb <fix_neb>` command, which must be used in conjunction
+with the neb command.  The group used to define the fix neb command
+defines the NEB atoms which are the only ones that inter-replica springs
+are applied to.  If the group does not include all atoms, then non-NEB
 atoms have no inter-replica springs and the forces they feel and their
 motion is computed in the usual way due only to other atoms within
 their replica.  Conceptually, the non-NEB atoms provide a background
@@ -445,7 +446,7 @@ Related commands
 """"""""""""""""
 
 :doc:`prd <prd>`, :doc:`temper <temper>`, :doc:`fix langevin <fix_langevin>`,
-:doc:`fix viscous <fix_viscous>`
+:doc:`fix viscous <fix_viscous>`, :doc:`fix neb <fix_neb>`
 
 Default
 """""""

lib/gpu/Makefile.cuda

@@ -134,11 +134,11 @@ $(OBJ_DIR)/scan_app.cu_o: cudpp_mini/scan_app.cu
 $(GPU_LIB): $(OBJS) $(CUDPP)
 	$(AR) -crusv $(GPU_LIB) $(OBJS) $(CUDPP)
 	@cp $(EXTRAMAKE) Makefile.lammps
- 
+
 # test app for querying device info
 
 $(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
-	$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda 
+	$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
 
 clean:
 	-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CUHS) *.linkinfo

lib/gpu/Makefile.cuda_mps

@@ -133,11 +133,11 @@ $(OBJ_DIR)/scan_app.cu_o: cudpp_mini/scan_app.cu
 $(GPU_LIB): $(OBJS) $(CUDPP)
 	$(AR) -crusv $(GPU_LIB) $(OBJS) $(CUDPP)
 	@cp $(EXTRAMAKE) Makefile.lammps
- 
+
 # test app for querying device info
 
 $(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
-	$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda 
+	$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
 
 clean:
 	-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CUHS) *.linkinfo

lib/gpu/Makefile.hip

@@ -98,10 +98,10 @@ HIP_GPU_OPTS += $(HIP_OPTS) -I./
 ifeq (spirv,$(HIP_PLATFORM))
 	HIP_HOST_OPTS += -fPIC
 	HIP_GPU_CC  = $(HIP_PATH)/bin/hipcc -c
-	HIP_GPU_OPTS_S = 
+	HIP_GPU_OPTS_S =
 	HIP_GPU_OPTS_E =
 	HIP_KERNEL_SUFFIX = .cpp
-	HIP_LIBS_TARGET = 
+	HIP_LIBS_TARGET =
 	export HCC_AMDGPU_TARGET := $(HIP_ARCH)
 else ifeq (clang,$(HIP_COMPILER))
 	HIP_HOST_OPTS += -fPIC

lib/gpu/Makefile.lammps.mac_ocl

@@ -2,4 +2,4 @@
 
 gpu_SYSINC = -DFFT_SINGLE
 gpu_SYSLIB = -framework OpenCL
-gpu_SYSPATH = 
+gpu_SYSPATH =

lib/gpu/Makefile.lammps.mingw-cross

@@ -2,5 +2,5 @@
 # settings for OpenCL builds
 gpu_SYSINC =
 gpu_SYSLIB = -Wl,--enable-stdcall-fixup -L../../tools/mingw-cross$(LIBOBJDIR) -Wl,-Bdynamic,-lOpenCL,-Bstatic
-gpu_SYSPATH = 
+gpu_SYSPATH =
 

lib/gpu/Makefile.lammps.opencl

@@ -2,4 +2,4 @@
 
 gpu_SYSINC =
 gpu_SYSLIB = -lOpenCL
-gpu_SYSPATH = 
+gpu_SYSPATH =

lib/gpu/Makefile.linux

@@ -1,4 +1,4 @@
-# /* ----------------------------------------------------------------------   
+# /* ----------------------------------------------------------------------
 #  Generic Linux Makefile for CUDA
 #     - Change CUDA_ARCH for your GPU
 # ------------------------------------------------------------------------- */

