From 4c2fb7a4312501d59ab530a09a5c5054272d53bf Mon Sep 17 00:00:00 2001
From: Nick Curtis <nicholas.curtis@amd.com>
Date: Thu, 1 Apr 2021 09:43:13 -0500
Subject: [PATCH 01/33] Porting to new default platform for AMD/HIP in ROCm 4.1

---
 cmake/Modules/Packages/GPU.cmake | 12 +++++++++---
 doc/src/Build_extras.rst         | 13 ++++++++++---
 lib/gpu/Makefile.hip             |  6 +++++-
 lib/gpu/README                   |  5 ++---
 lib/gpu/lal_pre_cuda_hip.h       |  8 ++++----
 5 files changed, 30 insertions(+), 14 deletions(-)

diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake
index 9aa917144b..68d74ea42e 100644
--- a/cmake/Modules/Packages/GPU.cmake
+++ b/cmake/Modules/Packages/GPU.cmake
@@ -218,7 +218,7 @@ elseif(GPU_API STREQUAL "HIP")
 
   if(NOT DEFINED HIP_PLATFORM)
       if(NOT DEFINED ENV{HIP_PLATFORM})
-          set(HIP_PLATFORM "hcc" CACHE PATH "HIP Platform to be used during compilation")
+          set(HIP_PLATFORM "amd" CACHE PATH "HIP Platform to be used during compilation")
       else()
           set(HIP_PLATFORM $ENV{HIP_PLATFORM} CACHE PATH "HIP Platform used during compilation")
       endif()
@@ -226,7 +226,7 @@ elseif(GPU_API STREQUAL "HIP")
 
   set(ENV{HIP_PLATFORM} ${HIP_PLATFORM})
 
-  if(HIP_PLATFORM STREQUAL "hcc")
+  if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
     set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
   elseif(HIP_PLATFORM STREQUAL "nvcc")
     find_package(CUDA REQUIRED)
@@ -284,7 +284,7 @@ elseif(GPU_API STREQUAL "HIP")
     set(CUBIN_FILE   "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin")
     set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h")
 
-    if(HIP_PLATFORM STREQUAL "hcc")
+    if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
         configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
 
         if(HIP_COMPILER STREQUAL "clang")
@@ -381,6 +381,12 @@ elseif(GPU_API STREQUAL "HIP")
 
     target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__)
     target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
+  elseif(HIP_PLATFORM STREQUAL "amd")
+    target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_AMD__)
+    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
+
+    target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_AMD__)
+    target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
   endif()
 
   target_link_libraries(lammps PRIVATE gpu)
diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst
index 2081dc4bcd..3af018c656 100644
--- a/doc/src/Build_extras.rst
+++ b/doc/src/Build_extras.rst
@@ -125,7 +125,7 @@ CMake build
                                 # default is sm_50
    -D HIP_ARCH=value            # primary GPU hardware choice for GPU_API=hip
                                 # value depends on selected HIP_PLATFORM
-                                # default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_50' for HIP_PLATFORM=nvcc
+                                # default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for HIP_PLATFORM=nvcc
    -D HIP_USE_DEVICE_SORT=value # enables GPU sorting
                                 # value = yes (default) or no
    -D CUDPP_OPT=value           # use GPU binning on with CUDA (should be off for modern GPUs)
@@ -169,17 +169,24 @@ desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
 
 If you are compiling with HIP, note that before running CMake you will have to
 set appropriate environment variables. Some variables such as
-:code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc`
+:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
 and the linker to work correctly.
 
 .. code:: bash
 
-   # AMDGPU target
+   # AMDGPU target (ROCm <= 4.0)
    export HIP_PLATFORM=hcc
    export HCC_AMDGPU_TARGET=gfx906
    cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
    make -j 4
 
+.. code:: bash
+
+   # AMDGPU target (ROCm >= 4.1)
+   export HIP_PLATFORM=amd
+   cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
+   make -j 4
+
 .. code:: bash
 
    # CUDA target (not recommended, use GPU_ARCH=cuda)
diff --git a/lib/gpu/Makefile.hip b/lib/gpu/Makefile.hip
index dbdef433ec..a736988596 100644
--- a/lib/gpu/Makefile.hip
+++ b/lib/gpu/Makefile.hip
@@ -1,6 +1,6 @@
 # /* ----------------------------------------------------------------------
 #  Generic Linux Makefile for HIP
-#     - export HIP_PLATFORM=hcc (or nvcc) before execution
+#     - export HIP_PLATFORM=amd (or nvcc) before execution
 #     - change HIP_ARCH for your GPU
 # ------------------------------------------------------------------------- */
 
@@ -42,6 +42,10 @@ ifeq (hcc,$(HIP_PLATFORM))
 	HIP_OPTS  += -ffast-math
 	# possible values: gfx803,gfx900,gfx906
 	HIP_ARCH = gfx906
+else ifeq (amd,$(HIP_PLATFORM))
+	HIP_OPTS  += -ffast-math
+	# possible values: gfx803,gfx900,gfx906
+	HIP_ARCH = gfx906
 else ifeq (nvcc,$(HIP_PLATFORM))
 	HIP_OPTS  += --use_fast_math
 	HIP_ARCH = -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_32,code=[sm_32,compute_32] -gencode arch=compute_35,code=[sm_35,compute_35] \
diff --git a/lib/gpu/README b/lib/gpu/README
index dfffe11b81..eb22839a59 100644
--- a/lib/gpu/README
+++ b/lib/gpu/README
@@ -212,8 +212,8 @@ additionally requires cub (https://nvlabs.github.io/cub). Download and
 extract the cub directory to lammps/lib/gpu/ or specify an appropriate
 path in lammps/lib/gpu/Makefile.hip.
 2. In Makefile.hip it is possible to specify the target platform via
-export HIP_PLATFORM=hcc or HIP_PLATFORM=nvcc as well as the target
-architecture (gfx803, gfx900, gfx906 etc.)
+export HIP_PLATFORM=amd (ROCm >= 4.1), HIP_PLATFORM=hcc (ROCm <= 4.0)
+or HIP_PLATFORM=nvcc as well as the target architecture (gfx803, gfx900, gfx906 etc.)
 3. If your MPI implementation does not support `mpicxx --showme` command,
 it is required to specify the corresponding MPI compiler and linker flags
 in lammps/lib/gpu/Makefile.hip and in lammps/src/MAKE/OPTIONS/Makefile.hip.
@@ -278,4 +278,3 @@ and
 Brown, W.M., Masako, Y. Implementing Molecular Dynamics on Hybrid High
 Performance Computers - Three-Body Potentials. Computer Physics Communications.
 2013. 184: p. 2785–2793.
-
diff --git a/lib/gpu/lal_pre_cuda_hip.h b/lib/gpu/lal_pre_cuda_hip.h
index d37b4a94c2..dfb6229bed 100644
--- a/lib/gpu/lal_pre_cuda_hip.h
+++ b/lib/gpu/lal_pre_cuda_hip.h
@@ -30,7 +30,7 @@
 // -------------------------------------------------------------------------
 
 
-#ifdef __HIP_PLATFORM_HCC__
+#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__)
 #define CONFIG_ID 303
 #define SIMD_SIZE 64
 #else
@@ -161,7 +161,7 @@
 //                         KERNEL MACROS - TEXTURES
 // -------------------------------------------------------------------------
 
-#ifdef __HIP_PLATFORM_HCC__
+#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__)
 #define _texture(name, type)  __device__ type* name
 #define _texture_2d(name, type)  __device__ type* name
 #else
@@ -201,7 +201,7 @@
   #define mu_tex mu_
 #endif
 
-#ifdef __HIP_PLATFORM_HCC__
+#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__)
 
 #undef fetch4
 #undef fetch
@@ -266,7 +266,7 @@ typedef struct _double4 double4;
 #endif
 #endif
 
-#if defined(CUDA_PRE_NINE) || defined(__HIP_PLATFORM_HCC__)
+#if defined(CUDA_PRE_NINE) || defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__)
 
   #ifdef _SINGLE_SINGLE
     #define shfl_down __shfl_down

From 160f2cc6307cb5c7e7b3179ca93e0d01de7b8b9f Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Fri, 2 Apr 2021 16:11:23 -0400
Subject: [PATCH 02/33] Update ROCm container definitions

---
 tools/singularity/ubuntu18.04_amd_rocm.def | 2 +-
 tools/singularity/ubuntu20.04_amd_rocm.def | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/tools/singularity/ubuntu18.04_amd_rocm.def b/tools/singularity/ubuntu18.04_amd_rocm.def
index bb04c738c4..7b06970110 100644
--- a/tools/singularity/ubuntu18.04_amd_rocm.def
+++ b/tools/singularity/ubuntu18.04_amd_rocm.def
@@ -94,7 +94,7 @@ From: ubuntu:18.04
     ###########################################################################
 
     export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
-    git clone -b rocm-3.7.x https://github.com/ROCmSoftwarePlatform/hipCUB.git
+    git clone -b rocm-4.1.x https://github.com/ROCmSoftwarePlatform/hipCUB.git
     mkdir hipCUB/build
     cd hipCUB/build
     CXX=hipcc cmake -D BUILD_TEST=off ..
diff --git a/tools/singularity/ubuntu20.04_amd_rocm.def b/tools/singularity/ubuntu20.04_amd_rocm.def
index 28d57be341..4eee97ffec 100644
--- a/tools/singularity/ubuntu20.04_amd_rocm.def
+++ b/tools/singularity/ubuntu20.04_amd_rocm.def
@@ -2,7 +2,7 @@ BootStrap: docker
 From: ubuntu:20.04
 
 %environment
-    export PATH=/usr/lib/ccache:/usr/local/cuda-11.0/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
+    export PATH=/usr/lib/ccache:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
 %post
     export DEBIAN_FRONTEND=noninteractive
     apt-get update
@@ -90,7 +90,7 @@ From: ubuntu:20.04
     ###########################################################################
 
     export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
-    git clone -b rocm-3.7.x https://github.com/ROCmSoftwarePlatform/hipCUB.git
+    git clone -b rocm-4.1.x https://github.com/ROCmSoftwarePlatform/hipCUB.git
     mkdir hipCUB/build
     cd hipCUB/build
     CXX=hipcc cmake -D BUILD_TEST=off ..

