Merge branch 'master' into new_collcommobj

ls1mardyn · Jan 29, 2025 · 2b7ac0e · 2b7ac0e
2 parents 31a5c6a + 2981975
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diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -17,3 +17,8 @@ Please describe the tests that you ran to verify your changes.
 
 - [ ] Test A
 - [ ] Test B
+
+## Documentation
+(Only relevant if this PR introduces new features)
+- [ ] `all-options.xml` documents how to use the feature.
+- [ ] The responsible `readXML()` documents how to use the feature.
diff --git a/.github/workflows/ls1_test.yml b/.github/workflows/ls1_test.yml
@@ -57,9 +57,11 @@ jobs:
         sudo apt-get update
         # MPICH 4.0.3 seems to have a bug that triggers a FP exception in our collective communication when doing 0+0.
         sudo apt-get install -y \
+          uuid-dev              \
           libcppunit-dev        \
           libopenmpi-dev        \
-          libomp-dev
+          libomp-dev            \
+          libxerces-c-dev
         echo "Running ${JOBNAME}"
         git status
         mkdir build_${JOBNAME}
@@ -85,10 +87,12 @@ jobs:
           cmake -DVECTOR_INSTRUCTIONS=${{ matrix.vector }} \
                 -DCMAKE_BUILD_TYPE=${{ matrix.target }} \
                 -DENABLE_AUTOPAS=${{ matrix.autopas }} \
+                -DAUTOPAS_ENABLE_RULES_BASED_AND_FUZZY_TUNING=ON \
                 -DENABLE_ALLLBL=$alllbl_enabled \
                 -DOPENMP=${{ matrix.openmp }} \
                 -DENABLE_MPI=$mpi_enabled \
                 -DENABLE_UNIT_TESTS=ON \
+                -DENABLE_VTK=ON \
               ..
         
           cmake --build . --parallel 1
@@ -146,9 +150,11 @@ jobs:
           cmake -DVECTOR_INSTRUCTIONS=${{ matrix.vector }} \
                 -DCMAKE_BUILD_TYPE=${{ matrix.target }} \
                 -DENABLE_AUTOPAS=${{ matrix.autopas }} \
+                -DAUTOPAS_ENABLE_RULES_BASED_AND_FUZZY_TUNING=ON \
                 -DENABLE_ALLLBL=$alllbl_enabled \
                 -DOPENMP=${{ matrix.openmp }} \
                 -DENABLE_MPI=$mpi_enabled \
+                -DENABLE_VTK=ON \
               ..
         
           cmake --build . --parallel 1

diff --git a/CITATION.cff b/CITATION.cff
@@ -1,4 +1,4 @@
-cff-version: 1.0.3
+cff-version: 1.2.0
 message: This file contains CFF citation information, cf. https://citation-file-format.github.io/, for the ls1 mardyn molecular dynamics code developed by the Boltzmann-Zuse Society for Computational Molecular Engineering.
 title: ls1 mardyn
 url: http://www.ls1-mardyn.de/
@@ -7,16 +7,16 @@ date-released: 2018-09-05
 commit: Revision 6473.
 version: Internal development version, situated between release 1.1.1 and prospective future release 1.2
 license-url: http://www.ls1-mardyn.de/license.html
-abstract: The molecular dynamics code ls1 mardyn (large systems 1: molecular dynamics), developed by the Boltzmann-Zuse Society for Computational Molecular Engineering, is a scalable massively-parallel molecular modelling and simulation code for classical-mechanical intermolecular pair potential models of low-molecular fluids.
+abstract: "The molecular dynamics code ls1 mardyn (large systems 1: molecular dynamics), developed by the Boltzmann-Zuse Society for Computational Molecular Engineering, is a scalable massively-parallel molecular modelling and simulation code for classical-mechanical intermolecular pair potential models of low-molecular fluids."
 contact:
  - given-names: Philipp
    family-names: Neumann
-author:
+authors:
  - name: Boltzmann-Zuse Society for Computational Molecular Engineering
    country: DE
-references:
- - type: article
-   title: ls1 mardyn: The massively parallel molecular dynamics code for large systems
+preferred-citation:
+   type: article
+   title: "ls1 mardyn: The massively parallel molecular dynamics code for large systems"
    year: 2014
    authors:
     - given-names: Christoph

