imdclient 0.1.3__py3-none-any.whl → 0.2.0b0__py3-none-any.whl

imdclient/tests/hpc_testing/gromacs/validate_gmx.sh

@@ -0,0 +1,90 @@
+#!/bin/bash
+
+# Default values
+GROMACS_BIN="gmx"
+MDP_FILE="gmx_gpu_test.mdp"
+STRUCT_FILE="struct.gro"
+TOP_FILE="gmx_gpu_test.top"
+MPI=false  # Default: single-node execution
+
+# GROMACS simulation parameters
+IMD_STRUCT_FILE="struct_imd.gro"
+TPR_FILE="gmx_gpu_test.tpr"
+TRAJ_FILE="gmx_gpu_test.trr"
+
+OUTPUT_FILE="gromacs_imd.out"
+
+# Parse arguments
+while [[ $# -gt 0 ]]; do
+    case $1 in
+        --gmx_bin)
+            GROMACS_BIN="$2"
+            shift 2
+            ;;
+        --mdp_file)
+            MDP_FILE="$2"
+            shift 2
+            ;;
+        --struct_file)
+            STRUCT_FILE="$2"
+            shift 2
+            ;;
+        --top_file)
+            TOP_FILE="$2"
+            shift 2
+            ;;
+        --mpi)
+            MPI=true
+            shift 1
+            ;;
+        *)
+            echo "Unknown argument: $1"
+            exit 1
+            ;;
+    esac
+done
+# Step 1: GROMACS Preprocessing (grompp)
+echo "Running GROMACS grompp..."
+$GROMACS_BIN grompp \
+    -f $MDP_FILE \
+    -c $STRUCT_FILE \
+    -p $TOP_FILE \
+    -imd $IMD_STRUCT_FILE \
+    -o $TPR_FILE \
+    -maxwarn 1
+
+# Step 2: GROMACS Simulation
+if [ "$MPI" = true ]; then
+    echo "Running GROMACS multi-node simulation with MPI..."
+
+    mpirun $GROMACS_BIN mdrun \
+        -s $TPR_FILE \
+        -o $TRAJ_FILE \
+        -imdwait &> $OUTPUT_FILE &
+else
+    echo "Running GROMACS single-node simulation..."
+    $GROMACS_BIN mdrun \
+        -s $TPR_FILE \
+        -o $TRAJ_FILE \
+        -imdwait &> $OUTPUT_FILE &
+fi
+
+# Wait for simulation to be ready
+
+await_gmx_imd() {
+    grep -q "IMD: Will wait until I have a connection and IMD_GO orders." "$OUTPUT_FILE"
+}
+
+while ! await_gmx_imd; do
+    echo "Waiting for GROMACS IMD readiness in $OUTPUT_FILE..."
+    sleep 5
+done
+
+# Step 3: Run IMDClient Test
+
+echo "Running IMDClient manual test..."
+python ../../test_manual.py \
+    --topol $IMD_STRUCT_FILE \
+    --traj $TRAJ_FILE \
+    --first_frame 0 
+