From 678302bfcb33486ea6cf1320538b203796e02306 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Fri, 2 Apr 2021 22:08:39 -0400
Subject: [PATCH 03/33] avoid a floating point exception in RanMars::rayleigh()
 from taking log(0)

---
 src/random_mars.cpp | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/src/random_mars.cpp b/src/random_mars.cpp
index 621d7d3008..78c6f93ba4 100644
--- a/src/random_mars.cpp
+++ b/src/random_mars.cpp
@@ -136,13 +136,16 @@ double RanMars::gaussian(double mu, double sigma)
 
 double RanMars::rayleigh(double sigma)
 {
-  double first,v1;
+  double v1;
 
-  if (sigma <= 0) error->all(FLERR,"Invalid Rayleigh parameter");
+  if (sigma <= 0.0) error->all(FLERR,"Invalid Rayleigh parameter");
 
   v1 = uniform();
-  first = sigma*sqrt(-2.0*log(v1));
-  return first;
+  // avoid a floating point exception due to log(0.0)
+  // and just return a very big number
+  if (v1 == 0.0) return 1.0e300;
+
+  return sigma*sqrt(-2.0*log(v1));
 }
 
 /* ----------------------------------------------------------------------

From b2e9ffa67371f340ebae59e1285b26e1945b8f07 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 3 Apr 2021 11:15:00 -0400
Subject: [PATCH 04/33] add missing entry to standard packages list

---
 doc/src/Packages_standard.rst | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/src/Packages_standard.rst b/doc/src/Packages_standard.rst
index ab9be69ab3..81623c8d4a 100644
--- a/doc/src/Packages_standard.rst
+++ b/doc/src/Packages_standard.rst
@@ -71,6 +71,8 @@ package:
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`PERI <PKG-PERI>`           | Peridynamics models                  | :doc:`pair_style peri <pair_peri>`                 | peri                                                 | no      |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
+| :ref:`PLUGIN <PKG-PLUGIN>`       | Plugin loader command                | :doc:`plugin <plugin>`                             | plugins                                              | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`POEMS <PKG-POEMS>`         | coupled rigid body motion            | :doc:`fix poems <fix_poems>`                       | rigid                                                | int     |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`PYTHON <PKG-PYTHON>`       | embed Python code in an input script | :doc:`python <python>`                             | python                                               | sys     |

From 5e0b017d30281b7fb94e23a4c53d84defb7467d2 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 4 Apr 2021 20:51:58 -0400
Subject: [PATCH 05/33] update information about adding unit tests to reflect
 recent changes

---
 doc/src/Developer_unittest.rst | 45 ++++++++++++++++++++++------------
 1 file changed, 29 insertions(+), 16 deletions(-)

diff --git a/doc/src/Developer_unittest.rst b/doc/src/Developer_unittest.rst
index 4487dff11c..52753ee1b4 100644
--- a/doc/src/Developer_unittest.rst
+++ b/doc/src/Developer_unittest.rst
@@ -4,10 +4,10 @@ Adding tests for unit testing
 This section discusses adding or expanding tests for the unit test
 infrastructure included into the LAMMPS source code distribution.
 Unlike example inputs, unit tests focus on testing the "local" behavior
-of individual features, tend to run very fast, and should be set up to
-cover as much of the added code as possible.  When contributing code to
-the distribution, the LAMMPS developers will appreciate if additions
-to the integrated unit test facility are included.
+of individual features, tend to run fast, and should be set up to cover
+as much of the added code as possible.  When contributing code to the
+distribution, the LAMMPS developers will appreciate if additions to the
+integrated unit test facility are included.
 
 Given the complex nature of MD simulations where many operations can
 only be performed when suitable "real" simulation environment has been
@@ -50,6 +50,9 @@ available:
    * - File name:
      - Test name:
      - Description:
+   * - ``test_argutils.cpp``
+     - ArgInfo
+     - Tests for ``ArgInfo`` class used by LAMMPS
    * - ``test_fmtlib.cpp``
      - FmtLib
      - Tests for ``fmtlib::`` functions used by LAMMPS
@@ -155,23 +158,27 @@ have the desired effect:
    {
        ASSERT_EQ(lmp->update->ntimestep, 0);
 
-       if (!verbose) ::testing::internal::CaptureStdout();
-       lmp->input->one("reset_timestep 10");
-       if (!verbose) ::testing::internal::GetCapturedStdout();
+       BEGIN_HIDE_OUTPUT();
+       command("reset_timestep 10");
+       END_HIDE_OUTPUT();
        ASSERT_EQ(lmp->update->ntimestep, 10);
 
-       if (!verbose) ::testing::internal::CaptureStdout();
-       lmp->input->one("reset_timestep 0");
-       if (!verbose) ::testing::internal::GetCapturedStdout();
+       BEGIN_HIDE_OUTPUT();
+       command("reset_timestep 0");
+       END_HIDE_OUTPUT();
        ASSERT_EQ(lmp->update->ntimestep, 0);
+
+       TEST_FAILURE(".*ERROR: Timestep must be >= 0.*", command("reset_timestep -10"););
+       TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep"););
+       TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep 10 10"););
+       TEST_FAILURE(".*ERROR: Expected integer .*", command("reset_timestep xxx"););
    }
 
-Please note the use of the (global) verbose variable to control whether
-the LAMMPS command will be silent by capturing the output or not.  In
-the default case, verbose == false, the test output will be compact and
-not mixed with LAMMPS output. However setting the verbose flag (via
-setting the ``TEST_ARGS`` environment variable, ``TEST_ARGS=-v``) can be
-helpful to understand why tests fail unexpectedly.
+Please note the use of the ``BEGIN_HIDE_OUTPUT`` and ``END_HIDE_OUTPUT``
+functions that will capture output from running LAMMPS.  This is normally
+discarded but by setting the verbose flag (via setting the ``TEST_ARGS``
+environment variable, ``TEST_ARGS=-v``) it can be printed and used to
+understand why tests fail unexpectedly.
 
 Another complexity of these tests stems from the need to capture
 situations where LAMMPS will stop with an error, i.e. handle so-called
@@ -210,6 +217,12 @@ The following test programs are currently available:
    * - ``test_lattice_region.cpp``
      - LatticeRegion
      - Tests to validate the :doc:`lattice <lattice>` and :doc:`region <region>` commands
+   * - ``test_groups.cpp``
+     - GroupTest
+     - Tests to validate the :doc:`group <group>` command
+   * - ``test_variables.cpp``
+     - VariableTest
+     - Tests to validate the :doc:`variable <variable>` command
    * - ``test_kim_commands.cpp``
      - KimCommands
      - Tests for several commands from the :ref:`KIM package <PKG-KIM>`

From d1b6aaa3f3a6e1524864c6d582b9a0220ea5980c Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 4 Apr 2021 20:57:29 -0400
Subject: [PATCH 06/33] plugins also have a .so suffix on MacOS (unlike shared
 libs)

---
 unittest/commands/test_simple_commands.cpp | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/unittest/commands/test_simple_commands.cpp b/unittest/commands/test_simple_commands.cpp
index 9173909806..9bd6e74c9b 100644
--- a/unittest/commands/test_simple_commands.cpp
+++ b/unittest/commands/test_simple_commands.cpp
@@ -328,11 +328,7 @@ TEST_F(SimpleCommandsTest, Units)
 #if defined(LMP_PLUGIN)
 TEST_F(SimpleCommandsTest, Plugin)
 {
-#if defined(__APPLE__)
-    std::string loadfmt("plugin load {}plugin.dylib");
-#else
     std::string loadfmt("plugin load {}plugin.so");
-#endif
     ::testing::internal::CaptureStdout();
     lmp->input->one(fmt::format(loadfmt, "hello"));
     auto text = ::testing::internal::GetCapturedStdout();

From 36c6410fd8fff5a583b8429f4a1c78cecdb87772 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 4 Apr 2021 21:14:12 -0400
Subject: [PATCH 07/33] make skip() function argument optional and default to 1

---
 src/tokenizer.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/tokenizer.h b/src/tokenizer.h
index 2db9870866..b3bbf05296 100644
--- a/src/tokenizer.h
+++ b/src/tokenizer.h
@@ -41,7 +41,7 @@ public:
     Tokenizer& operator=(Tokenizer&&) = default;
 
     void reset();
-    void skip(int n);
+    void skip(int n=1);
     bool has_next() const;
     bool contains(const std::string &str) const;
     std::string next();
@@ -104,7 +104,7 @@ public:
 
     bool has_next() const;
     bool contains(const std::string &value) const;
-    void skip(int ntokens);
+    void skip(int ntokens=1);
 
     size_t count();
 };

From 1e7e930d55ca27103cdc601860c6c53fbfaeef8f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 4 Apr 2021 21:14:40 -0400
Subject: [PATCH 08/33] generalize match to fit all rigid/small derived fixes

---
 src/velocity.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/velocity.cpp b/src/velocity.cpp
index b8d2e5229a..f4483074aa 100644
--- a/src/velocity.cpp
+++ b/src/velocity.cpp
@@ -108,7 +108,7 @@ void Velocity::command(int narg, char **arg)
 
   int initcomm = 0;
   if (style == ZERO && rfix >= 0 &&
-      utils::strmatch(modify->fix[rfix]->style,"^rigid/small")) initcomm = 1;
+      utils::strmatch(modify->fix[rfix]->style,"^rigid.*/small.*")) initcomm = 1;
   if ((style == CREATE || style == SET) && temperature &&
       strcmp(temperature->style,"temp/cs") == 0) initcomm = 1;
 

From 67d4302fc7befe67ff157b4e1584067efabea171 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 4 Apr 2021 21:51:06 -0400
Subject: [PATCH 09/33] add tests for tokenizer skip() function and throwing an
 exception

---
 unittest/utils/test_tokenizer.cpp | 44 +++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/unittest/utils/test_tokenizer.cpp b/unittest/utils/test_tokenizer.cpp
index 69ec7a55d2..ec097abf62 100644
--- a/unittest/utils/test_tokenizer.cpp
+++ b/unittest/utils/test_tokenizer.cpp
@@ -43,6 +43,18 @@ TEST(Tokenizer, two_words)
     ASSERT_EQ(t.count(), 2);
 }
 
+TEST(Tokenizer, skip)
+{
+    Tokenizer t("test word", " ");
+    ASSERT_TRUE(t.has_next());
+    t.skip();
+    ASSERT_TRUE(t.has_next());
+    t.skip(1);
+    ASSERT_FALSE(t.has_next());
+    ASSERT_EQ(t.count(), 2);
+    ASSERT_THROW(t.skip(), TokenizerException);
+}
+
 TEST(Tokenizer, prefix_separators)
 {
     Tokenizer t("  test word", " ");
@@ -63,6 +75,18 @@ TEST(Tokenizer, iterate_words)
     ASSERT_EQ(t.count(), 2);
 }
 