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -70,9 +70,6 @@ include(autopas)
 # ----- include mamico
 include(mamico)
 
-# ----- resilience plugin dependencies are set here
-include(compression)
-
 # ----- add adios2 dependency
 include(adios2)
 

diff --git a/README.md b/README.md
@@ -21,7 +21,7 @@ Prerequisites
 * [FFTW3](http://www.fftw.org)
 * [VTK](http://www.vtk.org)
 * [QuickSched](https://arxiv.org/abs/1601.05384)
-
+* If [AutoPas](https://autopas.github.io/doxygen_documentation/git-master/) is enabled, make sure to have [its requirements](https://github.com/AutoPas/AutoPas/blob/master/docs/userdoc/Building.md) installed.
 
 Installation
 ------------
@@ -161,10 +161,13 @@ MarDyn [options] <inputfile>
 ```
 where `MarDyn` is the executable build in the INSTALLATION section, `[options]` are any "--"-prefixed options as listed by `MarDyn --help` and `<inputfile>` is a input file.
 
-Detailed help can be obtained by running
+To get an overview of further command line options run
 ```sh
 MarDyn --help
 ```
+
+To understand how to write an input file check out [examples/all-options.xml](https://github.com/ls1mardyn/ls1-mardyn/blob/master/examples/all-options.xml), the various examples in the examples folder and the documentation of the various `readXML()` methods, e.g. via our doxygen documentation.
+
 ### running examples
 ls1-MarDyn comes with a set of examples, which can be found in the examples folder.
 ```sh

diff --git a/cmake/modules/autopas.cmake b/cmake/modules/autopas.cmake
@@ -23,8 +23,8 @@ if (ENABLE_AUTOPAS)
     set(AUTOPAS_USE_VECTORIZATION ${USE_VECTORIZATION} CACHE BOOL "Set via USE_VECTORIZATION" FORCE)
     set(AUTOPAS_VECTOR_INSTRUCTIONS ${VECTOR_INSTRUCTIONS} CACHE STRING "Set via VECTOR_INSTRUCTIONS_OPTIONS" FORCE)
 
-    # Merge of #830 (fixRegionIterators); includes #787 (combined tuning)
-    set(AUTOPAS_TAG faef573 CACHE STRING "AutoPas Git tag or commit id to use")
+    # Last version without 3 Body support. Newer versions have API changes
+    set(AUTOPAS_TAG v2.0.0 CACHE STRING "AutoPas Git tag or commit id to use")
 
