use consistent pygments language tags
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@ -152,14 +152,14 @@ 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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.. code-block:: python
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from lammps import PyLammps
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L = PyLammps()
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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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.. code-block:: python
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from lammps import lammps, PyLammps
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lmp = lammps()
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@ -180,14 +180,14 @@ 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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.. code-block:: python
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L.command("region box block 0 10 0 5 -0.5 0.5")
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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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.. code-block:: python
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L.region("box block", 0, 10, 0, 5, -0.5, 0.5)
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@ -199,14 +199,14 @@ 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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.. 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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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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.. code-block:: python
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L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
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@ -256,7 +256,7 @@ 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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.. code-block:: Python
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.. code-block:: python
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L.variable("a index 2")
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@ -265,14 +265,14 @@ 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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.. code-block:: python
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a = L.variables['a']
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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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.. code-block:: python
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print(a.value)
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a.value = 4
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@ -284,7 +284,7 @@ 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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.. 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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@ -298,7 +298,7 @@ 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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.. code-block:: python
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# access first atom
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L.atoms[0].id
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@ -311,7 +311,7 @@ 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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.. 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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@ -328,7 +328,7 @@ 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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.. 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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@ -339,14 +339,14 @@ 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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.. code-block:: python
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L.runs[0].thermo.Step # list of time steps in first run
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L.runs[0].thermo.Ke # list of kinetic energy values in first run
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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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.. code-block:: python
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import matplotlib.plot as plt
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steps = L.runs[0].thermo.Step
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@ -406,7 +406,7 @@ 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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.. code-block:: python
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phi = [d \* math.pi / 180 for d in range(360)]
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@ -439,7 +439,7 @@ 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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.. code-block:: Python
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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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@ -458,7 +458,7 @@ 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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.. code-block:: python
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estart = L.eval("pe")
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elast = estart
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@ -517,7 +517,7 @@ 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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.. code-block:: python
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from mpi4py import MPI
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from lammps import PyLammps
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