Remove Make.py reference in PyLammps examples (d3169eea) · Commits · 郑智淋 / lammps

python/examples/pylammps/.gitignore

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		*.orig
		*-checkpoint.ipynb
		*.png
		*.mp4

python/examples/pylammps/dihedrals/dihedral.ipynb

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python/examples/pylammps/interface_usage.ipynb

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		%% Cell type:markdown id: tags:

		# Using LAMMPS with iPython and Jupyter

		%% Cell type:markdown id: tags:

		LAMMPS can be run interactively using iPython easily. This tutorial shows how to set this up.

		%% Cell type:markdown id: tags:

		## Installation

		%% Cell type:markdown id: tags:

		1. Download the latest version of LAMMPS into a folder (we will calls this `$LAMMPS_DIR` from now on)
		2. Compile LAMMPS as a shared library and enable exceptions and PNG support
		```bash
		cd $LAMMPS_DIR/src
		python Make.py -m mpi -png -s exceptions -a file
		make mode=shlib auto
		make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_EXCEPTIONS" JPG_LIB="-lpng"
		```

		3. Create a python virtualenv
		```bash
		virtualenv testing
		source testing/bin/activate
		```

		4. Inside the virtualenv install the lammps package
		```
		(testing) cd $LAMMPS_DIR/python
		(testing) python install.py
		(testing) cd # move to your working directory
		```

		5. Install jupyter and ipython in the virtualenv
		```bash
		(testing) pip install ipython jupyter
		```

		6. Run jupyter notebook
		```bash
		(testing) jupyter notebook
		```

		%% Cell type:markdown id: tags:

		## Example

		%% Cell type:code id: tags:

		``` python
		from lammps import IPyLammps
		```

		%% Cell type:code id: tags:

		``` python
		L = IPyLammps()
		```

		%% Cell type:code id: tags:

		``` python
		# 3d Lennard-Jones melt

		L.units("lj")
		L.atom_style("atomic")
		L.atom_modify("map array")

		L.lattice("fcc", 0.8442)
		L.region("box block", 0, 4, 0, 4, 0, 4)
		L.create_box(1, "box")
		L.create_atoms(1, "box")
		L.mass(1, 1.0)

		L.velocity("all create", 1.44, 87287, "loop geom")

		L.pair_style("lj/cut", 2.5)
		L.pair_coeff(1, 1, 1.0, 1.0, 2.5)

		L.neighbor(0.3, "bin")
		L.neigh_modify("delay 0 every 20 check no")

		L.fix("1 all nve")

		L.variable("fx atom fx")

		L.run(10)
		```

		%% Cell type:code id: tags:

		``` python
		L.image(zoom=1)
		```

		%% Cell type:markdown id: tags:

		## Queries about LAMMPS simulation

		%% Cell type:code id: tags:

		``` python
		L.system
		```

		%% Cell type:code id: tags:

		``` python
		L.system.natoms
		```

		%% Cell type:code id: tags:

		``` python
		L.communication
		```

		%% Cell type:code id: tags:

		``` python
		L.fixes
		```

		%% Cell type:code id: tags:

		``` python
		L.computes
		```

		%% Cell type:code id: tags:

		``` python
		L.dumps
		```

		%% Cell type:code id: tags:

		``` python
		L.groups
		```

		%% Cell type:markdown id: tags:

		## Working with LAMMPS Variables

		%% Cell type:code id: tags:

		``` python
		L.variable("a index 2")
		```

		%% Cell type:code id: tags:

		``` python
		L.variables
		```

		%% Cell type:code id: tags:

		``` python
		L.variable("t equal temp")
		```

		%% Cell type:code id: tags:

		``` python
		L.variables
		```

		%% Cell type:code id: tags:

		``` python
		import sys

		if sys.version_info < (3, 0):
		# In Python 2 'print' is a restricted keyword, which is why you have to use the lmp_print function instead.
		x = float(L.lmp_print('"${a}"'))
		else:
		# In Python 3 the print function can be redefined.
		# x = float(L.print('"${a}"')")

		# To avoid a syntax error in Python 2 executions of this notebook, this line is packed into an eval statement
		x = float(eval("L.print('\"${a}\"')"))
		x
		```