+TEST(Tokenizer, copy_constructor)
+{
+    Tokenizer t("  test word   ", " ");
+    ASSERT_THAT(t.next(), Eq("test"));
+    ASSERT_THAT(t.next(), Eq("word"));
+    ASSERT_EQ(t.count(), 2);
+    Tokenizer u(t);
+    ASSERT_THAT(u.next(), Eq("test"));
+    ASSERT_THAT(u.next(), Eq("word"));
+    ASSERT_EQ(u.count(), 2);
+}
+
 TEST(Tokenizer, no_separator_path)
 {
     Tokenizer t("one", ":");
@@ -139,6 +163,26 @@ TEST(ValueTokenizer, empty_string)
     ASSERT_FALSE(values.has_next());
 }
 
+TEST(ValueTokenizer, two_words)
+{
+    ValueTokenizer t("test word", " ");
+    ASSERT_THAT(t.next_string(), Eq("test"));
+    ASSERT_THAT(t.next_string(), Eq("word"));
+    ASSERT_THROW(t.next_string(), TokenizerException);
+}
+
+TEST(ValueTokenizer, skip)
+{
+    ValueTokenizer t("test word", " ");
+    ASSERT_TRUE(t.has_next());
+    t.skip();
+    ASSERT_TRUE(t.has_next());
+    t.skip(1);
+    ASSERT_FALSE(t.has_next());
+    ASSERT_EQ(t.count(), 2);
+    ASSERT_THROW(t.skip(), TokenizerException);
+}
+
 TEST(ValueTokenizer, bad_integer)
 {
     ValueTokenizer values("f10");

From a858c07e8a7ff8c11a939fbb6a9c3e9430634ca9 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 4 Apr 2021 21:51:48 -0400
Subject: [PATCH 10/33] add unit tests for empty id, invalid timespecs, and
 merge sort

---
 unittest/utils/test_utils.cpp | 44 +++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/unittest/utils/test_utils.cpp b/unittest/utils/test_utils.cpp
index 81dda11615..0c6e38e342 100644
--- a/unittest/utils/test_utils.cpp
+++ b/unittest/utils/test_utils.cpp
@@ -331,6 +331,11 @@ TEST(Utils, valid_id7)
     ASSERT_TRUE(utils::is_id("___"));
 }
 
+TEST(Utils, empty_id)
+{
+    ASSERT_FALSE(utils::is_id(""));
+}
+
 TEST(Utils, invalid_id1)
 {
     ASSERT_FALSE(utils::is_id("+abc"));
@@ -780,6 +785,11 @@ TEST(Utils, unit_conversion)
     ASSERT_DOUBLE_EQ(factor, 1.0 / 23.060549);
 }
 
+TEST(Utils, timespec2seconds_off)
+{
+    ASSERT_DOUBLE_EQ(utils::timespec2seconds("off"), -1.0);
+}
+
 TEST(Utils, timespec2seconds_ss)
 {
     ASSERT_DOUBLE_EQ(utils::timespec2seconds("45"), 45.0);
@@ -795,6 +805,11 @@ TEST(Utils, timespec2seconds_hhmmss)
     ASSERT_DOUBLE_EQ(utils::timespec2seconds("2:10:45"), 7845.0);
 }
 
+TEST(Utils, timespec2seconds_invalid)
+{
+    ASSERT_DOUBLE_EQ(utils::timespec2seconds("2:aa:45"), -1.0);
+}
+
 TEST(Utils, date2num)
 {
     ASSERT_EQ(utils::date2num("1Jan05"), 20050101);
@@ -810,3 +825,32 @@ TEST(Utils, date2num)
     ASSERT_EQ(utils::date2num("30November 02"), 20021130);
     ASSERT_EQ(utils::date2num("31December100"), 1001231);
 }
+
+static int compare(int a, int b, void *)
+{
+    if (a < b)
+        return -1;
+    else if (a > b)
+        return 1;
+    else
+        return 0;
+}
+
+TEST(Utils, merge_sort)
+{
+    int data[] = {773, 405, 490, 830, 632, 96,  428, 728, 912, 840, 878, 745, 213, 219, 249, 380,
+                  894, 758, 575, 690, 61,  849, 19,  577, 338, 569, 898, 873, 448, 940, 431, 780,
+                  472, 289, 65,  491, 641, 37,  367, 33,  407, 854, 594, 611, 845, 136, 107, 592,
+                  275, 865, 158, 626, 399, 703, 686, 734, 188, 559, 781, 558, 737, 281, 638, 664,
+                  533, 529, 62,  969, 595, 661, 837, 463, 624, 568, 615, 936, 206, 637, 91,  694,
+                  214, 872, 468, 66,  775, 949, 486, 576, 255, 961, 480, 138, 177, 509, 333, 705,
+                  10,  375, 321, 952, 210, 111, 475, 268, 708, 864, 244, 121, 988, 540, 942, 682,
+                  750, 473, 478, 714, 955, 911, 482, 384, 144, 757, 697, 791, 420, 605, 447, 320};
+
+    const int num = sizeof(data) / sizeof(int);
+    utils::merge_sort(data, num, nullptr, &compare);
+    bool sorted = true;
+    for (int i = 1; i < num; ++i)
+        if (data[i - 1] > data[i]) sorted = false;
+    ASSERT_TRUE(sorted);
+}

From e00e2676fca98a56f87775fa7820aab19a6019b3 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 4 Apr 2021 22:23:13 -0400
Subject: [PATCH 11/33] add tests for utils::open_potential()

---
 .../formats/test_potential_file_reader.cpp    | 62 +++++++++++++++++++
 1 file changed, 62 insertions(+)

diff --git a/unittest/formats/test_potential_file_reader.cpp b/unittest/formats/test_potential_file_reader.cpp
index 1e3d96d6d7..f270f6e1f1 100644
--- a/unittest/formats/test_potential_file_reader.cpp
+++ b/unittest/formats/test_potential_file_reader.cpp
@@ -28,6 +28,7 @@
 #include "potential_file_reader.h"
 #include "gmock/gmock.h"
 #include "gtest/gtest.h"
+
 #include "../testing/core.h"
 
 #include <cstring>
@@ -257,6 +258,67 @@ TEST_F(PotentialFileReaderTest, UnitConvert)
     delete reader;
 }
 
+class OpenPotentialTest : public LAMMPSTest {
+};
+
+// open for native units
+TEST_F(OpenPotentialTest, Sw_native)
+{
+    int convert_flag = utils::get_supported_conversions(utils::ENERGY);
+    BEGIN_CAPTURE_OUTPUT();
+    command("units metal");
+    FILE *fp    = utils::open_potential("Si.sw", lmp, &convert_flag);
+    auto text   = END_CAPTURE_OUTPUT();
+    double conv = utils::get_conversion_factor(utils::ENERGY, convert_flag);
+
+    ASSERT_NE(fp, nullptr);
+    ASSERT_DOUBLE_EQ(conv, 1.0);
+    fclose(fp);
+}
+
+// open with supported conversion enabled
+TEST_F(OpenPotentialTest, Sw_conv)
+{
+    int convert_flag = utils::get_supported_conversions(utils::ENERGY);
+    ASSERT_EQ(convert_flag, utils::METAL2REAL | utils::REAL2METAL);
+    BEGIN_HIDE_OUTPUT();
+    command("units real");
+    FILE *fp    = utils::open_potential("Si.sw", lmp, &convert_flag);
+    auto text   = END_CAPTURE_OUTPUT();
+    double conv = utils::get_conversion_factor(utils::ENERGY, convert_flag);
+
+    ASSERT_NE(fp, nullptr);
+    ASSERT_EQ(convert_flag, utils::METAL2REAL);
+    ASSERT_DOUBLE_EQ(conv, 23.060549);
+    fclose(fp);
+}
+
+// open with conversion disabled
+TEST_F(OpenPotentialTest, Sw_noconv)
+{
+    BEGIN_HIDE_OUTPUT();
+    command("units real");
+    END_HIDE_OUTPUT();
+    TEST_FAILURE(".*potential.*requires metal units but real.*",
+                 utils::open_potential("Si.sw", lmp, nullptr););
+    BEGIN_HIDE_OUTPUT();
+    command("units lj");
+    END_HIDE_OUTPUT();
+    int convert_flag = utils::get_supported_conversions(utils::UNKNOWN);
+    ASSERT_EQ(convert_flag, utils::NOCONVERT);
+}
+
+// open non-existing potential
+TEST_F(OpenPotentialTest, No_file)
+{
+    int convert_flag = utils::get_supported_conversions(utils::ENERGY);
+    BEGIN_HIDE_OUTPUT();
+    command("units metal");
+    FILE *fp = utils::open_potential("Unknown.sw", lmp, &convert_flag);
+    END_HIDE_OUTPUT();
+    ASSERT_EQ(fp,nullptr);
+}
+
 int main(int argc, char **argv)
 {
     MPI_Init(&argc, &argv);

From 4e4a571dbda05a29dff342d163f4059b0aac5117 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 5 Apr 2021 14:31:13 -0400
Subject: [PATCH 12/33] Add advanced LAMMPS_DOWNLOADS_URL cmake option

---
 cmake/CMakeLists.txt            | 5 +++++
 cmake/Modules/LAMMPSUtils.cmake | 1 -
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 21d965ebba..4c94a5037a 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -22,6 +22,11 @@ set(LAMMPS_TOOLS_DIR      ${LAMMPS_DIR}/tools)
 set(LAMMPS_PYTHON_DIR     ${LAMMPS_DIR}/python)
 set(LAMMPS_POTENTIALS_DIR ${LAMMPS_DIR}/potentials)
 
+set(LAMMPS_DOWNLOADS_URL "https://download.lammps.org" CACHE STRING "Base URL for LAMMPS downloads")
+set(LAMMPS_POTENTIALS_URL "${LAMMPS_DOWNLOADS_URL}/potentials")
+set(LAMMPS_THIRDPARTY_URL "${LAMMPS_DOWNLOADS_URL}/thirdparty")
+mark_as_advanced(LAMMPS_DOWNLOADS_URL)
+
 find_package(Git)
 
