WIP: lammps

CMake/options.cmake

@@ -79,6 +79,7 @@ option(ENABLE_MANDELBROT "Enable Mandelbrot AMR miniapp" ON)
 option(ENABLE_VORTEX "Enable Vortex miniapp (experimental)" OFF)
 option(ENABLE_CONDUITTEST "Enable Conduit miniapp (experimental)" OFF)
 option(ENABLE_KRIPKE "Enable Kripke miniapp (experimental)" OFF)
+option(ENABLE_LAMMPS "Enable LAMMPS driver" OFF)
 option(SENSEI_USE_EXTERNAL_pugixml "Use external pugixml library" OFF)
 
 message(STATUS "ENABLE_SENSEI=${ENABLE_SENSEI}")
@@ -104,6 +105,7 @@ message(STATUS "ENABLE_OPTS=${ENABLE_OPTS}")
 message(STATUS "ENABLE_OSCILLATORS=${ENABLE_OSCILLATORS}")
 message(STATUS "ENABLE_CONDUITTEST=${ENABLE_CONDUITTEST}")
 message(STATUS "ENABLE_KRIPKE=${ENABLE_KRIPKE}")
+message(STATUS "ENABLE_LAMMPS=${ENABLE_LAMMPS}")
 message(STATUS "SENSEI_USE_EXTERNAL_pugixml=${SENSEI_USE_EXTERNAL_pugixml}")
 
 if (ENABLE_ADIOS1 AND ENABLE_ADIOS2)

endpoints/SENSEIEndPoint.cpp

@@ -17,6 +17,7 @@ using AnalysisAdaptorPtr = vtkSmartPointer<sensei::ConfigurableAnalysis>;
 
 int main(int argc, char **argv)
 {
+  sensei::Profiler::Initialize();
   sensei::MPIManager mpiMan(argc, argv);
   int rank = mpiMan.GetCommRank();
 

miniapps/CMakeLists.txt

@@ -33,3 +33,10 @@ else()
   message(STATUS "Disabled: Vortex miniapp.")
 endif()
 
+if(ENABLE_LAMMPS)
+  message(STATUS "Enabled: LAMMPS driver.")
+  add_subdirectory(lammps)
+else()
+  message(STATUS "Disabled: LAMMPS driver.")
+endif()
+

miniapps/lammps/CMakeLists.txt

@@ -0,0 +1,33 @@
+if (NOT LAMMPS_DIR)
+  message(FATAL_ERROR "To build LAMMPS driver you must set -DLAMMPS_DIR=<root of lammps dir>")
+else()
+  message(STATUS "LAMMPS_DIR: ${LAMMPS_DIR}")
+endif()
+
+include_directories(${LAMMPS_DIR}/src)
+
+set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -DLAMMPS_LIB_MPI")
+
+set(sources lammpsDriver.cxx)
+
+set(libs 
+    ${LAMMPS_DIR}/src/liblammps_mpi.a
+)
+
+if(ENABLE_SENSEI)
+  list(APPEND sources
+    lammpsDataAdaptor.h
+    lammpsDataAdaptor.cxx
+    lammpsBridge.h
+    lammpsBridge.cxx
+  )
+  list(APPEND libs sensei)
+endif()
+
+add_executable(lammpsDriver ${sources})
+
+target_link_libraries(lammpsDriver ${libs})
+
+install(TARGETS lammpsDriver
+  RUNTIME DESTINATION bin
+)

miniapps/lammps/configs/adiostransport.xml

@@ -0,0 +1,17 @@
+<sensei>
+  <transport type="adios2" filename="test_%05d.bp" debug_mode="1" engine="bp4">
+    <engine_parameters>
+        NumAggregators = 0
+        InitialBufferSize = 1Mb
+        BufferGrowthFactor = 2
+        MaxBufferSize = 1024Mb
+        StatsLevel = 0
+        Profile = Off
+      </engine_parameters>
+
+      <!-- subset by mesh and array -->
+      <mesh name="atoms">
+        <point_arrays> type,id </point_arrays>
+      </mesh>
+    </transport>
+</sensei>

miniapps/lammps/configs/adioswrite.xml

@@ -0,0 +1,23 @@
+<sensei>
+
+  <!-- configure ADIOS2 write -->
+  <analysis type="adios2" filename="test_%05d.bp" engine="BP4"
+    debug_mode="1" enabled="1" steps_per_file="1" >
+
+    <!-- ADIOS2 engine parameters -->
+    <engine_parameters>
+      NumAggregators = 0
+      InitialBufferSize = 1Mb
+      BufferGrowthFactor = 2
+      MaxBufferSize = 1024Mb
+      StatsLevel = 0
+      Profile = Off
+    </engine_parameters>
+
+    <!-- subset by mesh and array -->
+    <mesh name="atoms">
+      <point_arrays>type,id </point_arrays>
+    </mesh>
+
+  </analysis>
+</sensei>