		%% Cell type:code id: tags:

		``` python
		L.variables['t'].value
		```

		%% Cell type:code id: tags:

		``` python
		L.eval("v_t/2.0")
		```

		%% Cell type:code id: tags:

		``` python
		L.variable("b index a b c")
		```

		%% Cell type:code id: tags:

		``` python
		L.variables['b'].value
		```

		%% Cell type:code id: tags:

		``` python
		L.eval("v_b")
		```

		%% Cell type:code id: tags:

		``` python
		L.variables['b'].definition
		```

		%% Cell type:code id: tags:

		``` python
		L.variable("i loop 10")
		```

		%% Cell type:code id: tags:

		``` python
		L.variables['i'].value
		```

		%% Cell type:code id: tags:

		``` python
		L.next("i")
		L.variables['i'].value
		```

		%% Cell type:code id: tags:

		``` python
		L.eval("ke")
		```

		%% Cell type:markdown id: tags:

		## Accessing Atom data

		%% Cell type:code id: tags:

		``` python
		L.atoms[0]
		```

		%% Cell type:code id: tags:

		``` python
		[x for x in dir(L.atoms[0]) if not x.startswith('__')]
		```

		%% Cell type:code id: tags:

		``` python
		L.atoms[0].position
		```

		%% Cell type:code id: tags:

		``` python
		L.atoms[0].id
		```

		%% Cell type:code id: tags:

		``` python
		L.atoms[0].velocity
		```

		%% Cell type:code id: tags:

		``` python
		L.atoms[0].force
		```

		%% Cell type:code id: tags:

		``` python
		L.atoms[0].type
		```

		%% Cell type:code id: tags:

		``` python
		L.variables['fx'].value
		```

		%% Cell type:markdown id: tags:

		## Accessing thermo data

		%% Cell type:code id: tags:

		``` python
		L.runs
		```

		%% Cell type:code id: tags:

		``` python
		L.runs[0]
		```

		%% Cell type:code id: tags:

		``` python
		L.runs[0].thermo
		```

		%% Cell type:code id: tags:

		``` python
		L.runs[0].thermo.Temp
		L.runs[0].thermo
		```

		%% Cell type:markdown id: tags:

		## Saving session to as LAMMPS input file

		%% Cell type:code id: tags:

		``` python
		L.write_script("in.output")
		```

		%% Cell type:code id: tags:

		``` python
		dir(L.runs[0].thermo)
		```

		%% Cell type:code id: tags:

		``` python
		```

python/examples/pylammps/interface_usage_bonds.ipynb

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Original line number	Diff line number	Diff line
		%% Cell type:markdown id: tags:

		# Using LAMMPS with iPython and Jupyter

		%% Cell type:markdown id: tags:

		LAMMPS can be run interactively using iPython easily. This tutorial shows how to set this up.

		%% Cell type:markdown id: tags:

		## Installation

		%% Cell type:markdown id: tags:

		1. Download the latest version of LAMMPS into a folder (we will calls this `$LAMMPS_DIR` from now on)
		2. Compile LAMMPS as a shared library and enable exceptions and PNG support
		```bash
		cd $LAMMPS_DIR/src
		make yes-molecule
		python Make.py -m mpi -png -s exceptions -a file
		make mode=shlib auto
		make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_EXCEPTIONS" JPG_LIB="-lpng"
		```

		3. Create a python virtualenv
		```bash
		virtualenv testing
		source testing/bin/activate
		```

		4. Inside the virtualenv install the lammps package
		```
		(testing) cd $LAMMPS_DIR/python
		(testing) python install.py
		(testing) cd # move to your working directory
		```

		5. Install jupyter and ipython in the virtualenv
		```bash
		(testing) pip install ipython jupyter
		```

		6. Run jupyter notebook
		```bash
		(testing) jupyter notebook
		```

		%% Cell type:markdown id: tags:

		## Example

		%% Cell type:code id: tags:

		``` python
		from lammps import IPyLammps
		```

		%% Cell type:code id: tags:

		``` python
		L = IPyLammps()
		```

		%% Cell type:code id: tags:

		``` python
		# 2d circle of particles inside a box with LJ walls
		import math

		b = 0
		x = 50
		y = 20
		d = 20

		# careful not to slam into wall too hard

		v = 0.3
		w = 0.08

		L.units("lj")
		L.dimension(2)
		L.atom_style("bond")
		L.boundary("f f p")

		L.lattice("hex", 0.85)
		L.region("box", "block", 0, x, 0, y, -0.5, 0.5)
		L.create_box(1, "box", "bond/types", 1, "extra/bond/per/atom", 6)
		L.region("circle", "sphere", d/2.0+1.0, d/2.0/math.sqrt(3.0)+1, 0.0, d/2.0)
		L.create_atoms(1, "region", "circle")
		L.mass(1, 1.0)

		L.velocity("all create 0.5 87287 loop geom")
		L.velocity("all set", v, w, 0, "sum yes")

		L.pair_style("lj/cut", 2.5)
		L.pair_coeff(1, 1, 10.0, 1.0, 2.5)

		L.bond_style("harmonic")
		L.bond_coeff(1, 10.0, 1.2)

		L.create_bonds("all", "all", 1, 1.0, 1.5)
		L.create_bonds("many", "all", "all", 1, 1.0, 1.5)

		L.neighbor(0.3, "bin")
		L.neigh_modify("delay", 0, "every", 1, "check yes")

		L.fix(1, "all", "nve")

		L.fix(2, "all wall/lj93 xlo 0.0 1 1 2.5 xhi", x, "1 1 2.5")
		L.fix(3, "all wall/lj93 ylo 0.0 1 1 2.5 yhi", y, "1 1 2.5")
		```

