Update Howto_pylammps.rst and remove Howto_pylammps.txt
This commit is contained in:
Richard Berger
@ -57,7 +57,7 @@ output support enabled.
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Step 1a: For the CMake based build system, the steps are:
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.. parsed-literal::
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.. code-block:: bash
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mkdir $LAMMPS_DIR/build-shared
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cd $LAMMPS_DIR/build-shared
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@ -69,7 +69,7 @@ Step 1a: For the CMake based build system, the steps are:
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Step 1b: For the legacy, make based build system, the steps are:
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.. parsed-literal::
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.. code-block:: bash
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cd $LAMMPS_DIR/src
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@ -86,7 +86,7 @@ PyLammps is part of the lammps Python package. To install it simply install
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that package into your current Python installation with:
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.. parsed-literal::
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.. code-block:: bash
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make install-python
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@ -111,7 +111,7 @@ Benefits of using a virtualenv
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**Prerequisite (e.g. on Ubuntu)**
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.. parsed-literal::
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.. code-block:: bash
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apt-get install python-virtualenv
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@ -119,7 +119,7 @@ Creating a virtualenv with lammps installed
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"""""""""""""""""""""""""""""""""""""""""""
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.. parsed-literal::
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.. code-block:: bash
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# create virtualenv named 'testing'
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virtualenv $HOME/python/testing
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@ -133,7 +133,7 @@ need to re-run CMake to update the location of the python executable
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to the location in the virtual environment with:
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.. parsed-literal::
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.. code-block:: bash
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cmake . -DPYTHON_EXECUTABLE=$(which python)
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@ -155,7 +155,7 @@ To create a PyLammps object you need to first import the class from the lammps
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module. By using the default constructor, a new *lammps* instance is created.
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.. parsed-literal::
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.. code-block:: Python
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from lammps import PyLammps
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L = PyLammps()
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@ -163,7 +163,7 @@ module. By using the default constructor, a new *lammps* instance is created.
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You can also initialize PyLammps on top of this existing *lammps* object:
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.. parsed-literal::
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.. code-block:: Python
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from lammps import lammps, PyLammps
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lmp = lammps()
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@ -178,7 +178,7 @@ the command method of the lammps object instance.
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For instance, let's take the following LAMMPS command:
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.. parsed-literal::
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.. code-block:: LAMMPS
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region box block 0 10 0 5 -0.5 0.5
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@ -186,7 +186,7 @@ In the original interface this command can be executed with the following
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Python code if *L* was a lammps instance:
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.. parsed-literal::
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.. code-block:: Python
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L.command("region box block 0 10 0 5 -0.5 0.5")
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@ -194,7 +194,7 @@ With the PyLammps interface, any command can be split up into arbitrary parts
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separated by white-space, passed as individual arguments to a region method.
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.. parsed-literal::
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.. code-block:: Python
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L.region("box block", 0, 10, 0, 5, -0.5, 0.5)
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@ -207,7 +207,7 @@ parameterization. In the original interface parameterization needed to be done
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manually by creating formatted strings.
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.. parsed-literal::
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.. code-block:: Python
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L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
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@ -215,7 +215,7 @@ In contrast, methods of PyLammps accept parameters directly and will convert
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them automatically to a final command string.
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.. parsed-literal::
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.. code-block:: Python
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L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
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@ -270,7 +270,7 @@ LAMMPS variables can be both defined and accessed via the PyLammps interface.
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To define a variable you can use the :doc:`variable <variable>` command:
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.. parsed-literal::
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.. code-block:: Python
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L.variable("a index 2")
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@ -280,7 +280,7 @@ you can access an individual variable by retrieving a variable object from the
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L.variables dictionary by name
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.. parsed-literal::
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.. code-block:: Python
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a = L.variables['a']
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@ -288,7 +288,7 @@ The variable value can then be easily read and written by accessing the value
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property of this object.
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.. parsed-literal::
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.. code-block:: Python
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print(a.value)
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a.value = 4
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@ -301,7 +301,7 @@ passed string parameter can be any expression containing global thermo values,
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variables, compute or fix data.
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.. parsed-literal::
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.. code-block:: Python
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result = L.eval("ke") # kinetic energy
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result = L.eval("pe") # potential energy
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@ -316,7 +316,7 @@ Each element of this list is an object which exposes its properties (id, type,
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position, velocity, force, etc.).
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.. parsed-literal::
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.. code-block:: Python
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# access first atom
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L.atoms[0].id
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@ -330,7 +330,7 @@ position, velocity, force, etc.).
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Some properties can also be used to set:
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.. parsed-literal::
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.. code-block:: Python
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# set position in 2D simulation
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L.atoms[0].position = (1.0, 0.0)
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@ -348,7 +348,7 @@ The first element is the output of the first run, the second element that of
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the second run.
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.. parsed-literal::
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.. code-block:: Python
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L.run(1000)
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L.runs[0] # data of first 1000 time steps
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@ -360,7 +360,7 @@ Each run contains a dictionary of all trajectories. Each trajectory is
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accessible through its thermo name:
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.. parsed-literal::
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.. code-block:: Python
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L.runs[0].step # list of time steps in first run
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L.runs[0].ke # list of kinetic energy values in first run
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@ -370,7 +370,7 @@ Together with matplotlib plotting data out of LAMMPS becomes simple:
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import matplotlib.plot as plt
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.. parsed-literal::
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.. code-block:: Python
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steps = L.runs[0].step
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ke = L.runs[0].ke
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@ -408,7 +408,7 @@ To launch an instance of Jupyter simply run the following command inside your
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Python environment (this assumes you followed the Quick Start instructions):
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.. parsed-literal::
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.. code-block:: bash
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jupyter notebook
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@ -431,7 +431,7 @@ them using a datafile. Then one of the atoms is rotated along the central axis b
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setting its position from Python, which changes the dihedral angle.
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.. parsed-literal::
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.. code-block:: Python
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phi = [d \* math.pi / 180 for d in range(360)]
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@ -465,7 +465,7 @@ Initially, a 2D system is created in a state with minimal energy.
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It is then disordered by moving each atom by a random delta.
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.. parsed-literal::
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.. code-block:: Python
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random.seed(27848)
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deltaperturb = 0.2
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@ -485,7 +485,7 @@ Finally, the Monte Carlo algorithm is implemented in Python. It continuously
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moves random atoms by a random delta and only accepts certain moves.
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.. parsed-literal::
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.. code-block:: Python
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estart = L.eval("pe")
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elast = estart
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@ -538,7 +538,7 @@ Using PyLammps and mpi4py (Experimental)
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PyLammps can be run in parallel using mpi4py. This python package can be installed using
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.. parsed-literal::
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.. code-block:: bash
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pip install mpi4py
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@ -546,7 +546,7 @@ The following is a short example which reads in an existing LAMMPS input file an
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executes it in parallel. You can find in.melt in the examples/melt folder.
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.. parsed-literal::
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.. code-block:: Python
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from mpi4py import MPI
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from lammps import PyLammps
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@ -563,7 +563,7 @@ To run this script (melt.py) in parallel using 4 MPI processes we invoke the
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following mpirun command:
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.. parsed-literal::
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.. code-block:: bash
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mpirun -np 4 python melt.py
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