miniapps/lammps/configs/adioswriteosc.xml

@@ -0,0 +1,23 @@
+<sensei>
+
+  <!-- configure ADIOS2 write -->
+  <analysis type="adios2" filename="test_%05d.bp" engine="BP4"
+    debug_mode="1" enabled="1" steps_per_file="1" >
+
+    <!-- ADIOS2 engine parameters -->
+    <engine_parameters>
+      NumAggregators = 0
+      InitialBufferSize = 1Mb
+      BufferGrowthFactor = 2
+      MaxBufferSize = 1024Mb
+      StatsLevel = 0
+      Profile = Off
+    </engine_parameters>
+
+    <!-- subset by mesh and array -->
+    <mesh name="mesh">
+      <cell_arrays>data</cell_arrays>
+    </mesh>
+
+  </analysis>
+</sensei>

miniapps/lammps/configs/cmakeconfig_adios.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+export CC=`which gcc`
+export CXX=`which g++`
+
+
+cmake -S ./src/ADIOS2 -B ./build/adios \
+ -DCMAKE_INSTALL_PREFIX=`pwd`/install/adios \
+ -DADIOS2_USE_Fortran=OFF \
+ -DADIOS2_BUILD_EXAMPLES=OFF \
+ -DCMAKE_BUILD_TYPE=Debug

miniapps/lammps/configs/cmakeconfig_sensei.sh

@@ -0,0 +1,17 @@
+
+export CC=`which gcc`
+export CXX=`which g++`
+export LAMMPS_DIR=`pwd`/src/lammps/
+
+
+
+cmake -S ./src/SENSEI -B ./build/sensei \
+  -DCMAKE_INSTALL_PREFIX=`pwd`/install/sensei \
+  -DVTK_DIR=`pwd`/install/vtk/lib64/cmake/vtk-8.2 \
+  -DENABLE_VTK_IO=ON \
+  -DLAMMPS_DIR=$LAMMPS_DIR \
+  -DENABLE_LAMMPS=ON \
+  -DENABLE_MANDELBROT=OFF \
+  -DENABLE_OSCILLATORS=OFF \
+  -DENABLE_ADIOS2=ON \
+  -DADIOS2_DIR=`pwd`/install/adios/lib64/cmake/adios2

miniapps/lammps/configs/cmakeconfig_vtk8.sh

@@ -0,0 +1,17 @@
+
+export CC=`which gcc`
+export CXX=`which g++`
+
+cmake -S src/vtk -B build/vtk \
+ -DVTK_Group_Imaging=OFF \
+ -DVTK_Group_MPI=OFF \
+ -DVTK_Group_Qt=OFF \
+ -DVTK_Group_Rendering=OFF \
+ -DVTK_Group_StandAlone=ON \
+ -DVTK_Group_Tk=OFF \
+ -DVTK_Group_Views=OFF \
+ -DVTK_Group_Web=OFF \
+ -DVTK_RENDERING_BACKEND=None \
+ -DCMAKE_BUILD_TYPE=Debug \
+ -DBUILD_TESTING=OFF \
+ -DCMAKE_INSTALL_PREFIX=`pwd`/install/vtk

miniapps/lammps/configs/config.xml

@@ -0,0 +1,34 @@
+<sensei>
+  <analysis type="PosthocIO"
+    output_dir="./vtkfiles" file_name="output" mode="paraview"
+    enabled="0">
+    <mesh name="atoms" structure_only="0" ghost_cells="1" ghost_nodes="0">
+      <point_arrays>type,id</point_arrays>
+    </mesh>
+  </analysis>
+
+   <!-- configure ADIOS2 write -->
+   <analysis type="adios2" filename="test_%05d.bp”
+      engine="BP4" enabled="1”
+      steps_per_file="1" >
+
+      <!-- ADIOS2 engine parameters -->
+      <engine_parameters>
+          NumAggregators = 0
+          InitialBufferSize = 1Mb
+          BufferGrowthFactor = 2
+          MaxBufferSize = 1024Mb
+          StatsLevel = 0
+          Profile = Off
+      </engine_parameters>
+
+      <!-- subset by mesh and array -->
+      <mesh name="atoms">
+         <point_arrays>type,id </point_arrays>
+      </mesh>
+
+  </analysis>
+
+
+
+</sensei>

miniapps/lammps/configs/endpoint.sh

@@ -0,0 +1,6 @@
+
+export LD_LIBRARY_PATH=/lus/grand/projects/visualization/srizzi/BUILDS/sensei-lammps/install/vtk/lib64:/lus/grand/projects/visualization/srizzi/BUILDS/sensei-lammps/install/adios/lib64:$LD_LIBRARY_PATH
+
+#mpiexec -n 4 ./lammpsDriver in.rhodo -n 5 -sensei config.xml
+#mpiexec -n 4 ./lammpsDriver in.rhodo -n 5 -sensei adioswrite.xml
+./SENSEIEndPoint -a vtkosc.xml -t adiostransport.xml