lib/gpu/Makefile.linux_multi

@@ -1,4 +1,4 @@
-# /* ----------------------------------------------------------------------   
+# /* ----------------------------------------------------------------------
 #  Generic Linux Makefile for CUDA complied for multiple compute capabilities
 #     - Add your GPU to CUDA_CODE
 # ------------------------------------------------------------------------- */

lib/gpu/Makefile.linux_opencl

@@ -1,4 +1,4 @@
-# /* ----------------------------------------------------------------------   
+# /* ----------------------------------------------------------------------
 #  Generic Linux Makefile for OpenCL - Mixed precision
 # ------------------------------------------------------------------------- */
 
@@ -11,7 +11,7 @@ EXTRAMAKE = Makefile.lammps.opencl
 
 LMP_INC = -DLAMMPS_SMALLBIG
 
-OCL_INC = 
+OCL_INC =
 OCL_CPP = mpic++ -std=c++11 -O3 -DMPICH_IGNORE_CXX_SEEK $(LMP_INC) $(OCL_INC)
 OCL_LINK = -lOpenCL
 OCL_PREC = -D_SINGLE_DOUBLE

lib/gpu/Makefile.mac_opencl

@@ -1,4 +1,4 @@
-# /* ----------------------------------------------------------------------   
+# /* ----------------------------------------------------------------------
 #  Generic Mac Makefile for OpenCL - Single precision with FFT_SINGLE
 # ------------------------------------------------------------------------- */
 

lib/gpu/Makefile.mac_opencl_mpi

@@ -1,4 +1,4 @@
-# /* ----------------------------------------------------------------------   
+# /* ----------------------------------------------------------------------
 #  Generic Mac Makefile for OpenCL - Single precision with FFT_SINGLE
 # ------------------------------------------------------------------------- */
 

lib/gpu/Makefile.oneapi

@@ -1,4 +1,4 @@
-# /* ----------------------------------------------------------------------   
+# /* ----------------------------------------------------------------------
 #  Linux Makefile for Intel oneAPI - Mixed precision
 # ------------------------------------------------------------------------- */
 

lib/gpu/Makefile.oneapi_prof

@@ -1,4 +1,4 @@
-# /* ----------------------------------------------------------------------   
+# /* ----------------------------------------------------------------------
 #  Linux Makefile for Intel oneAPI - Mixed precision (with timing enabled)
 # ------------------------------------------------------------------------- */
 

lib/gpu/Makefile.serial

@@ -1,4 +1,4 @@
-# /* ----------------------------------------------------------------------   
+# /* ----------------------------------------------------------------------
 #  Generic Linux Makefile for CUDA without MPI libraries
 #     - Change CUDA_ARCH for your GPU
 # ------------------------------------------------------------------------- */

lib/gpu/Nvidia.makefile

@@ -11,7 +11,7 @@ HOST_H = lal_answer.h lal_atom.h lal_balance.h lal_base_atomic.h lal_base_amoeba
          lal_base_charge.h lal_base_dipole.h lal_base_dpd.h \
          lal_base_ellipsoid.h lal_base_three.h lal_device.h lal_neighbor.h \
          lal_neighbor_shared.h lal_pre_ocl_config.h $(NVD_H)
-         
+
 # Source files
 SRCS := $(wildcard ./lal_*.cpp)
 OBJS := $(subst ./,$(OBJ_DIR)/,$(SRCS:%.cpp=%.o))
@@ -127,7 +127,7 @@ $(GPU_LIB): $(OBJS) $(CUDPP)
 # test app for querying device info
 
 $(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
-	$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda 
+	$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
 
 clean:
 	-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CUHS) *.cubin *.linkinfo

lib/gpu/Nvidia.makefile_multi

@@ -89,7 +89,7 @@ $(GPU_LIB): $(OBJS) $(CUDPP)
 # test app for querying device info
 
 $(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
-	$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda 
+	$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
 
 clean:
 	-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CUHS) *.linkinfo