 # by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
diff --git a/cmake/Modules/LAMMPSUtils.cmake b/cmake/Modules/LAMMPSUtils.cmake
index 37275843fa..acaef19498 100644
--- a/cmake/Modules/LAMMPSUtils.cmake
+++ b/cmake/Modules/LAMMPSUtils.cmake
@@ -86,7 +86,6 @@ endfunction(GenerateBinaryHeader)
 # fetch missing potential files
 function(FetchPotentials pkgfolder potfolder)
   if (EXISTS "${pkgfolder}/potentials.txt")
-    set(LAMMPS_POTENTIALS_URL "https://download.lammps.org/potentials")
     file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
     foreach(line ${linelist})
       string(FIND ${line} " " blank)

From 8533bb17e7cf3913600f139de54edaab2cf01108 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 5 Apr 2021 14:36:38 -0400
Subject: [PATCH 13/33] Update cmake/Modules/OpenCLLoader.cmake

---
 cmake/Modules/OpenCLLoader.cmake | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/cmake/Modules/OpenCLLoader.cmake b/cmake/Modules/OpenCLLoader.cmake
index 5ab121f841..54eaab4795 100644
--- a/cmake/Modules/OpenCLLoader.cmake
+++ b/cmake/Modules/OpenCLLoader.cmake
@@ -1,11 +1,13 @@
 message(STATUS "Downloading and building OpenCL loader library")
+set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+set(OPENCL_LOADER_MD5 "011cdcbd41030be94f3fced6d763a52a" CACHE STRING "MD5 checksum of OpenCL loader tarball")
+mark_as_advanced(OPENCL_LOADER_URL)
+mark_as_advanced(OPENCL_LOADER_MD5)
 
 include(ExternalProject)
-set(OPENCL_LOADER_URL "https://download.lammps.org/thirdparty/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
-mark_as_advanced(OPENCL_LOADER_URL)
 ExternalProject_Add(opencl_loader
-                    URL ${OPENCL_LOADER_URL}
-                    URL_MD5         011cdcbd41030be94f3fced6d763a52a
+                    URL             ${OPENCL_LOADER_URL}
+                    URL_MD5         ${OPENCL_LOADER_MD5}
                     SOURCE_DIR      "${CMAKE_BINARY_DIR}/opencl_loader-src"
                     BINARY_DIR      "${CMAKE_BINARY_DIR}/opencl_loader-build"
                     CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_OPENCL_LOADER_OPTS}

From 3b14606f063f8fa72470697a495a3441df2e00ca Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 5 Apr 2021 14:43:05 -0400
Subject: [PATCH 14/33] Update cmake/Modules/MPI4WIN.cmake

---
 cmake/Modules/MPI4WIN.cmake | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/cmake/Modules/MPI4WIN.cmake b/cmake/Modules/MPI4WIN.cmake
index 529cefeab0..aa0c9e1833 100644
--- a/cmake/Modules/MPI4WIN.cmake
+++ b/cmake/Modules/MPI4WIN.cmake
@@ -1,16 +1,25 @@
 # Download and configure custom MPICH files for Windows
 message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
+set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
+set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
+set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
+set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
+mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
+mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
+
 include(ExternalProject)
 if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
   ExternalProject_Add(mpi4win_build
-    URL https://download.lammps.org/thirdparty/mpich2-win64-devel.tar.gz
-    URL_MD5 4939fdb59d13182fd5dd65211e469f14
+    URL     ${MPICH2_WIN64_DEVEL_URL}
+    URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
     CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
     BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
 else()
   ExternalProject_Add(mpi4win_build
-    URL https://download.lammps.org/thirdparty/mpich2-win32-devel.tar.gz
-    URL_MD5 a61d153500dce44e21b755ee7257e031
+    URL     ${MPICH2_WIN32_DEVEL_URL}
+    URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
     CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
     BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
 endif()

From 614411130b2aa3312b5ab12a02db3132f31a56ec Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 5 Apr 2021 14:44:27 -0400
Subject: [PATCH 15/33] Update cmake/Modules/Documentation.cmake

---
 cmake/Modules/Documentation.cmake | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/cmake/Modules/Documentation.cmake b/cmake/Modules/Documentation.cmake
index 5a42244b9e..c0028676b7 100644
--- a/cmake/Modules/Documentation.cmake
+++ b/cmake/Modules/Documentation.cmake
@@ -55,11 +55,15 @@ if(BUILD_DOC)
     COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
   )
 
+  set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz" CACHE STRING "URL for MathJax tarball")
+  set(MATHJAX_MD5 "a4a6a093a89bc2ccab1452d766b98e53" CACHE STRING "MD5 checksum of MathJax tarball")
+  mark_as_advanced(MATHJAX_URL)
+
   # download mathjax distribution and unpack to folder "mathjax"
   if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5)
-    file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz"
+    file(DOWNLOAD ${MATHJAX_URL}
       "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
-      EXPECTED_MD5 a4a6a093a89bc2ccab1452d766b98e53)
+      EXPECTED_MD5 ${MATHJAX_MD5})
     execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
     file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
     execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)

From 192ee276b16c3d67838ce58d50f9a85c41abe141 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 5 Apr 2021 14:46:50 -0400
Subject: [PATCH 16/33] Update cmake/Modules/Packages/KOKKOS.cmake

---
 cmake/Modules/Packages/KOKKOS.cmake | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake
index 1dfb0bf389..1f00516e08 100644
--- a/cmake/Modules/Packages/KOKKOS.cmake
+++ b/cmake/Modules/Packages/KOKKOS.cmake
@@ -37,9 +37,13 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "08201d1c7cf5bc458ce0f5b44a629d5a" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  mark_as_advanced(KOKKOS_URL)
+  mark_as_advanced(KOKKOS_MD5)
   ExternalProject_Add(kokkos_build
-    URL https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz
-    URL_MD5 08201d1c7cf5bc458ce0f5b44a629d5a
+    URL     ${KOKKOS_URL}
+    URL_MD5 ${KOKKOS_MD5}
     CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
     BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
   )

From 42ca8c5ba09762c43602614feee0363a25f9273d Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 5 Apr 2021 14:55:56 -0400
Subject: [PATCH 17/33] Update cmake/Modules/Packages/VORONOI.cmake

---
 cmake/Modules/Packages/VORONOI.cmake | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/cmake/Modules/Packages/VORONOI.cmake b/cmake/Modules/Packages/VORONOI.cmake
index 1d6893a978..7feea4c52e 100644
--- a/cmake/Modules/Packages/VORONOI.cmake
+++ b/cmake/Modules/Packages/VORONOI.cmake
@@ -7,6 +7,11 @@ endif()
 option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
 if(DOWNLOAD_VORO)
   message(STATUS "Voro++ download requested - we will build our own")
+  set(VORO_URL "${LAMMPS_THIRDPARTY_URL}/voro++-0.4.6.tar.gz" CACHE STRING "URL for Voro++ tarball")
+  set(VORO_MD5 "2338b824c3b7b25590e18e8df5d68af9" CACHE STRING "MD5 checksum for Voro++ tarball")
+  mark_as_advanced(VORO_URL)
+  mark_as_advanced(VORO_MD5)
+
   include(ExternalProject)
 
   if(BUILD_SHARED_LIBS)
@@ -22,8 +27,8 @@ if(DOWNLOAD_VORO)
   endif()
 
   ExternalProject_Add(voro_build
-    URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
-    URL_MD5 2338b824c3b7b25590e18e8df5d68af9
+    URL     ${VORO_URL}
+    URL_MD5 ${VORO_MD5}
     PATCH_COMMAND patch -b -p0 < ${LAMMPS_LIB_SOURCE_DIR}/voronoi/voro-make.patch
     CONFIGURE_COMMAND ""
     BUILD_COMMAND make ${VORO_BUILD_OPTIONS}

From 725332614a95131a855cfc8bc74edd98dcb5dccd Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 5 Apr 2021 14:56:47 -0400
Subject: [PATCH 18/33] Update cmake/Modules/Packages/MSCG.cmake

---
 cmake/Modules/Packages/MSCG.cmake | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/cmake/Modules/Packages/MSCG.cmake b/cmake/Modules/Packages/MSCG.cmake
index 6cb389fb13..6ac62cb012 100644
--- a/cmake/Modules/Packages/MSCG.cmake
+++ b/cmake/Modules/Packages/MSCG.cmake
@@ -7,10 +7,15 @@ else()
 endif()
 option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
 if(DOWNLOAD_MSCG)
+  set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz" CACHE STRING "URL for MSCG tarball")
+  set(MSCG_MD5 "8c45e269ee13f60b303edd7823866a91" CACHE STRING "MD5 checksum of MSCG tarball")
+  mark_as_advanced(MSCG_URL)
+  mark_as_advanced(MSCG_MD5)
+
   include(ExternalProject)
   ExternalProject_Add(mscg_build
-    URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
-    URL_MD5 8c45e269ee13f60b303edd7823866a91
+    URL     ${MSCG_URL}
+    URL_MD5 ${MSCG_MD5}
     SOURCE_SUBDIR src/CMake
     CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
                -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}

From 0277883fb2271a31ed0d07f4b64098ee4655b436 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 5 Apr 2021 15:00:06 -0400
Subject: [PATCH 19/33] Update cmake/Modules/Packages/USER-SCAFACOS.cmake

---
 cmake/Modules/Packages/USER-SCAFACOS.cmake | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/cmake/Modules/Packages/USER-SCAFACOS.cmake b/cmake/Modules/Packages/USER-SCAFACOS.cmake
index dc5c400c36..fd355420c3 100644
--- a/cmake/Modules/Packages/USER-SCAFACOS.cmake
+++ b/cmake/Modules/Packages/USER-SCAFACOS.cmake
@@ -14,15 +14,19 @@ endif()
 option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
 if(DOWNLOAD_SCAFACOS)
   message(STATUS "ScaFaCoS download requested - we will build our own")
+  set(SCAFACOS_URL "https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz" CACHE STRING "URL for SCAFACOS tarball")
+  set(SCAFACOS_MD5 "bd46d74e3296bd8a444d731bb10c1738" CACHE STRING "MD5 checksum of SCAFACOS tarball")
+  mark_as_advanced(SCAFACOS_URL)
+  mark_as_advanced(SCAFACOS_MD5)
 