imdclient/tests/hpc_testing/lammps/README.md

@@ -0,0 +1,62 @@
+# Manual validation of different compiler options for LAMMPS using ASU's SOL
+
+### Running tests
+
+To validate all IMDv3 output (time, integration step, box, positions, velocities, and forces)
+against H5MD output with a simple sample simulation, first ensure you're using a 
+python environment which has the testing requirements of IMDClient installed.
+
+If not already installed, do:
+```bash
+conda env create -n imdclient-test -f devtools/conda-envs/test_env.yaml -y
+conda activate imdclient-test
+```
+
+Equivalently, on ASU's Sol, do:
+```bash
+module load mamba
+# Only needed for MPI builds
+module load openmpi/4.1.5
+conda env create -n imdclient-test -f devtools/conda-envs/test_env.yaml -y
+source activate imdclient-test
+```
+
+Then, to run the tests, do:
+```bash
+cd imdclient/tests/hpc_testing/lammps
+chmod +x validate_lmp.sh
+
+./validate_lmp.sh \
+    -lmp_bin /path/to/lmp
+```
+
+Or, for MPI builds,
+```bash
+./validate_lmp.sh \
+    --lmp_bin /path/to/lmp \
+    --mpi
+```
+
+To validate against your own simulation files, see `validate_lmp.sh` for 
+command line arguments.
+
+### Compiling on ASU's Sol supercomputer with MPI and GPU support
+
+Allocate a GPU node on SOL and clone in https://github.com/ljwoods2/lammps/tree/imd-v3
+
+After cloning, do:
+
+```bash
+git checkout imd-v3-integration
+module load cmake-3.21.4-gcc-11.2.0
+module load gcc-10.3.0-gcc-11.2.0
+module load cuda-11.7.0-gcc-11.2.0
+module load hdf5-develop-1.13-gcc-11.2.0
+module load openmpi/4.1.5
+
+mkdir -p build_gpu
+cd build_gpu
+
+cmake ../cmake/ -D PKG_MISC=yes -D PKG_GPU=on -D GPU_API=cuda -D PKG_H5MD=yes -D BUILD_MPI=yes -DCMAKE_CXX_FLAGS="-DLAMMPS_ASYNC_IMD"
+make -j 4
+```

imdclient/tests/hpc_testing/lammps/lammps_v3_nst_1.in

@@ -0,0 +1,71 @@
+## Setup
+units metal 
+boundary p p p #Specify periodic boundary condition are needed in all three faces
+atom_style atomic #What style of atoms is to be used in the simulation
+log   logfile.txt #Write the log file to this text file. All thermodynamic information applicable to the entire system
+
+## Create Box
+#Refers to an abstract geometric region of space. units box refers to the fact that the size of the box is specified in the units as given in the units command. 
+# The name "forbox" refers to the region ID so that you can refer to it somewhere else in this input script.
+region forbox block 0 45.8 0 45.8 0 45.8 units box
+create_box 1 forbox 
+# Since we have given fcc as lattice type no need to mention basis for this
+lattice fcc 4.58 
+
+## Create atoms & define interactions
+# basis arg defines which atoms are created based on their lattice position (all are atom type 1)
+create_atoms 1 region forbox  basis 1 1 basis 2 1 basis 3 1 basis 4 1 units box
+# Mass of atom type 1 is 39.48 [mass units grams/mole]
+mass 1 39.948 
+# lj potential describes potential energy between two atoms as function of the dist between them
+# don't apply lj interactions beyond cutoff dist
+pair_style lj/cut 10 
+# The coefficient of the lj potential for the interactions of atom type 1 with atom type 1
+pair_coeff  1 1 0.01006418 3.3952 
+
+## Create atom group for argon atoms
+group ar type 1 #Group all the argon types (argon type is of type 1). All atoms of type 1 are in group with the name 'ar'
+
+
+## Write initial configuration
+dump dump_1 all custom 1 dump_initial_config.dump id type x y z ix iy iz vx vy vz
+
+
+## Perform energy minimization
+run 1
+# Stop dumping to this file
+undump dump_1 
+# Minimize the energy using a conjugate gradient step.
+minimize 1e-25 1e-19 10000 10000 
+print "Finished Minimizing"
+variable ener equal pe
+
+## Output the topology after minimization
+write_data topology_after_min.data
+
+## Prepare MD simulation
+timestep  0.001
+# Set the velocities of all the atoms so that the temperature of the system
+# is 300K. Make the distribution Gaussian.
+velocity all create 300 102939 dist gaussian mom yes rot yes
+# this is equlibration process.
+fix 1 all nve 
+
+# Create source of truth trajectory
+dump h5md1 all h5md 1 lammps_trj.h5md position velocity force box yes
+dump_modify h5md1 unwrap no
+
+## IMD settings
+# https://docs.lammps.org/fix_imd.html
+fix 2 all imd 8888 version 3 unwrap off nowait off
+
+## Run MD sim
+run 100
+
+# Stop dumping information to the dump file.
+undump h5md1 
+
+# Unfix the NVE. Additional lines if any will assume that this fix is off.
+unfix 1
+
+#End