     FetchContent_Declare(
             autopasfetch

diff --git a/cmake/modules/compression.cmake b/cmake/modules/compression.cmake
diff --git a/cmake/modules/lz4.cmake b/cmake/modules/lz4.cmake
diff --git a/cmake/modules/mamico.cmake b/cmake/modules/mamico.cmake
@@ -1,18 +1,15 @@
 option(MAMICO_COUPLING "Couple with MaMiCo" OFF)
 if (MAMICO_COUPLING)
-	message(STATUS "MaMiCo coupling enabled. ls1 mardyn will compile as library. No executable will be created.")
-	set(MAMICO_COMPILE_DEFINITIONS MAMICO_COUPLING MDDim3)
-	option(MAMICO_ENABLE_FPIC "Enable -fPIC flag for MaMiCo python bindings" OFF)
-	set(MAMICO_SRC_DIR CACHE PATH "Root directory of the MaMiCo codebase")
+    message(STATUS "MaMiCo coupling enabled. ls1 mardyn will compile as library. No executable will be created.")
+    set(MAMICO_COMPILE_DEFINITIONS MAMICO_COUPLING MDDim3)
+    option(MAMICO_ENABLE_FPIC "Enable -fPIC flag for MaMiCo python bindings" OFF)
+    set(MAMICO_SRC_DIR CACHE PATH "Root directory of the MaMiCo codebase")
     if(NOT MAMICO_SRC_DIR)
-		message(FATAL_ERROR "MaMiCo source directory not specified.")
-	endif()
-	if(ENABLE_MPI)
-		set(MAMICO_MPI_DEFINITIONS MDCoupledParallel TarchParallel)
-	endif()
-	if(MAMICO_ENABLE_FPIC)
-		set(MAMICO_COMPILE_OPTIONS "${MAMICO_COMPILE_OPTIONS} -fPIC")
-	endif()
+        message(FATAL_ERROR "MaMiCo source directory not specified.")
+    endif()
+    if(ENABLE_MPI)
+        set(MAMICO_MPI_DEFINITIONS MDCoupledParallel TarchParallel)
+    endif()
 else()
     message(STATUS "MaMiCo coupling disabled.")
 endif()
diff --git a/doc/Plugins_Summary.dox b/doc/Plugins_Summary.dox
@@ -10,7 +10,7 @@ Plugin name | Up to 5 Keywords | Short Description (one line)
 Adios2Reader | input, checkpoint, visualization, parallel, particle configurations, MegaMol | Requires ENABLE_ADIOS2=ON (downloads and installs ADIOS2 automatically, alternatively can use your preinstalled ADIOS2 with FIND_PACKAGE_ADIOS2=ON). Reads checkpoint for further computation. Use bpls tool (next to MarDyn executable) for investigation of ADIOS2 files or directories (*.bp).
 Adios2Writer | output, checkpoint, visualization, parallel, particle configurations, MegaMol | Requires ENABLE_ADIOS2=ON (downloads and installs ADIOS2 automatically, alternatively can use your preinstalled ADIOS2 with FIND_PACKAGE_ADIOS2=ON). Writes out particle configuration including position, velocity, angular momentum, quaternions for all components. Also provides meta information such as the full configuration file, component information, process count, and bounding box.
 CavityWriter | cavity, output, profile, grid | Sets up a grid of pseudo-molecules that check for neighbours in radius. Threshold determines if grid point counts as cavity or not. Output in .xyz format.
-CheckpointWriter | checkpoint, legacy | (Legacy) Checkpoint writer. Hint: use <type>binary</type> to speed-up. See also MPICheckpointWriter and MPI_IOCheckpointWriter.
+CheckpointWriter | checkpoint, legacy | (Legacy) Checkpoint writer. Hint: use <type>binary</type> to speed-up.
 COMaligner | alignment, particleContainer utility, visualization | Calculates Center of Mass (COM) of all particles and aligns it with center of simulation box. Dimension/frequency/speed of alignment can be controlled via XML.
 CommunicationPartnerWriter | mpi, communication, output, debugging | Prints the CommunicationPartners for each rank in a separate file.
 DecompWriter | mpi, print | Writes information on the MPI Domain Decomposition. For each rank the boxmin and boxmax is printed.
@@ -46,7 +46,6 @@ MettDeamonFeedrateDirector | feed rate, director, reservoir, stationary, evapora
 Mirror | reflection, mirror plane, wall, boundary condition | Reflect particles at a mirror plane employing different algorithms. This can be used as a simple wall or even more complex boundary conditions.
 MmpldWriter | visualization, particle configurations, MegaMol, mmpld, binary | Output plugin writing visualization files containing multiple subsequently sampled frames of particle configurations in the binary MegaMol Particle List Data file format (MMPLD).
 MmspdBinWriter | visualization, particle configurations, MegaMol, mmspd, binary | Output plugin writing visualization files containing multiple subsequently sampled frames of particle configurations in the binary MegaMol Simple Particle Data file format (MMSPD).
-MPI_IOCheckpointWriter | checkpointing | WIP, not functionable
 MPICheckpointWriter | checkpointing | WIP, not functionable (no proper reader existing)
 ODF | orientation distribution function | Calculates the distribution of mutual orientations between dipolar molecules and writes them into an output. Always use dipolar vector [0 0 1] in the input when using this plugin. Only tested for molecules with exactly one dipole site. Application to other molecules should be possible with minor adjustments and some testing.
 Permittivity | todo | Samples the relative permittivity for pure/mixed Stockmayer fluids and mixtures containing Stockmayer fluids and unpolar fluids. Requires long sampling times (i.e. several million steps). Using global thermostat is recommended.