   # version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later.
-  file(DOWNLOAD https://download.lammps.org/thirdparty/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
+  file(DOWNLOAD ${LAMMPS_THIRDPARTY_URL}/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
           EXPECTED_HASH MD5=4baa1333bb28fcce102d505e1992d032)
 
   include(ExternalProject)
   ExternalProject_Add(scafacos_build
-    URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
-    URL_MD5 bd46d74e3296bd8a444d731bb10c1738
+    URL     ${SCAFACOS_URL}
+    URL_MD5 ${SCAFACOS_MD5}
     PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
                                              --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m

From 8ccc19bb2a272ec593da61515a1a313e1ff6d35f Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 5 Apr 2021 15:03:05 -0400
Subject: [PATCH 20/33] Update cmake/Modules/Packages/LATTE.cmake

---
 cmake/Modules/Packages/LATTE.cmake | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/cmake/Modules/Packages/LATTE.cmake b/cmake/Modules/Packages/LATTE.cmake
index e66f83fa43..ddf31a68ed 100644
--- a/cmake/Modules/Packages/LATTE.cmake
+++ b/cmake/Modules/Packages/LATTE.cmake
@@ -15,10 +15,14 @@ endif()
 option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
 if(DOWNLOAD_LATTE)
   message(STATUS "LATTE download requested - we will build our own")
+  set(LATTE_URL "https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz" CACHE STRING "URL for LATTE tarball")
+  set(LATTE_MD5 "820e73a457ced178c08c71389a385de7" CACHE STRING "MD5 checksum of LATTE tarball")
+  mark_as_advanced(LATTE_URL)
+  mark_as_advanced(LATTE_MD5)
   include(ExternalProject)
   ExternalProject_Add(latte_build
-    URL https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz
-    URL_MD5 820e73a457ced178c08c71389a385de7
+    URL     ${LATTE_URL}
+    URL_MD5 ${LATTE_MD5}
     SOURCE_SUBDIR cmake
     CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
     -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}

From b718903efc36ce9d15218f425cc74a4f180170d6 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 5 Apr 2021 15:10:01 -0400
Subject: [PATCH 21/33] Update cmake/Modules/Packages/USER-PLUMED.cmake

---
 cmake/Modules/Packages/USER-PLUMED.cmake | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/cmake/Modules/Packages/USER-PLUMED.cmake b/cmake/Modules/Packages/USER-PLUMED.cmake
index 53abf5771a..8719e8179d 100644
--- a/cmake/Modules/Packages/USER-PLUMED.cmake
+++ b/cmake/Modules/Packages/USER-PLUMED.cmake
@@ -53,10 +53,16 @@ if(DOWNLOAD_PLUMED)
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
     set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
   endif()
+
+  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_MD5 "95f29dd0c067577f11972ff90dfc7d12" CACHE STRING "MD5 checksum of PLUMED tarball")
+  mark_as_advanced(PLUMED_URL)
+  mark_as_advanced(PLUMED_MD5)
+
   include(ExternalProject)
   ExternalProject_Add(plumed_build
-    URL https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz
-    URL_MD5 95f29dd0c067577f11972ff90dfc7d12
+    URL     ${PLUMED_URL}
+    URL_MD5 ${PLUMED_MD5}
     BUILD_IN_SOURCE 1
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                              ${CONFIGURE_REQUEST_PIC}

From 88b9e99707c95bd6ede9f47672536ded23fe66d0 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 5 Apr 2021 15:26:58 -0400
Subject: [PATCH 22/33] Update cmake/Modules/Packages/GPU.cmake

---
 cmake/Modules/Packages/GPU.cmake | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake
index 9aa917144b..115d81af2a 100644
--- a/cmake/Modules/Packages/GPU.cmake
+++ b/cmake/Modules/Packages/GPU.cmake
@@ -338,11 +338,16 @@ elseif(GPU_API STREQUAL "HIP")
 
       if(DOWNLOAD_CUB)
         message(STATUS "CUB download requested")
+        set(CUB_URL "https://github.com/NVlabs/cub/archive/1.12.0.tar.gz" CACHE STRING "URL for CUB tarball")
+        set(CUB_MD5 "1cf595beacafff104700921bac8519f3" CACHE STRING "MD5 checksum of CUB tarball")
+        mark_as_advanced(CUB_URL)
+        mark_as_advanced(CUB_MD5)
+
         include(ExternalProject)
 
         ExternalProject_Add(CUB
-          GIT_REPOSITORY https://github.com/NVlabs/cub
-          TIMEOUT 5
+          URL     ${CUB_URL}
+          URL_MD5 ${CUB_MD5}
           PREFIX "${CMAKE_CURRENT_BINARY_DIR}"
           CONFIGURE_COMMAND ""
           BUILD_COMMAND ""
@@ -354,7 +359,7 @@ elseif(GPU_API STREQUAL "HIP")
       else()
         find_package(CUB)
         if(NOT CUB_FOUND)
-          message(FATAL_ERROR "CUB library not found. Help CMake to find it by setting CUB_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
+          message(FATAL_ERROR "CUB library not found. Help CMake to find it by setting CUB_INCLUDE_DIR, or set DOWNLOAD_CUB=ON to download it")
         endif()
       endif()
 

From 2509190daec63d7942334ed5556ff72abc175574 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 5 Apr 2021 15:29:33 -0400
Subject: [PATCH 23/33] Update cmake/Modules/YAML.cmake

---
 cmake/Modules/YAML.cmake | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/cmake/Modules/YAML.cmake b/cmake/Modules/YAML.cmake
index f2ba34e1b6..c50773568c 100644
--- a/cmake/Modules/YAML.cmake
+++ b/cmake/Modules/YAML.cmake
@@ -2,10 +2,13 @@ message(STATUS "Downloading and building YAML library")
 
 include(ExternalProject)
 set(YAML_URL "https://pyyaml.org/download/libyaml/yaml-0.2.5.tar.gz" CACHE STRING "URL for libyaml tarball")
+set(YAML_MD5 "bb15429d8fb787e7d3f1c83ae129a999" CACHE STRING "MD5 checksum of libyaml tarball")
 mark_as_advanced(YAML_URL)
+mark_as_advanced(YAML_MD5)
+
 ExternalProject_Add(libyaml
                     URL               ${YAML_URL}
-                    URL_MD5           bb15429d8fb787e7d3f1c83ae129a999
+                    URL_MD5           ${YAML_MD5}
                     SOURCE_DIR        "${CMAKE_BINARY_DIR}/yaml-src"
                     BINARY_DIR        "${CMAKE_BINARY_DIR}/yaml-build"
                     CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}

From d4550dbb4b218541af2754bba41db856ad227f6e Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 5 Apr 2021 15:32:18 -0400
Subject: [PATCH 24/33] Update cmake/Modules/Packages/USER-SMD.cmake

---
 cmake/Modules/Packages/USER-SMD.cmake | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/cmake/Modules/Packages/USER-SMD.cmake b/cmake/Modules/Packages/USER-SMD.cmake
index 67f4aae99d..6d941f9798 100644
--- a/cmake/Modules/Packages/USER-SMD.cmake
+++ b/cmake/Modules/Packages/USER-SMD.cmake
@@ -7,10 +7,14 @@ endif()
 option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
 if(DOWNLOAD_EIGEN3)
   message(STATUS "Eigen3 download requested - we will build our own")
+  set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz" CACHE STRING "URL for Eigen3 tarball")
+  set(EIGEN3_MD5 "9e30f67e8531477de4117506fe44669b" CACHE STRING "MD5 checksum of Eigen3 tarball")
+  mark_as_advanced(EIGEN3_URL)
+  mark_as_advanced(EIGEN3_MD5)
   include(ExternalProject)
   ExternalProject_Add(Eigen3_build
-    URL https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz
-    URL_MD5 9e30f67e8531477de4117506fe44669b
+    URL     ${EIGEN3_URL}
+    URL_MD5 ${EIGEN3_MD5}
     CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
   )
   ExternalProject_get_property(Eigen3_build SOURCE_DIR)

From cbd439692ebfb2c070ed307998471b4e15523849 Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 5 Apr 2021 15:36:14 -0400
Subject: [PATCH 25/33] Update cmake/Modules/Packages/KIM.cmake

---
 cmake/Modules/Packages/KIM.cmake | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/cmake/Modules/Packages/KIM.cmake b/cmake/Modules/Packages/KIM.cmake
index 5482d3071c..2a2a1cde78 100644
--- a/cmake/Modules/Packages/KIM.cmake
+++ b/cmake/Modules/Packages/KIM.cmake
@@ -35,9 +35,13 @@ if(DOWNLOAD_KIM)
   include(ExternalProject)
   enable_language(C)
   enable_language(Fortran)
+  set(KIM_URL "https://s3.openkim.org/kim-api/kim-api-2.2.1.txz" CACHE STRING "URL for KIM tarball")
+  set(KIM_MD5 "ae1ddda2ef7017ea07934e519d023dca" CACHE STRING "MD5 checksum of KIM tarball")
+  mark_as_advanced(KIM_URL)
+  mark_as_advanced(KIM_MD5)
   ExternalProject_Add(kim_build
-    URL https://s3.openkim.org/kim-api/kim-api-2.2.1.txz
-    URL_MD5 ae1ddda2ef7017ea07934e519d023dca
+    URL     ${KIM_URL}
+    URL_MD5 ${KIM_MD5}
     BINARY_DIR build
     CMAKE_ARGS ${CMAKE_REQUEST_PIC}
                -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}

From fc6e10921d26c5c9e0a446cec7246dad005324f6 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 5 Apr 2021 15:38:59 -0400
Subject: [PATCH 26/33] add post yes/no keyword to rerun commmand (with default
 to no)

---
 doc/src/rerun.rst |  9 +++++++--
 src/rerun.cpp     | 12 +++++++++++-
 2 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/doc/src/rerun.rst b/doc/src/rerun.rst
index 7d51fba868..e9e23afba8 100644
--- a/doc/src/rerun.rst
+++ b/doc/src/rerun.rst
@@ -15,7 +15,7 @@ Syntax
 
   .. parsed-literal::
 
-     keyword = *first* or *last* or *every* or *skip* or *start* or *stop* or *dump*
+     keyword = *first* or *last* or *every* or *skip* or *start* or *stop* or *post* or *dump*
       *first* args = Nfirst
         Nfirst = dump timestep to start on
       *last* args = Nlast
@@ -28,6 +28,7 @@ Syntax
         Nstart = timestep on which pseudo run will start
       *stop* args = Nstop
         Nstop = timestep to which pseudo run will end
+      *post* value = *yes* or *no*
       *dump* args = same as :doc:`read_dump <read_dump>` command starting with its field arguments
 
 Examples
@@ -154,6 +155,10 @@ Also note that an error will occur if you read a snapshot from the
 dump file with a timestep value larger than the *stop* setting you
 have specified.
 
