adds MD example

Atomistic_experiments/BPNN_model/install_dependencies.sh

@@ -73,10 +73,33 @@ pip install $PIP_FLAGS "rascaline-torch @ git+https://github.com/luthaf/rascalin
 
 pip install -r requirements.txt
 
-echo "All dependencies have been installed. - running a minimal test of the install"
+#echo "All dependencies have been installed. - running a minimal test of the install"
 
-cd ./test_install
+#cd ./test_install
 
-python training.py
+#python training.py
 #no ensure that this does not exit with fail
-python -u compare.py
+#python -u compare.py
+
+# clones the my ipi
+git clone [email protected]:bananenpampe/i-pi.git
+
+# change into the directory change the absolute path LIGHNING_CALCULATOR_PATH
+# in ./i-pi/drivers/py/pes/lightning.py to the absolute location of '/H2O/driver/'
+
+cd ./H2O/driver/
+
+LIGHNING_CALCULATOR_PATH=$(pwd)
+
+cd ../../
+
+cd ./i-pi/drivers/py/pes
+
+# change the absolute path in the lightning.py file
+sed -i '' "s|/Users/matthiaskellner/Documents/PhD/H2O/driver/|${LIGHNING_CALCULATOR_PATH}|g" lightning.py
+
+cd ../../../
+
+pip install -e .
+
+cd ..

Atomistic_experiments/MD/H2O/300K_64/run.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+
+which python
+rm -f /tmp/ipi_alchem_H2O_5
+
+i-pi simulation.xml &
+
+sleep 10s
+
+echo "Current time: $(date +"%H:%M:%S")"
+
+i-pi-py_driver -m lightning -a alchem_H2O_5 -u -o ../../../eval/H2O/shallow_ens/example.ckpt,start_64.xyz
+
+

Atomistic_experiments/MD/H2O/300K_64/simulation.xml

@@ -0,0 +1,47 @@
+<simulation verbosity= "low">
+<output prefix="BPNN-H2O-md">
+<properties stride="100" filename="out">  [ step, time{picosecond},  conserved{electronvolt},
+        temperature{kelvin}, kinetic_md{electronvolt}, potential{electronvolt}, pressure_md{bar}, volume{angstrom3},
+        ensemble_temperature{kelvin}, cell_abcABC] </properties>
+        <trajectory filename="xc" stride="100" cell_units="angstrom"> x_centroid{angstrom} </trajectory>
+        <trajectory filename='committee_pot' stride='100' extra_type='committee_pot'> extras </trajectory>
+        <checkpoint stride="1000"/>
+        </output>
+        <total_steps> 2000000 </total_steps>
+        <prng><seed>64</seed></prng>
+        <ffsocket mode='unix' name='driver'  matching='any'>
+                <latency>  1.00000000e-02</latency>
+                <slots>4</slots>
+                <port>12345</port>
+                <timeout>60.000000e+00</timeout>
+                <address>alchem_H2O_5</address>
+        </ffsocket>
+        <system>
+                <initialize nbeads="1">
+                        <file mode="ase" units="angstrom" cell_units="angstrom"> start_64.xyz </file>
+                        <velocities mode="thermal" units="kelvin">300 </velocities>
+                </initialize>
+                <forces>
+                        <force forcefield='driver'/>
+                 </forces>
+                <motion mode="dynamics">
+                        <dynamics mode="nvt">
+                                <timestep units="femtosecond"> 0.5 </timestep>
+                                <thermostat mode='gle'>
+                                        <A shape='(5,5)'>
+                                                                [
+                                4.498098855452e-3,    6.594810718477e-6,    2.788030342989e-4,   -8.808265165053e-4,    5.605371493938e-3,
+                                -6.726802271646e-6,    2.079069559861e-9,    1.746169548818e-5,   -4.800164465960e-6,    1.025830873432e-5,
+                                -3.586191452340e-4,   -1.746169548818e-5,    3.287481976399e-5,    1.245698716799e-4,   -2.417657162526e-4,
+                                -2.508912543565e-4,    4.800164465960e-6,   -1.245698716799e-4,    6.449207766266e-4,    2.783583234046e-4,
+                                5.273493443008e-3,   -1.025830873432e-5,    2.417657162526e-4,   -2.783583234046e-4,    7.488477456790e-3
+                                                                ]
+                                </A>
+                                </thermostat>
+                        </dynamics>
+                </motion>
+                <ensemble>
+                        <temperature units="kelvin"> 300 </temperature>
+                </ensemble>
+         </system>
+</simulation>