i-PI version 2.0.0

As archived with the publication: https://doi.org/10.1016/j.cpc.2018.09.020

.gitignore

@@ -1,11 +1,15 @@
 #ignored patterns
 
-bin/*
+bin/i-pi-driver
+doc/manual.pdf
+doc/manual.xml
 *.pyc
 *.pyo
 *.x
 *.mod
 *.out
 *.o
-*.pdf
 *~
+\#*
+*.orig
+regtest-ref

README.rst

@@ -1,42 +1,81 @@
-i-PI V1.0
---------
+====
+i-PI: a Universal Force Engine
+====
 
-A Python interface for ab initio path integral molecular dynamics simulations. 
-i-PI is composed of a Python server (i-pi itself, that does not need to be 
+A Python interface for ab initio path integral molecular dynamics simulations.
+i-PI is composed of a Python server (i-pi itself, that does not need to be
 compiled but only requires a relatively recent version of Python and Numpy)
 that propagates the (path integral) dynamics of the nuclei, and of an external
-code that acts as client and computes the electronic energy and forces.
+code that acts as a client and computes the electronic energy and forces.
 
-This is typically a patched version of an electronic structure code, but a 
-simple self-contained Fortran driver that implements Lennard-Jones and 
-Silveira-Goldman potentials is included for test purposes.
+This is typically a patched version of an electronic structure code, but a
+simple self-contained Fortran driver that implements Lennard-Jones and
+Silvera-Goldman potentials is included for test purposes.
 
 
-Quick Installation and Test 
----------------------------
+Quick Setup and Test
+====================
 
-Follow these instruction to test i-PI. These assume to be run from a Linux 
-environment, with a recent version of Python, Numpy and gfortran, and that 
-the terminal is initially in the i-pi package directory (the directory 
-containing this file).
+Follow these instructions to set up and test i-PI. It is assumed that i-PI will
+be run from a Linux environment, with a recent version of Python, Numpy and
+gfortran, and that the terminal is initially in the i-pi package directory (the
+directory containing this file).
 
-* Generate the driver code
+Source the environment settings file :code:`env.sh` as :code:`$ source env.sh` or :code:`$ .
+env.sh`.  It is useful to put this in your :code:`.bashrc` or other settings file if
+you always want to have i-PI available.
 
-$ cd driver
-$ make
-$ cd ..
 
-* Run one of the examples
+Compile the driver code
+-----------------------
 
-This will first start the wrapper in the background, redirecting the output on 
-a log file, then run a couple of instances of the driver code and then follow
-the progress of the wrapper by monitoring the log file
+::
 
-$ cd examples/tutorial/tutorial-1/
-$ ../../../i-pi tutorial-1.xml > log &
-$ ../../../drivers/driver.x -h localhost -p 31415 -m sg -o 15 &
-$ ../../../drivers/driver.x -h localhost -p 31415 -m sg -o 15 &
-$ tail -f log
+  $ cd drivers
+  $ make
+  $ cd ..
 
-The monitoring can be interrupted with CTRL+C when the run has finished (5000 steps)
 
+Run one of the examples
+-----------------------
+
+This will first start the wrapper in the background, redirecting the output to
+a log file, and then run a couple of instances of the driver code. The progress
+of the wrapper is followed by monitoring the log file with the `tail` Linux
+command.
+
+Optionally, you can make a copy of the directory with the example somewhere
+else if you want to keep the i-PI directory clean.
+
+::
+
+  $ cd examples/tutorial/tutorial-1/
+  $ i-pi tutorial-1.xml > log &
+  $ i-pi-driver -h localhost -p 31415 -m sg -o 15 &
+  $ i-pi-driver -h localhost -p 31415 -m sg -o 15 &
+  $ tail -f log
+
+The monitoring can be interrupted with CTRL+C when the run has finished (5000 steps).
+
+
+Run the automatic test suite
+----------------------------
+
+The automatic test suite can be run with the Python package `pytest` from the
+root directory of the i-PI project.
+
+::
+
+  $ pytest -v
+
+
+PEP-8 Compliance
+================
+
+i-PI code should be compliant to a minimal subset of PEP-8 recommendations.
+Before proceeding to a pull request, or to the merging of a large commit, you
+can use the following script to automatically prettify the code
+
+```
+i-pi-pepper -p $IPI_ROOT 
+```