+The *post* keyword can be used to minimize the output to the screen that
+happens after a *rerun* command, similar to the post keyword of the
+:doc:`run command <run>`. It is set to *no* by default.
+
 The *dump* keyword is required and must be the last keyword specified.
 Its arguments are passed internally to the :doc:`read_dump <read_dump>`
 command.  The first argument following the *dump* keyword should be
@@ -226,4 +231,4 @@ Default
 
 The option defaults are first = 0, last = a huge value (effectively
 infinity), start = same as first, stop = same as last, every = 0, skip
-= 1;
+= 1, post = no;
diff --git a/src/rerun.cpp b/src/rerun.cpp
index 648874420a..8615b02d95 100644
--- a/src/rerun.cpp
+++ b/src/rerun.cpp
@@ -51,6 +51,7 @@ void Rerun::command(int narg, char **arg)
     if (strcmp(arg[iarg],"start") == 0) break;
     if (strcmp(arg[iarg],"stop") == 0) break;
     if (strcmp(arg[iarg],"dump") == 0) break;
+    if (strcmp(arg[iarg],"post") == 0) break;
     iarg++;
   }
   int nfile = iarg;
@@ -65,6 +66,7 @@ void Rerun::command(int narg, char **arg)
   int nskip = 1;
   int startflag = 0;
   int stopflag = 0;
+  int postflag = 0;
   bigint start = -1;
   bigint stop = -1;
 
@@ -101,6 +103,14 @@ void Rerun::command(int narg, char **arg)
       stop = utils::bnumeric(FLERR,arg[iarg+1],false,lmp);
       if (stop < 0) error->all(FLERR,"Illegal rerun command");
       iarg += 2;
+    } else if (strcmp(arg[iarg],"post") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal rerun command");
+      if (strcmp(arg[iarg+1],"yes") == 0) {
+        postflag = 1;
+      } else if (strcmp(arg[iarg+1],"no") == 0) {
+        postflag = 0;
+      } else error->all(FLERR,"Illegal rerun command");
+      iarg += 2;
     } else if (strcmp(arg[iarg],"dump") == 0) {
       break;
     } else error->all(FLERR,"Illegal rerun command");
@@ -182,7 +192,7 @@ void Rerun::command(int narg, char **arg)
   update->nsteps = ndump;
 
   Finish finish(lmp);
-  finish.end(1);
+  finish.end(postflag);
 
   update->whichflag = 0;
   update->firststep = update->laststep = 0;

From 7e57d6a334b0493698827f4a78b204ec5e064de9 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Mon, 5 Apr 2021 15:39:31 -0400
Subject: [PATCH 27/33] add tests for "rerun"

---
 unittest/formats/test_dump_atom.cpp   | 50 ++++++++++++++++--
 unittest/formats/test_dump_custom.cpp | 73 +++++++++++++++++++++++++--
 2 files changed, 115 insertions(+), 8 deletions(-)

diff --git a/unittest/formats/test_dump_atom.cpp b/unittest/formats/test_dump_atom.cpp
index 46c6b7dfa7..5161eece3e 100644
--- a/unittest/formats/test_dump_atom.cpp
+++ b/unittest/formats/test_dump_atom.cpp
@@ -15,6 +15,8 @@
 #include "../testing/systems/melt.h"
 #include "../testing/utils.h"
 #include "fmt/format.h"
+#include "output.h"
+#include "thermo.h"
 #include "utils.h"
 #include "gmock/gmock.h"
 #include "gtest/gtest.h"
@@ -24,7 +26,7 @@
 using ::testing::Eq;
 
 char *BINARY2TXT_BINARY = nullptr;
-bool verbose = false;
+bool verbose            = false;
 
 class DumpAtomTest : public MeltTest {
     std::string dump_style = "atom";
@@ -46,7 +48,14 @@ public:
             command(fmt::format("dump_modify id {}", dump_modify_options));
         }
 
-        command(fmt::format("run {}", ntimesteps));
+        command(fmt::format("run {} post no", ntimesteps));
+        END_HIDE_OUTPUT();
+    }
+
+    void continue_dump(int ntimesteps)
+    {
+        BEGIN_HIDE_OUTPUT();
+        command(fmt::format("run {} pre no post no", ntimesteps));
         END_HIDE_OUTPUT();
     }
 
@@ -62,7 +71,7 @@ public:
             command(fmt::format("dump_modify id1 {}", dump_modify_options));
         }
 
-        command(fmt::format("run {}", ntimesteps));
+        command(fmt::format("run {} post no", ntimesteps));
         END_HIDE_OUTPUT();
     }
 
@@ -446,13 +455,16 @@ TEST_F(DumpAtomTest, binary_triclinic_with_image_run0)
     delete_file(converted_file);
 }
 
-TEST_F(DumpAtomTest, run1)
+TEST_F(DumpAtomTest, run1plus1)
 {
-    auto dump_file = "dump_run1.melt";
+    auto dump_file = "dump_run1plus1.melt";
     generate_dump(dump_file, "", 1);
 
     ASSERT_FILE_EXISTS(dump_file);
     ASSERT_EQ(count_lines(dump_file), 82);
+    continue_dump(1);
+    ASSERT_FILE_EXISTS(dump_file);
+    ASSERT_EQ(count_lines(dump_file), 123);
     delete_file(dump_file);
 }
 
@@ -466,6 +478,34 @@ TEST_F(DumpAtomTest, run2)
     delete_file(dump_file);
 }
 
+TEST_F(DumpAtomTest, rerun)
+{
+    auto dump_file = "dump_rerun.melt";
+    HIDE_OUTPUT([&] {
+        command("fix 1 all nve");
+    });
+    generate_dump(dump_file, "format line \"%d %d %20.15g %20.15g %20.15g\"", 1);
+    double pe_1, pe_2, pe_rerun;
+    lmp->output->thermo->evaluate_keyword("pe", &pe_1);
+    ASSERT_FILE_EXISTS(dump_file);
+    ASSERT_EQ(count_lines(dump_file), 82);
+    continue_dump(1);
+    lmp->output->thermo->evaluate_keyword("pe", &pe_2);
+    ASSERT_FILE_EXISTS(dump_file);
+    ASSERT_EQ(count_lines(dump_file), 123);
+    HIDE_OUTPUT([&] {
+        command(fmt::format("rerun {} first 1 last 1 every 1 post no dump x y z", dump_file));
+    });
+    lmp->output->thermo->evaluate_keyword("pe", &pe_rerun);
+    ASSERT_DOUBLE_EQ(pe_1, pe_rerun);
+    HIDE_OUTPUT([&] {
+        command(fmt::format("rerun {} first 2 last 2 every 1 post yes dump x y z", dump_file));
+    });
+    lmp->output->thermo->evaluate_keyword("pe", &pe_rerun);
+    ASSERT_DOUBLE_EQ(pe_2, pe_rerun);
+    delete_file(dump_file);
+}
+
 TEST_F(DumpAtomTest, multi_file_run1)
 {
     auto dump_file = "dump_run1_*.melt";
diff --git a/unittest/formats/test_dump_custom.cpp b/unittest/formats/test_dump_custom.cpp
index b90d77e966..f8a55bb2fb 100644
--- a/unittest/formats/test_dump_custom.cpp
+++ b/unittest/formats/test_dump_custom.cpp
@@ -15,6 +15,8 @@
 #include "../testing/systems/melt.h"
 #include "../testing/utils.h"
 #include "fmt/format.h"
+#include "output.h"
+#include "thermo.h"
 #include "utils.h"
 #include "gmock/gmock.h"
 #include "gtest/gtest.h"
@@ -22,7 +24,7 @@
 using ::testing::Eq;
 
 char *BINARY2TXT_BINARY = nullptr;
-bool verbose = false;
+bool verbose            = false;
 
 class DumpCustomTest : public MeltTest {
     std::string dump_style = "custom";
@@ -45,7 +47,14 @@ public:
             command(fmt::format("dump_modify id {}", dump_modify_options));
         }
 
-        command(fmt::format("run {}", ntimesteps));
+        command(fmt::format("run {} post no", ntimesteps));
+        END_HIDE_OUTPUT();
+    }
+
+    void continue_dump(int ntimesteps)
+    {
+        BEGIN_HIDE_OUTPUT();
+        command(fmt::format("run {} pre no post no", ntimesteps));
         END_HIDE_OUTPUT();
     }
 
@@ -62,7 +71,7 @@ public:
             command(fmt::format("dump_modify id1 {}", dump_modify_options));
         }
 
-        command(fmt::format("run {}", ntimesteps));
+        command(fmt::format("run {} post no", ntimesteps));
         END_HIDE_OUTPUT();
     }
 
@@ -262,6 +271,64 @@ TEST_F(DumpCustomTest, with_variable_run1)
     delete_file(dump_file);
 }
 
+TEST_F(DumpCustomTest, run1plus1)
+{
+    auto dump_file = "dump_custom_run1plus1.melt";
+    auto fields    = "id type x y z";
+
+    generate_dump(dump_file, fields, "units yes", 1);
+
+    ASSERT_FILE_EXISTS(dump_file);
+    auto lines = read_lines(dump_file);
+    ASSERT_EQ(lines.size(), 84);
+    continue_dump(1);
+    ASSERT_FILE_EXISTS(dump_file);
+    lines = read_lines(dump_file);
+    ASSERT_EQ(lines.size(), 125);
+    delete_file(dump_file);
+}
+
+TEST_F(DumpCustomTest, run2)
+{
+    auto dump_file = "dump_custom_run2.melt";
+    auto fields    = "id type x y z";
+    generate_dump(dump_file, fields, "", 2);
+
+    ASSERT_FILE_EXISTS(dump_file);
+    ASSERT_EQ(count_lines(dump_file), 123);
+    delete_file(dump_file);
+}
+
+TEST_F(DumpCustomTest, rerun)
+{
+    auto dump_file = "dump_rerun.melt";
+    auto fields    = "id type xs ys zs";
+
+    HIDE_OUTPUT([&] {
+        command("fix 1 all nve");
+    });
+    generate_dump(dump_file, fields, "format float %20.15g", 1);
+    double pe_1, pe_2, pe_rerun;
+    lmp->output->thermo->evaluate_keyword("pe", &pe_1);
+    ASSERT_FILE_EXISTS(dump_file);
+    ASSERT_EQ(count_lines(dump_file), 82);
+    continue_dump(1);
+    lmp->output->thermo->evaluate_keyword("pe", &pe_2);
+    ASSERT_FILE_EXISTS(dump_file);
+    ASSERT_EQ(count_lines(dump_file), 123);
+    HIDE_OUTPUT([&] {
+        command(fmt::format("rerun {} first 1 last 1 every 1 post no dump x y z", dump_file));
+    });
+    lmp->output->thermo->evaluate_keyword("pe", &pe_rerun);
+    ASSERT_DOUBLE_EQ(pe_1, pe_rerun);
+    HIDE_OUTPUT([&] {
+        command(fmt::format("rerun {} first 2 last 2 every 1 post yes dump x y z", dump_file));
+    });
+    lmp->output->thermo->evaluate_keyword("pe", &pe_rerun);
+    ASSERT_DOUBLE_EQ(pe_2, pe_rerun);
+    delete_file(dump_file);
+}
+
 int main(int argc, char **argv)
 {
     MPI_Init(&argc, &argv);