diff --git a/doc/compression.dox b/doc/compression.dox
diff --git a/examples/Adsorption-plugin-version/CO2/CO2_LJ93Wall.xdr b/examples/Adsorption-plugin-version/CO2/CO2_LJ93Wall.xdr
diff --git a/examples/Adsorption-plugin-version/CO2/CO2_LJ93Wall_snapshot.png b/examples/Adsorption-plugin-version/CO2/CO2_LJ93Wall_snapshot.png
diff --git a/examples/Adsorption-plugin-version/CO2/components_co2_stoll.xml b/examples/Adsorption-plugin-version/CO2/components_co2_stoll.xml
diff --git a/examples/Adsorption-plugin-version/CO2/run01/config.xml b/examples/Adsorption-plugin-version/CO2/run01/config.xml
diff --git a/examples/Adsorption-plugin-version/CO2/sphereparams_co2_stoll.xml b/examples/Adsorption-plugin-version/CO2/sphereparams_co2_stoll.xml
diff --git a/examples/Adsorption/Generator/adsorption.xml b/examples/Adsorption/Generator/adsorption.xml
@@ -27,7 +27,7 @@
       </domain>
       <components>
         <moleculetype id="1" name="fluid">
-          <site type="LJ126" id="1">
+          <site type="LJ126" id="1" name="LJTS">
             <coords>
               <x>0.0</x>
               <y>0.0</y>

diff --git a/examples/Adsorption/Generator/adsorption_autopas_default.xml b/examples/Adsorption/Generator/adsorption_autopas_default.xml
@@ -27,7 +27,7 @@
       </domain>
       <components>
         <moleculetype id="1" name="fluid">
-          <site type="LJ126" id="1">
+          <site type="LJ126" id="1" name="LJTS">
             <coords>
               <x>0.0</x>
               <y>0.0</y>

diff --git a/examples/Adsorption/Generator/adsorption_autopas_tuning.xml b/examples/Adsorption/Generator/adsorption_autopas_tuning.xml
@@ -27,7 +27,7 @@
       </domain>
       <components>
         <moleculetype id="1" name="fluid">
-          <site type="LJ126" id="1">
+          <site type="LJ126" id="1" name="LJTS">
             <coords>
               <x>0.0</x>
               <y>0.0</y>

diff --git a/examples/Argon/components.xml b/examples/Argon/components.xml
@@ -2,7 +2,7 @@
 <components version="20100525" >
 
 	<moleculetype id="1" name="Argon">
-		<site type="LJ126" id="1" >
+		<site type="LJ126" id="1" name="Ar">
 			<coords> <x>0.0</x> <y>0.0</y> <z>0.0</z> </coords>
 			<mass>0.039948</mass>
 			<sigma>6.4160007</sigma>

diff --git a/examples/CO2/components.xml b/examples/CO2/components.xml
@@ -2,21 +2,21 @@
 <components version="20100525" >
 
 	<moleculetype id="1" name="CO2">
-		<site type="LJ126" id="1" >
+		<site type="LJ126" id="1" name="C">
 			<coords> <x>0.0</x> <y>0.0</y> <z>0.0</z> </coords>
 			<mass>0.012</mass>
 			<sigma>5.31712452</sigma>
 			<epsilon>3.91811245e-05</epsilon>
 			<shifted>false</shifted>
 		</site>
-		<site type="LJ126" id="2" >
+		<site type="LJ126" id="2" name="O">
 			<coords> <x>0.0</x> <y>0.0</y> <z>-2.43188952</z> </coords>
 			<mass>0.016</mass>
 			<sigma>5.62288233</sigma>
 			<epsilon>0.00031824324</epsilon>
 			<shifted>false</shifted>
 		</site>
-		<site type="LJ126" id="3" >
+		<site type="LJ126" id="3" name="O">
 			<coords> <x>0.0</x> <y>0.0</y> <z>2.43188952</z> </coords>
 			<mass>0.016</mass>
 			<sigma>5.62288233</sigma>

diff --git a/examples/DropletCoalescence/components.xml b/examples/DropletCoalescence/components.xml
@@ -3,7 +3,7 @@
 <components>
 