miniapps/lammps/configs/in.rhodo

@@ -0,0 +1,28 @@
+# Rhodopsin model
+
+units           real  
+neigh_modify    delay 5 every 1   
+
+atom_style      full  
+bond_style      harmonic 
+angle_style     charmm 
+dihedral_style  charmm 
+improper_style  harmonic 
+pair_style      lj/charmm/coul/long 8.0 10.0 
+pair_modify     mix arithmetic 
+kspace_style    pppm 1e-4 
+
+read_data       data.rhodo
+
+fix             1 all shake 0.0001 5 0 m 1.0 a 232
+fix             2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+fix		3 all external pf/callback 1 10000
+
+special_bonds   charmm
+
+thermo          50
+thermo_style    multi 
+timestep        2.0
+
+#run		100
+

miniapps/lammps/configs/run.sh

@@ -0,0 +1,7 @@
+
+export LD_LIBRARY_PATH=/lus/grand/projects/visualization/srizzi/BUILDS/sensei-lammps/install/vtk/lib64:/lus/grand/projects/visualization/srizzi/BUILDS/sensei-lammps/install/adios/lib64:$LD_LIBRARY_PATH
+
+#mpiexec -n 4 ./lammpsDriver in.rhodo -n 5 -sensei config.xml
+#mpiexec -n 4 ./lammpsDriver in.rhodo -n 5 -sensei adioswrite.xml
+#./lammpsDriver in.rhodo -n 5 -sensei adioswrite.xml
+./oscillator --t-end 0.05 -f adioswriteosc.xml sample.osc

miniapps/lammps/configs/sample.osc

@@ -0,0 +1,6 @@
+# type      center      r       omega0      zeta
+damped      32 32 32    10.     3.14        .3
+damped      16 32 16    10.     9.5         .1
+damped      48 32 48    5.      3.14        .1
+decaying    16 32 48    15      3.14
+periodic    48 32 16    15      3.14

miniapps/lammps/configs/vtk.xml

@@ -0,0 +1,9 @@
+<sensei>
+  <analysis type="PosthocIO"
+    output_dir="./vtkfiles" file_name="output" mode="paraview"
+    enabled="1">
+    <mesh name="atoms" structure_only="0" ghost_cells="1" ghost_nodes="0">
+      <point_arrays>type,id</point_arrays>
+    </mesh>
+  </analysis>
+</sensei>

miniapps/lammps/configs/vtkosc.xml

@@ -0,0 +1,9 @@
+<sensei>
+  <analysis type="PosthocIO"
+    output_dir="./vtkfiles" file_name="output" mode="paraview"
+    enabled="1">
+    <mesh name="mesh" structure_only="0" ghost_cells="1" ghost_nodes="0">
+      <cell_arrays>data</cell_arrays>
+    </mesh>
+  </analysis>
+</sensei>

miniapps/lammps/lammpsBridge.cxx

@@ -0,0 +1,49 @@
+#include "lammpsBridge.h"
+#include "lammpsDataAdaptor.h"
+#include <vtkSmartPointer.h>
+#include <ConfigurableAnalysis.h>
+#include <vtkDataObject.h>
+
+namespace lammpsBridge
+{
+  static vtkSmartPointer<senseiLammps::lammpsDataAdaptor>  DataAdaptor;
+  static vtkSmartPointer<sensei::ConfigurableAnalysis>     AnalysisAdaptor;
+
+void Initialize(MPI_Comm world, const std::string& config_file)
+{ 
+  DataAdaptor = vtkSmartPointer<senseiLammps::lammpsDataAdaptor>::New();
+  DataAdaptor->Initialize();
+  DataAdaptor->SetCommunicator(world);
+  DataAdaptor->SetDataTimeStep(-1);
+
+  AnalysisAdaptor = vtkSmartPointer<sensei::ConfigurableAnalysis>::New();
+  AnalysisAdaptor->Initialize(config_file);
+}
+
+void SetData(long ntimestep, int nlocal, int *id, 
+             int nghost, int *type, double **x, 
+             double xsublo, double xsubhi, 
+             double ysublo, double ysubhi, 
+             double zsublo, double zsubhi )
+{
+  DataAdaptor->AddLAMMPSData( ntimestep, nlocal, id, nghost, type, x, \
+                              xsublo, xsubhi, ysublo, ysubhi, zsublo, zsubhi);
+  DataAdaptor->SetDataTimeStep(ntimestep);
+  DataAdaptor->SetDataTime(ntimestep);
+}
+
+void Analyze()
+{
+  AnalysisAdaptor->Execute(DataAdaptor.GetPointer());
+  DataAdaptor->ReleaseData();
+}
+
+//-----------------------------------------------------------------------------
+void Finalize()
+{
+  AnalysisAdaptor->Finalize();
+  AnalysisAdaptor = nullptr;
+  DataAdaptor = nullptr;
+}
+
+} // namespace lammpsBridge

miniapps/lammps/lammpsBridge.h

@@ -0,0 +1,15 @@
+#pragma once
+#include <mpi.h>
+#include <string>
+
+namespace lammpsBridge
+{
+  void Initialize(MPI_Comm world, const std::string& config_file);
+  void SetData(long ntimestep, int nlocal, int *id, 
+               int    nghost, int *type, double **x, 
+               double xsublo, double xsubhi, 
+               double ysublo, double ysubhi, 
+               double zsublo, double zsubhi );
+  void Analyze();
+  void Finalize();
+}