bin/i-pi

@@ -0,0 +1,105 @@
+#!/usr/bin/env python2
+
+"""Main script from which the simulation is run.
+
+Deals with creation of the simulation object, reading the input file and
+initialising the system.
+
+Run using:
+      i-pi input_file.xml
+
+Where 'input_file.xml' should be replaced by the name of the xml input file
+from which the system data will be read. For a description of how the input
+file should be formatted, see the reference manual.
+"""
+
+# This file is part of i-PI.
+# i-PI Copyright (C) 2014-2015 i-PI developers
+# See the "licenses" directory for full license information.
+
+
+import sys
+import os
+
+# Check that we have the import path for this i-PI set and if not, add it.
+dir_root = os.path.realpath(
+    os.path.join(os.path.dirname(os.path.realpath(__file__)), '..'))
+if not dir_root in sys.path:
+    sys.path.insert(0, dir_root)
+
+from ipi.utils.softexit import softexit
+from ipi.engine.simulation import Simulation
+
+
+def main(fn_input, options):
+    """Loads and runs the simulation stored in `fn_input`."""
+
+    # optionally profile this run - set up
+    # ~ if do_yappi:
+    # ~ try:
+    # ~ import yappi
+    #~ yappi.start(builtins=True, profile_threads=True)
+    # ~ except ImportError:
+    # ~ print 'Profiling with yappi was enabled but could not be imported.'
+    # ~ print "Profiling with yappi was enabled but could not be imported."
+    #~ sys.exit(1)
+
+    # construct simulation based on input file
+    simulation = Simulation.load_from_xml(fn_input, request_banner=True, custom_verbosity=options.verbosity)
+
+    # run the simulation
+    simulation.run()
+
+    # optionally profile this run - wrap up
+    # TODO
+    # We do not get to this if the run is ctrl interrupted and exits cleanly.
+    # Maybe the profiler should be global and cleaned up on exit?
+    if options.do_yappi:
+        yappi.stop()
+        yappi.get_thread_stats().print_all()
+        yfs = yappi.get_func_stats()
+        yfs.save("profile.kgrind", type="callgrind")
+        ypo = open("profile.yappi", "w")
+        yfs.print_all(out=ypo)
+        ypo.close()
+
+    # It seems that checkpoints are written by the following.
+    # TODO: Have them written when simulation.run() finishes instead.
+    # It should be sufficient to run `self.softexit() at the end of
+    # `Simulation.run()`. Anything else missing?
+    softexit.trigger(" @ SIMULATION: Exiting cleanly.")
+
+
+if __name__ == '__main__':
+
+    # TODO: Use argparse once we move to Python 2.7.
+
+    from optparse import OptionParser
+
+    parser = OptionParser(usage='%prog [options] <input file>',
+                          description='The main i-PI executable used to run '
+                                      'a simulation, given an XML input file.'
+                          )
+
+    parser.add_option('-p', '--profile',
+                      action='store_true', dest='do_yappi', default=False,
+                      help='Profile this run using Yappi.')
+
+    parser.add_option('-V', '--verbosity', dest='verbosity', default=None,
+                      choices=['quiet', 'low', 'medium', 'high', 'debug'],
+                      help='Define the verbosity level.')
+
+    options, args = parser.parse_args()
+
+    # make sure that we have exactly one input file and it exists
+    if len(args) == 0:
+        parser.error('No input file name provided.')
+    elif len(args) > 1:
+        parser.error('Provide only one input file name.')
+    else:
+        fn_in = args[0]
+        if not os.path.exists(fn_in):
+            parser.error('Input file not found: {:s}'.format(fn_in))
+
+    # Everything is ready. Go!
+    main(args[0], options)

bin/i-pi-contract-trajectory

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+../tools/py/contract-trajectory.py

bin/i-pi-getacf

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+../tools/py/getacf.py

bin/i-pi-getproperty

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+../tools/py/getproperty.py

bin/i-pi-gleacf

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+../tools/py/gleacf.py

bin/i-pi-kinetic2tag

@@ -0,0 +1 @@
+../tools/py/kinetic2tag.py

bin/i-pi-mergebeadspdb

@@ -0,0 +1 @@
+../tools/py/mergebeadspdb.py

bin/i-pi-mux-positions

@@ -0,0 +1 @@
+../tools/py/mux-positions.py

bin/i-pi-paraweights

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+../tools/py/paraweights.py

bin/i-pi-pepper

@@ -0,0 +1 @@
+../tools/py/pepper.py

bin/i-pi-posforce2kinetic

@@ -0,0 +1 @@
+../tools/py/posforce2kinetic.py

bin/i-pi-regtest

@@ -0,0 +1 @@
+../tools/py/regtest.py

bin/i-pi-remdsort

@@ -0,0 +1 @@
+../tools/py/remdsort.py

bin/i-pi-trimsim

@@ -0,0 +1 @@
+../tools/py/trimsim.py