collapse multiple empty lines into a single empty line
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Axel Kohlmeyer
@ -56,7 +56,6 @@ output support enabled.
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Step 1a: For the CMake based build system, the steps are:
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.. code-block:: bash
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mkdir $LAMMPS_DIR/build-shared
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@ -68,7 +67,6 @@ 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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.. code-block:: bash
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cd $LAMMPS_DIR/src
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@ -85,7 +83,6 @@ Step 2: Installing the LAMMPS Python package
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PyLammps is part of the lammps Python package. To install it simply install
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that package into your current Python installation with:
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.. code-block:: bash
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make install-python
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@ -110,7 +107,6 @@ Benefits of using a virtualenv
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**Prerequisite (e.g. on Ubuntu)**
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.. code-block:: bash
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apt-get install python-virtualenv
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@ -118,7 +114,6 @@ Benefits of using a virtualenv
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Creating a virtualenv with lammps installed
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"""""""""""""""""""""""""""""""""""""""""""
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.. code-block:: bash
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# create virtualenv named 'testing'
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@ -132,7 +127,6 @@ When using CMake and the shared library has already been build, you
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need to re-run CMake to update the location of the python executable
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to the location in the virtual environment with:
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.. code-block:: bash
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cmake . -DPYTHON_EXECUTABLE=$(which python)
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@ -154,7 +148,6 @@ Creating a new instance of PyLammps
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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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.. code-block:: Python
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from lammps import PyLammps
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@ -162,7 +155,6 @@ 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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.. code-block:: Python
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from lammps import lammps, PyLammps
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@ -177,7 +169,6 @@ 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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.. code-block:: LAMMPS
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region box block 0 10 0 5 -0.5 0.5
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@ -185,7 +176,6 @@ For instance, let's take the following LAMMPS command:
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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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.. code-block:: Python
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L.command("region box block 0 10 0 5 -0.5 0.5")
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@ -193,7 +183,6 @@ Python code if *L* was a lammps instance:
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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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.. code-block:: Python
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L.region("box block", 0, 10, 0, 5, -0.5, 0.5)
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@ -206,7 +195,6 @@ The benefit of this approach is avoiding redundant command calls and easier
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parameterization. In the original interface parameterization needed to be done
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manually by creating formatted strings.
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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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@ -214,7 +202,6 @@ manually by creating formatted strings.
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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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.. code-block:: Python
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L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
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@ -225,8 +212,6 @@ System state
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In addition to dispatching commands directly through the PyLammps object, it
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also provides several properties which allow you to query the system state.
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L.system
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Is a dictionary describing the system such as the bounding box or number of atoms
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@ -260,8 +245,6 @@ L.dump
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L.groups
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List of groups present in the current system
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Working with LAMMPS variables
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-----------------------------
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@ -269,7 +252,6 @@ 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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.. code-block:: Python
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L.variable("a index 2")
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@ -279,7 +261,6 @@ A dictionary of all variables is returned by L.variables
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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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.. code-block:: Python
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a = L.variables['a']
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@ -287,7 +268,6 @@ L.variables dictionary by name
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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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.. code-block:: Python
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print(a.value)
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@ -300,7 +280,6 @@ LAMMPS expressions can be immediately evaluated by using the eval method. The
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passed string parameter can be any expression containing global thermo values,
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variables, compute or fix data.
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.. code-block:: Python
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result = L.eval("ke") # kinetic energy
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@ -315,7 +294,6 @@ All atoms in the current simulation can be accessed by using the L.atoms list.
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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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.. code-block:: Python
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# access first atom
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@ -329,7 +307,6 @@ position, velocity, force, etc.).
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Some properties can also be used to set:
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.. code-block:: Python
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# set position in 2D simulation
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@ -347,7 +324,6 @@ after a run via the L.runs list. This list contains a growing list of run data.
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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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.. code-block:: Python
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L.run(1000)
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@ -359,7 +335,6 @@ the second run.
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Each run contains a dictionary of all trajectories. Each trajectory is
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accessible through its thermo name:
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.. code-block:: Python
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L.runs[0].thermo.Step # list of time steps in first run
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@ -367,7 +342,6 @@ accessible through its thermo name:
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Together with matplotlib plotting data out of LAMMPS becomes simple:
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.. code-block:: Python
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import matplotlib.plot as plt
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@ -406,7 +380,6 @@ tutorials and showcasing your latest research.
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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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.. code-block:: bash
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jupyter notebook
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@ -429,7 +402,6 @@ Four atoms are placed in the simulation and the dihedral potential is applied on
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them using a datafile. Then one of the atoms is rotated along the central axis by
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setting its position from Python, which changes the dihedral angle.
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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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@ -463,7 +435,6 @@ 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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.. code-block:: Python
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random.seed(27848)
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@ -483,7 +454,6 @@ It is then disordered by moving each atom by a random delta.
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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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.. code-block:: Python
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estart = L.eval("pe")
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@ -536,7 +506,6 @@ 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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.. code-block:: bash
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pip install mpi4py
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@ -544,7 +513,6 @@ PyLammps can be run in parallel using mpi4py. This python package can be install
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The following is a short example which reads in an existing LAMMPS input file and
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executes it in parallel. You can find in.melt in the examples/melt folder.
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.. code-block:: Python
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from mpi4py import MPI
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@ -561,7 +529,6 @@ executes it in parallel. You can find in.melt in the examples/melt folder.
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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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.. code-block:: bash
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mpirun -np 4 python melt.py
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