Pimd (#61)

* An example for path integral simulations of water
An example of running PIMD simulations using i-PI, LAMMPS and visualizing them in chemiscope, including some fancy tricks

examples/path-integrals/README.rst

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+Running, analizing and visualizing a path integral MD simulation
+================================================================
+
+This example shows how to run a path integral molecular dynamics 
+simulation using ``i-PI``, analyze the output and visualize the 
+trajectory in ``chemiscope``. It uses `LAMMPS <http://lammps.org>`_
+as the driver to simulate the q-TIP4P/f water model. 

examples/path-integrals/environment.yml

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+channels:
+  - conda-forge
+dependencies:
+  - python=3.11
+  - pip
+  - lammps  
+  - pip:
+    - ase
+    - ipi  
+    - chemiscope
+    - matplotlib
+    - skmatter

examples/path-integrals/in.lmp

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+units		electron
+atom_style	full
+
+#pair_style	lj/cut/coul/long 17.01
+pair_style      lj/cut/tip4p/long 1 2 1 1 0.278072379 17.007
+#bond_style      harmonic
+bond_style      class2 
+angle_style     harmonic
+#kspace_style	pppm 0.0001
+kspace_style	pppm/tip4p 0.0001
+
+read_data	water_32_data.lmp
+pair_coeff  * * 0 0
+pair_coeff  1  1  0.000295147 5.96946
+
+neighbor	2.0 bin
+
+timestep	0.00025
+
+#velocity all create 298.0 2345187
+
+#thermo_style	multi
+#thermo		1
+
+#fix		1 all nvt temp 298.0 298.0 30.0 tchain 1
+#fix 1 all nve
+fix 1 all ipi h2o-lammps 32342 unix
+
+
+#dump		1 all xyz 25 dump.xyz
+
+run		100000000
+

examples/path-integrals/input_pimd.xml

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+<simulation verbosity='medium' safe_stride='100'>
+  <output prefix='simulation'>
+    <properties stride='1' filename='out'>  [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_cv{electronvolt}, potential{electronvolt}, pressure_cv{megapascal}, kinetic_td{electronvolt} ] </properties>
+    <trajectory filename='pos' stride='20'> positions </trajectory>
+    <trajectory filename='kin' stride='20'> kinetic_cv </trajectory>
+    <trajectory filename='kod' stride='20'> kinetic_od </trajectory>
+  </output>
+  <total_steps> 200 </total_steps>
+  <prng>
+    <seed> 32342 </seed>
+  </prng>
+  <ffsocket name='lmpserial' mode='unix'>
+      <address>h2o-lammps</address> <latency> 1e-4 </latency>
+  </ffsocket>
+  <system>
+    <initialize nbeads='8'>
+      <file mode='pdb'> water_32.pdb </file>
+      <velocities mode='thermal' units='kelvin'> 298 </velocities>
+    </initialize>
+    <forces>
+      <force forcefield='lmpserial'> lmpserial </force>
+    </forces>
+    <ensemble>
+      <temperature units='kelvin'>298</temperature>
+    </ensemble>
+    <motion mode='dynamics'>
+      <dynamics mode='nvt'>
+        <thermostat mode='pile_g'>
+          <tau units="femtosecond"> 5.0 </tau>     
+        </thermostat>
+        <timestep units='femtosecond'> 0.5 </timestep>
+      </dynamics>
+    </motion>
+  </system>
+</simulation>