   <moleculetype id="1" name="Argon">
-    <site type="LJ126" id="1" >
+    <site type="LJ126" id="1" name="Ar">
       <coords> <x>0.0</x> <y>0.0</y> <z>0.0</z> </coords>
       <mass>39.948</mass>
       <sigma>3.3916</sigma>
@@ -18,7 +18,7 @@
   </moleculetype>
 
   <moleculetype id="2" name="Argon">
-    <site type="LJ126" id="1" >
+    <site type="LJ126" id="1" name="Ar">
       <coords> <x>0.0</x> <y>0.0</y> <z>0.0</z> </coords>
       <mass>39.948</mass>
       <sigma>3.3916</sigma>

diff --git a/examples/DropletCoalescence/liq/config_2_replicateLiq.xml b/examples/DropletCoalescence/liq/config_2_replicateLiq.xml
diff --git a/examples/DropletCoalescence/mixing_2c.xml b/examples/DropletCoalescence/mixing_2c.xml
diff --git a/examples/DropletCoalescence/vap/config_4_replicateVap.xml b/examples/DropletCoalescence/vap/config_4_replicateVap.xml
diff --git a/examples/DropletCoalescence/vle/config_5_droplet.xml b/examples/DropletCoalescence/vle/config_5_droplet.xml
diff --git a/examples/Evaporation/stationary/components_3c.xml b/examples/Evaporation/stationary/components_3c.xml
@@ -2,7 +2,7 @@
 
 <components>
 	<moleculetype id="1" name="1CLJTS_freeze">
-		<site type="LJ126" id="1" >
+		<site type="LJ126" id="1" name="LJTS">
 			<coords> <x>0.0</x> <y>0.0</y> <z>0.0</z> </coords>
 			<mass>1.0</mass>
 			<sigma>1.0</sigma>
@@ -17,7 +17,7 @@
 	</moleculetype>
 
 	<moleculetype id="2" name="1CLJTS_j+">
-		<site type="LJ126" id="1" >
+		<site type="LJ126" id="1" name="LJTS">
 			<coords> <x>0.0</x> <y>0.0</y> <z>0.0</z> </coords>
 			<mass>1.0</mass>
 			<sigma>1.0</sigma>
@@ -32,7 +32,7 @@
 	</moleculetype>
 
 	<moleculetype id="3" name="1CLJTS_j-">
-		<site type="LJ126" id="1" >
+		<site type="LJ126" id="1" name="LJTS">
 			<coords> <x>0.0</x> <y>0.0</y> <z>0.0</z> </coords>
 			<mass>1.0</mass>
 			<sigma>1.0</sigma>

diff --git a/examples/Evaporation/stationary/sphereparams_3c.xml b/examples/Evaporation/stationary/sphereparams_3c.xml
@@ -28,7 +28,7 @@
 		<color>
 			<r>0</r>
 			<g>0</g>
-			<b>255</b>>
+			<b>255</b>
 			<alpha>255</alpha>
 		</color>
 	</site>

diff --git a/examples/ExplodingLiquid/components.xml b/examples/ExplodingLiquid/components.xml
@@ -2,7 +2,7 @@
 
 <components>
 	<moleculetype id="1" name="1CLJTS">
-	<site type="LJ126" id="1" >
+	<site type="LJ126" id="1" name="LJTS">
 		<coords> <x>0.0</x> <y>0.0</y> <z>0.0</z> </coords>
 		<mass>1</mass>
 		<sigma>1</sigma>