From 94068cc4c7b8465dc3beb91dde1eecfc0cbeb33e Mon Sep 17 00:00:00 2001
From: Richard Berger <richard.berger@temple.edu>
Date: Mon, 5 Apr 2021 16:17:41 -0400
Subject: [PATCH 28/33] Add missing GTEST_MD5

---
 cmake/Modules/GTest.cmake | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/cmake/Modules/GTest.cmake b/cmake/Modules/GTest.cmake
index 0c62291d5e..677ed5f4af 100644
--- a/cmake/Modules/GTest.cmake
+++ b/cmake/Modules/GTest.cmake
@@ -8,10 +8,12 @@ endif()
 
 include(ExternalProject)
 set(GTEST_URL "https://github.com/google/googletest/archive/release-1.10.0.tar.gz" CACHE STRING "URL for GTest tarball")
+set(GTEST_MD5 "ecd1fa65e7de707cd5c00bdac56022cd" CACHE STRING "MD5 checksum of GTest tarball")
 mark_as_advanced(GTEST_URL)
+mark_as_advanced(GTEST_MD5)
 ExternalProject_Add(googletest
-                    URL ${GTEST_URL}
-                    URL_MD5         ecd1fa65e7de707cd5c00bdac56022cd
+                    URL             ${GTEST_URL}
+                    URL_MD5         ${GTEST_MD5}
                     SOURCE_DIR      "${CMAKE_BINARY_DIR}/gtest-src"
                     BINARY_DIR      "${CMAKE_BINARY_DIR}/gtest-build"
                     CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS}

From 11d62b71c382ef202cee84602e35984b3e0b98a7 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Apr 2021 11:11:01 -0400
Subject: [PATCH 29/33] use clang preset when compiling on MacOS

---
 .github/workflows/unittest-macos.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/unittest-macos.yml b/.github/workflows/unittest-macos.yml
index a65db7636b..f62b3046c9 100644
--- a/.github/workflows/unittest-macos.yml
+++ b/.github/workflows/unittest-macos.yml
@@ -24,7 +24,9 @@ jobs:
       shell: bash
       working-directory: ${{github.workspace}}/build
       run: |
-        cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake \
+        cmake -C $GITHUB_WORKSPACE/cmake/presets/clang.cmake \
+              -C $GITHUB_WORKSPACE/cmake/presets/most.cmake \
+                 $GITHUB_WORKSPACE/cmake \
               -DENABLE_TESTING=ON -DBUILD_SHARED_LIBS=ON -DLAMMPS_EXCEPTIONS=ON
         cmake --build . --parallel 2
 

From d346c539147ae666741494657646a8d885741312 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Apr 2021 11:28:19 -0400
Subject: [PATCH 30/33] silence compiler warnings about formats

---
 src/USER-REAXC/reaxc_tool_box.cpp | 45 +++++++++++++++----------------
 src/USER-REAXC/reaxc_traj.h       | 16 ++++++-----
 2 files changed, 31 insertions(+), 30 deletions(-)

diff --git a/src/USER-REAXC/reaxc_tool_box.cpp b/src/USER-REAXC/reaxc_tool_box.cpp
index f0171d2108..abab3f2b43 100644
--- a/src/USER-REAXC/reaxc_tool_box.cpp
+++ b/src/USER-REAXC/reaxc_tool_box.cpp
@@ -25,10 +25,11 @@
   ----------------------------------------------------------------------*/
 
 #include "reaxc_tool_box.h"
+#include "reaxc_defs.h"
+
 #include <cstdio>
 #include <cstdlib>
 #include <cstring>
-#include "reaxc_defs.h"
 
 #include "error.h"
 
@@ -49,62 +50,58 @@ int Tokenize( char* s, char*** tok )
   return count;
 }
 
-
-
 /* safe malloc */
 void *smalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, const char *name )
 {
   void *ptr;
-  char errmsg[256];
 
   if (n <= 0) {
-    snprintf(errmsg, 256, "Trying to allocate %ld bytes for array %s. "
-              "returning NULL.", n, name);
+    auto errmsg = fmt::format("Trying to allocate {} bytes for array {}. "
+                              "returning NULL.", n, name);
     if (error_ptr) error_ptr->one(FLERR,errmsg);
-    else fputs(errmsg,stderr);
+    else fputs(errmsg.c_str(),stderr);
 
     return nullptr;
   }
 
   ptr = malloc( n );
   if (ptr == nullptr) {
-    snprintf(errmsg, 256, "Failed to allocate %ld bytes for array %s", n, name);
+    auto errmsg = fmt::format("Failed to allocate {} bytes for array {}",
+                              n, name);
     if (error_ptr) error_ptr->one(FLERR,errmsg);
-    else fputs(errmsg,stderr);
+    else fputs(errmsg.c_str(),stderr);
   }
 
   return ptr;
 }
 
-
 /* safe calloc */
 void *scalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, rc_bigint size, const char *name )
 {
   void *ptr;
-  char errmsg[256];
 
   if (n <= 0) {
-    snprintf(errmsg, 256, "Trying to allocate %ld elements for array %s. "
-            "returning NULL.\n", n, name );
+    auto errmsg = fmt::format("Trying to allocate {} elements for array {}. "
+            "returning NULL.\n", n, name);
     if (error_ptr) error_ptr->one(FLERR,errmsg);
-    else fputs(errmsg,stderr);
+    else fputs(errmsg.c_str(),stderr);
     return nullptr;
   }
 
   if (size <= 0) {
-    snprintf(errmsg, 256, "Elements size for array %s is %ld. "
-             "returning NULL", name, size );
+    auto errmsg = fmt::format("Elements size for array {} is {}. "
+             "returning NULL", name, size);
     if (error_ptr) error_ptr->one(FLERR,errmsg);
-    else fputs(errmsg,stderr);
+    else fputs(errmsg.c_str(),stderr);
     return nullptr;
   }
 
   ptr = calloc( n, size );
   if (ptr == nullptr) {
-    char errmsg[256];
-    snprintf(errmsg, 256, "Failed to allocate %ld bytes for array %s", n*size, name);
+    auto errmsg = fmt::format("Failed to allocate {} bytes for array {}",
+                              n*size, name);
     if (error_ptr) error_ptr->one(FLERR,errmsg);
-    else fputs(errmsg,stderr);
+    else fputs(errmsg.c_str(),stderr);
   }
 
   return ptr;
@@ -115,14 +112,14 @@ void *scalloc( LAMMPS_NS::Error *error_ptr, rc_bigint n, rc_bigint size, const c
 void sfree( LAMMPS_NS::Error* error_ptr, void *ptr, const char *name )
 {
   if (ptr == nullptr) {
-    char errmsg[256];
-    snprintf(errmsg, 256, "Trying to free the already NULL pointer %s", name );
+    auto errmsg = fmt::format("Trying to free the already free()'d pointer {}",
+                              name);
     if (error_ptr) error_ptr->one(FLERR,errmsg);
-    else fputs(errmsg,stderr);
+    else fputs(errmsg.c_str(),stderr);
     return;
   }
 
-  free( ptr );
+  free(ptr);
   ptr = nullptr;
 }
 
diff --git a/src/USER-REAXC/reaxc_traj.h b/src/USER-REAXC/reaxc_traj.h
index 4966bf11d8..2ff5995204 100644
--- a/src/USER-REAXC/reaxc_traj.h
+++ b/src/USER-REAXC/reaxc_traj.h
@@ -36,14 +36,18 @@
 #define HEADER_LINE_LEN 62
 #define STR_LINE  "%-37s%-24s\n"
 #define INT_LINE  "%-37s%-24d\n"
-#define BIGINT_LINE  "%-37s%-24ld\n"
+#if defined(LAMMPS_SMALLSMALL)
+#define BIGINT_LINE  "%-37s%-24d\n"
+#else
+#define BIGINT_LINE  "%-37s%-24lld\n"
+#endif
 #define INT2_LINE  "%-36s%-12d,%-12d\n"
 #define REAL_LINE "%-37s%-24.3f\n"
 #define SCI_LINE  "%-37s%-24g\n"
 #define REAL3_LINE "%-32s%9.3f,%9.3f,%9.3f\n"
 
 #if defined(LAMMPS_BIGBIG)
-#define INIT_DESC "%9ld%3d%9s%10.3f\n" //AtomID - AtomType, AtomName, AtomMass
+#define INIT_DESC "%9lld%3d%9s%10.3f\n" //AtomID - AtomType, AtomName, AtomMass
 #else
 #define INIT_DESC "%9d%3d%9s%10.3f\n" //AtomID - AtomType, AtomName, AtomMass
 #endif
@@ -56,7 +60,7 @@
 #define SIZE_INFO_LEN3 31
 
 #if defined(LAMMPS_BIGBIG)
-#define ATOM_BASIC "%9ld%10.3f%10.3f%10.3f%10.3f\n" //AtomID AtomType (X Y Z) Charge
+#define ATOM_BASIC "%9lld%10.3f%10.3f%10.3f%10.3f\n" //AtomID AtomType (X Y Z) Charge
 #define ATOM_wV    "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) Charge
 #define ATOM_wF    "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Fx Fy Fz) Charge
 #define ATOM_FULL  "%9ld%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f%10.3f\n" //AtomID (X Y Z) (Vx Vy Vz) (Fx Fy Fz) Charge
@@ -72,9 +76,9 @@
 #define ATOM_FULL_LEN 110
 