		%% Cell type:code id: tags:

		``` python
		L.image(zoom=1.8)
		```

		%% Cell type:code id: tags:

		``` python
		L.thermo_style("custom step temp epair press")
		L.thermo(100)
		output = L.run(40000)
		L.image(zoom=1.8)
		```

		%% Cell type:markdown id: tags:

		## Queries about LAMMPS simulation

		%% Cell type:code id: tags:

		``` python
		L.system
		```

		%% Cell type:code id: tags:

		``` python
		L.system.natoms
		```

		%% Cell type:code id: tags:

		``` python
		L.system.nbonds
		```

		%% Cell type:code id: tags:

		``` python
		L.system.nbondtypes
		```

		%% Cell type:code id: tags:

		``` python
		L.communication
		```

		%% Cell type:code id: tags:

		``` python
		L.fixes
		```

		%% Cell type:code id: tags:

		``` python
		L.computes
		```

		%% Cell type:code id: tags:

		``` python
		L.dumps
		```

		%% Cell type:code id: tags:

		``` python
		L.groups
		```

		%% Cell type:markdown id: tags:

		## Working with LAMMPS Variables

		%% Cell type:code id: tags:

		``` python
		L.variable("a index 2")
		```

		%% Cell type:code id: tags:

		``` python
		L.variables
		```

		%% Cell type:code id: tags:

		``` python
		L.variable("t equal temp")
		```

		%% Cell type:code id: tags:

		``` python
		L.variables
		```

		%% Cell type:code id: tags:

		``` python
		import sys

		if sys.version_info < (3, 0):
		# In Python 2 'print' is a restricted keyword, which is why you have to use the lmp_print function instead.
		x = float(L.lmp_print('"${a}"'))
		else:
		# In Python 3 the print function can be redefined.
		# x = float(L.print('"${a}"')")

		# To avoid a syntax error in Python 2 executions of this notebook, this line is packed into an eval statement
		x = float(eval("L.print('\"${a}\"')"))
		x
		```

		%% Cell type:code id: tags:

		``` python
		L.variables['t'].value
		```

		%% Cell type:code id: tags:

		``` python
		L.eval("v_t/2.0")
		```

		%% Cell type:code id: tags:

		``` python
		L.variable("b index a b c")
		```

		%% Cell type:code id: tags:

		``` python
		L.variables['b'].value
		```

		%% Cell type:code id: tags:

		``` python
		L.eval("v_b")
		```

		%% Cell type:code id: tags:

		``` python
		L.variables['b'].definition
		```

		%% Cell type:code id: tags:

		``` python
		L.variable("i loop 10")
		```

		%% Cell type:code id: tags:

		``` python
		L.variables['i'].value
		```

		%% Cell type:code id: tags:

		``` python
		L.next("i")
		L.variables['i'].value
		```

		%% Cell type:code id: tags:

		``` python
		L.eval("ke")
		```

		%% Cell type:markdown id: tags:

		## Accessing Atom data

		%% Cell type:code id: tags:

		``` python
		L.atoms[0]
		```

		%% Cell type:code id: tags:

		``` python
		[x for x in dir(L.atoms[0]) if not x.startswith('__')]
		```

		%% Cell type:code id: tags:

		``` python
		L.atoms[0].position
		```

		%% Cell type:code id: tags:

		``` python
		L.atoms[0].id
		```

		%% Cell type:code id: tags:

		``` python
		L.atoms[0].velocity
		```

		%% Cell type:code id: tags:

		``` python
		L.atoms[0].force
		```

		%% Cell type:code id: tags:

		``` python
		L.atoms[0].type
		```

		%% Cell type:code id: tags:

		``` python
		```

python/examples/pylammps/montecarlo/mc.ipynb

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