magrate admp; update .gitignore; replace abnormal water1024.pdb

dmff/admp/README.md

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+# ADMP
+
+Automatic Differentiable Multipolar Polarizable (ADMP) force field calculator. 
+
+This module provides an auto-differentiable implementation of multipolar polarizable force fields, that resembles the behavior of [MPID](https://github.com/andysim/MPIDOpenMMPlugin) plugin of OpenMM. Supposedly, this module is developed for the following purposes:
+
+1. Achieving an easy calculation of force and virial of the multipolar polarizable forcefield. 
+2. Allowing fluctuating (geometric-dependent) multipoles/polarizabilities in multipolar polarizable potentials.
+3. Allowing the calculation of derivatives of various force field parameters, thus achieving a more systematic and automatic parameter optimization scheme.
+
+The module is based on [JAX](https://github.com/google/jax) and [JAX-MD](https://github.com/google/jax-md) projects. 
+
+
+
+## Installation
+
+### Dependencies
+
+ADMP module depends on the following packages, install them before using ADMP:
+
+1. Install [jax](https://github.com/google/jax) (pick the correct cuda version, see more details on their installation guide):
+
+   ```bash
+   pip install jax[cuda11_cudnn82] -f https://storage.googleapis.com/jax-releases/jax_releases.html
+   ```
+
+2. Install [jax-md](https://github.com/google/jax-md) :
+
+   ```bash
+   pip install jax-md --upgrade
+   ```
+
+   ADMP currently relies on the space and partition modules to provide neighbor list
+
+3. Install ADMP:
+
+   ADMP is a pure python module, just simply put it in your $PYTHONPATH.
+
+   ```bash
+   export PYTHONPATH=$PYTHONPATH:/path/to/admp	
+   ```
+
+
+
+## Settings
+
+In `admp/settings.py`, you can modify some global settings, including:
+
+**PRECISION**: single or double precision
+
+**DO_JIT**: whether do jit or not.
+
+
+
+## Example
+
+We provide a MPID 1024 water box example. In water_1024 and water_pol_1024, we show both the nonpolarizable and the polarizable cases.
+
+```bash
+cd ./examples/water_1024
+./run_admp.py
+
+cd ./examples/water_pol_1024
+./run_admp.py
+```
+
+if `DO_JIT = True`, then the first run would be a bit slow, since it tries to do the jit compilation. Further executions of `get_forces` or `get_energy` should be much faster.
+