 #if defined(LAMMPS_BIGBIG)
-#define BOND_BASIC "%9ld%9ld%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO
-#define BOND_FULL  "%9ld%9ld%10.3f%10.3f%10.3f%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO BOs BOpi BOpi2
-#define ANGLE_BASIC "%9ld%9ld%9ld%10.3f\n" // Atom1 Atom2 Atom3 Theta
+#define BOND_BASIC "%9lld%9lld%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO
+#define BOND_FULL  "%9lld%9lld%10.3f%10.3f%10.3f%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO BOs BOpi BOpi2
+#define ANGLE_BASIC "%9lld%9lld%9lld%10.3f\n" // Atom1 Atom2 Atom3 Theta
 #else
 #define BOND_BASIC "%9d%9d%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO
 #define BOND_FULL  "%9d%9d%10.3f%10.3f%10.3f%10.3f%10.3f\n" // Atom1 Atom2 Dist Total_BO BOs BOpi BOpi2

From db400c91aec560f8b04a83c8de4141724d1df89e Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Apr 2021 11:37:59 -0400
Subject: [PATCH 31/33] relax error a little bit to avoid failure on macos

---
 unittest/force-styles/tests/fix-timestep-adapt_coul.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml b/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml
index 4bf25f3b33..cd7f9aa87d 100644
--- a/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml
+++ b/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml
@@ -1,7 +1,7 @@
 ---
 lammps_version: 10 Mar 2021
 date_generated: Thu Mar 25 14:07:45 202
-epsilon: 1e-14
+epsilon: 7.5e-14
 prerequisites: ! |
   atom full
   fix adapt

From e01e0298cb9587cac513face286643ff1e7d6b07 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Apr 2021 13:25:24 -0400
Subject: [PATCH 32/33] fix uninitialized data access after restart bug in
 USER-YAFF pair styles

also fix some source formatting issues
---
 src/KSPACE/pair_lj_cut_coul_long.cpp          | 16 +++++++-------
 .../pair_lj_switch3_coulgauss_long.cpp        | 22 ++++++++++---------
 .../pair_mm3_switch3_coulgauss_long.cpp       | 20 +++++++++--------
 3 files changed, 31 insertions(+), 27 deletions(-)

diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp
index fcb39b8c6e..5d04fd1cfb 100644
--- a/src/KSPACE/pair_lj_cut_coul_long.cpp
+++ b/src/KSPACE/pair_lj_cut_coul_long.cpp
@@ -17,21 +17,21 @@
 
 #include "pair_lj_cut_coul_long.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
+#include "error.h"
 #include "force.h"
 #include "kspace.h"
-#include "update.h"
-#include "respa.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
 #include "math_const.h"
 #include "memory.h"
-#include "error.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+#include "respa.h"
+#include "update.h"
 
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp
index 6e4c0587f7..2247a9467c 100644
--- a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp
+++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp
@@ -106,6 +106,7 @@ void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag)
   firstneigh = list->firstneigh;
 
   // loop over neighbors of my atoms
+
   for (ii = 0; ii < inum; ii++) {
     i = ilist[ii];
     qtmp = q[i];
@@ -193,7 +194,7 @@ void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag)
               offset[itype][jtype];
         } else evdwl = 0.0;
 
-        // Truncation, see Yaff Switch33
+        // Truncation, see Yaff Switch3
         if (truncw>0) {
           if (rsq < cut_ljsq[itype][jtype]) {
             if (r>cut_lj[itype][jtype]-truncw) {
@@ -262,19 +263,18 @@ void PairLJSwitch3CoulGaussLong::allocate()
 
 void PairLJSwitch3CoulGaussLong::settings(int narg, char **arg)
 {
- if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command");
+  if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command");
 
   cut_lj_global = utils::numeric(FLERR,arg[0],false,lmp);
+
   if (narg == 2) {
     cut_coul = cut_lj_global;
     truncw = utils::numeric(FLERR,arg[1],false,lmp);
-  }
-  else {
+  } else {
     cut_coul = utils::numeric(FLERR,arg[1],false,lmp);
     truncw = utils::numeric(FLERR,arg[2],false,lmp);
   }
-  if (truncw>0.0) truncwi = 1.0/truncw;
-  else truncwi = 0.0;
+
   // reset cutoffs that have been explicitly set
 
   if (allocated) {
@@ -332,6 +332,9 @@ void PairLJSwitch3CoulGaussLong::init_style()
 
   cut_coulsq = cut_coul * cut_coul;
 
+  if (truncw>0.0) truncwi = 1.0/truncw;
+  else truncwi = 0.0;
+
   // insure use of KSpace long-range solver, set g_ewald
 
   if (force->kspace == nullptr)
@@ -375,8 +378,7 @@ double PairLJSwitch3CoulGaussLong::init_one(int i, int j)
       double r6inv = r2inv*r2inv*r2inv;
       double r12inv = r6inv*r6inv;
       offset[i][j] = lj3[i][j]*r12inv-lj4[i][j]*r6inv;
-    }
-    else {offset[i][j] = 0.0;}
+    } else {offset[i][j] = 0.0;}
   } else offset[i][j] = 0.0;
 
   cut_ljsq[j][i] = cut_ljsq[i][j];
@@ -431,8 +433,7 @@ double PairLJSwitch3CoulGaussLong::init_one(int i, int j)
       double t71 = -0.4e1 * cg * (0.2e1 * t10 * t11 - 0.2e1 * t10 * t14 + (cg5 - 0.2e1 * cg1) * t58 * cg5) * t26 / t4 / t41 / t9;
       etail_ij = 2.0*MY_PI*all[0]*all[1]*t71;
       ptail_ij = 2.0*MY_PI*all[0]*all[1]*t71;
-    }
-    else {
+    } else {
       double t1 = pow(cg3, 0.2e1);
       double t2 = t1 * t1;
       double t3 = t2 * t1;
@@ -618,6 +619,7 @@ double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype,
       expn2 = 0.0;
       erfc2 = 0.0;
       forcecoul2 = 0.0;
+      prefactor2 = 0.0;
     } else {
       r = sqrt(rsq);
       rrij = lj2[itype][jtype]*r;
diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp
index 67a322ca24..c7fcac855a 100644
--- a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp
+++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp
@@ -106,6 +106,7 @@ void PairMM3Switch3CoulGaussLong::compute(int eflag, int vflag)
   firstneigh = list->firstneigh;
 
   // loop over neighbors of my atoms
+
   for (ii = 0; ii < inum; ii++) {
     i = ilist[ii];
     qtmp = q[i];
@@ -170,6 +171,7 @@ void PairMM3Switch3CoulGaussLong::compute(int eflag, int vflag)
             expn2 = 0.0;
             erfc2 = 0.0;
             forcecoul2 = 0.0;
+            prefactor2 = 0.0;
           } else {
             rrij = lj2[itype][jtype]*r;
             expn2 = exp(-rrij*rrij);
@@ -263,19 +265,18 @@ void PairMM3Switch3CoulGaussLong::allocate()
 
 void PairMM3Switch3CoulGaussLong::settings(int narg, char **arg)
 {
- if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command");
+  if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command");
 
   cut_lj_global = utils::numeric(FLERR,arg[0],false,lmp);
+
   if (narg == 2) {
     cut_coul = cut_lj_global;
     truncw = utils::numeric(FLERR,arg[1],false,lmp);
-  }
-  else {
+  } else {
     cut_coul = utils::numeric(FLERR,arg[1],false,lmp);
     truncw = utils::numeric(FLERR,arg[2],false,lmp);
   }
-  if (truncw>0.0) truncwi = 1.0/truncw;
-  else truncwi = 0.0;
+
   // reset cutoffs that have been explicitly set
 
   if (allocated) {
@@ -333,6 +334,9 @@ void PairMM3Switch3CoulGaussLong::init_style()
 
   cut_coulsq = cut_coul * cut_coul;
 
+  if (truncw>0.0) truncwi = 1.0/truncw;
+  else truncwi = 0.0;
+
   // insure use of KSpace long-range solver, set g_ewald
 
   if (force->kspace == nullptr)
@@ -375,8 +379,7 @@ double PairMM3Switch3CoulGaussLong::init_one(int i, int j)
       double r6inv = r2inv*r2inv*r2inv;
       double expb = lj3[i][j]*exp(-lj1[i][j]*r);
       offset[i][j] = expb-lj4[i][j]*r6inv;
-    }
-    else {offset[i][j] = 0.0;}
+    } else {offset[i][j] = 0.0;}
   } else offset[i][j] = 0.0;
 
   cut_ljsq[j][i] = cut_ljsq[i][j];
@@ -426,8 +429,7 @@ double PairMM3Switch3CoulGaussLong::init_one(int i, int j)
         double t64 = cg * (0.6388888889e3 * ((-t3 + (0.7e1 / 0.36e2 * cg5 - t5) * t1 - 0.2e1 / 0.3e1 * t8 * (cg5 - cg1 / 0.4e1) * cg3 + cg5 * t14) * t20 + t3 + (cg5 / 0.12e2 + t5) * t1 + (cg5 + cg1 / 0.3e1) * cg1 * cg3 / 0.2e1 + t30 * cg5) * t2 * t36 * t39 - 0.225e1 * (0.2e1 * t43 * t44 - 0.2e1 * t43 * t47 + cg5 * (cg5 - 0.2e1 * cg1)) * t54 * t1 / cg1 / t8 * t39);
         etail_ij = 2.0*MY_PI*all[0]*all[1]*t64;
         ptail_ij = 2.0*MY_PI*all[0]*all[1]*t64;
-    }
-    else {
+    } else {
         double t2 = pow(cg3, 0.2e1);
         double t3 = t2 * t2;
         double t7 = 0.12e2 / cg3 * cg1;

From 698b9b9519000b8976084714a977a6ce25a880d3 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Tue, 6 Apr 2021 13:36:27 -0400
Subject: [PATCH 33/33] relax epsilon some more

---
 unittest/force-styles/tests/fix-timestep-adapt_coul.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml b/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml
index cd7f9aa87d..f0ec2f1292 100644
--- a/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml
+++ b/unittest/force-styles/tests/fix-timestep-adapt_coul.yaml
@@ -1,7 +1,7 @@
 ---
 lammps_version: 10 Mar 2021
 date_generated: Thu Mar 25 14:07:45 202
-epsilon: 7.5e-14
+epsilon: 5e-13
 prerequisites: ! |
   atom full
   fix adapt