switch parsed-literal to code-block in Howto files where applicable (3c277409) · Commits · 郑智淋 / lammps

doc/Makefile

+0 −1

Original line number	Diff line number	Diff line
		@@ -71,7 +71,6 @@ html: $(ANCHORCHECK) $(MATHJAX)
		echo "############################################" ;\
		deactivate ;\
		)
		-rm html/searchindex.js
		@rm -rf html/_sources
		@rm -rf html/PDF
		@rm -rf html/USER

doc/src/Howto_2d.rst

+1 −1

Original line number	Diff line number	Diff line
		@@ -12,7 +12,7 @@ create\_atoms command will tile the 3d simulation box with a single z
		plane of atoms - e.g.


		.. parsed-literal::
		.. code-block:: LAMMPS

		:doc:`create box <create_box>` 1 -10 10 -10 10 -0.25 0.25

doc/src/Howto_bash.rst

+18 −18

Original line number	Diff line number	Diff line
		@@ -98,7 +98,7 @@ Installing prerequisite packages
		First upgrade all existing packages using


		.. parsed-literal::
		.. code-block:: bash

		sudo apt update
		sudo apt upgrade -y
		@@ -107,7 +107,7 @@ Next install the following packages, which include compilers and libraries
		needed for various LAMMPS features:


		.. parsed-literal::
		.. code-block:: bash

		sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng12-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools

		@@ -127,7 +127,7 @@ Option 1: Downloading LAMMPS tarball using wget
		"""""""""""""""""""""""""""""""""""""""""""""""


		.. parsed-literal::
		.. code-block:: bash

		wget http://lammps.sandia.gov/tars/lammps-stable.tar.gz
		tar xvzf lammps-stable.tar.gz
		@@ -137,7 +137,7 @@ Option 2: Obtaining LAMMPS code from GitHub
		"""""""""""""""""""""""""""""""""""""""""""


		.. parsed-literal::
		.. code-block:: bash

		git clone https://github.com/lammps/lammps.git
		cd lammps
		@@ -151,7 +151,7 @@ Compiling serial version
		""""""""""""""""""""""""


		.. parsed-literal::
		.. code-block:: bash

		cd src/
		make -j 4 serial
		@@ -162,7 +162,7 @@ Compiling MPI version
		"""""""""""""""""""""


		.. parsed-literal::
		.. code-block:: bash

		cd src/
		make -j 4 mpi
		@@ -176,14 +176,14 @@ This will create an executable called lmp\_mpi in the src/ directory
		Finally, please note the absolute path of your src folder. You can get this using


		.. parsed-literal::
		.. code-block:: bash

		pwd

		or


		.. parsed-literal::
		.. code-block:: bash

		echo $PWD

		@@ -191,7 +191,7 @@ To run any examples you need the location of the executable. For now, let us
		save this location in a temporary variable


		.. parsed-literal::
		.. code-block:: bash

		LAMMPS_DIR=$PWD

		@@ -206,7 +206,7 @@ Once compiled you can execute some of the LAMMPS examples. Switch into the
		examples/melt folder


		.. parsed-literal::
		.. code-block:: bash

		cd ../examples/melt

		@@ -215,14 +215,14 @@ version is $LAMMPS\_DIR/lmp\_mpi. You can run the melt example with either
		version as follows:


		.. parsed-literal::
		.. code-block:: bash

		$LAMMPS_DIR/lmp_serial -in in.melt

		or


		.. parsed-literal::
		.. code-block:: bash

		mpirun -np 4 $LAMMPS_DIR/lmp_mpi -in in.melt

		@@ -236,21 +236,21 @@ You can avoid having to type the full path of your LAMMPS binary by adding its
		parent folder to the PATH environment variable as follows:


		.. parsed-literal::
		.. code-block:: bash

		export PATH=$LAMMPS_DIR:$PATH

		Input scripts can then be run like this:


		.. parsed-literal::
		.. code-block:: bash

		lmp_serial -in in.melt

		or


		.. parsed-literal::
		.. code-block:: bash

		mpirun -np 4 lmp_mpi -in in.melt

		@@ -259,7 +259,7 @@ To persist this setting edit the $HOME/.bashrc file using your favorite editor
		and add this line


		.. parsed-literal::
		.. code-block:: bash

		export PATH=/full/path/to/your/lammps/src:$PATH

		@@ -268,14 +268,14 @@ and add this line
		For an executable lmp\_serial with a full path


		.. parsed-literal::
		.. code-block:: bash

		/home/richard/lammps/src/lmp_serial

		the PATH variable should be


		.. parsed-literal::
		.. code-block:: bash

		export PATH=/home/richard/lammps/src:$PATH

doc/src/Howto_chunk.rst

+6 −6

Original line number	Diff line number	Diff line
		@@ -151,7 +151,7 @@ properties:
		(1) Average velocity in each of 1000 2d spatial bins:


		.. parsed-literal::
		.. code-block:: LAMMPS

		compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.01 units reduced
		fix 1 all ave/chunk 100 10 1000 cc1 vx vy file tmp.out
		@@ -160,7 +160,7 @@ properties:
		velocity:


		.. parsed-literal::
		.. code-block:: LAMMPS

		compute cc1 all chunk/atom bin/2d x 0.0 0.1 y lower 0.1 units reduced
		compute vbias all temp/profile 1 0 0 y 10
		@@ -169,16 +169,16 @@ velocity:
		(3) Center of mass of each molecule:


		.. parsed-literal::
		.. code-block:: LAMMPS

		compute cc1 all chunk/atom molecule
		compute myChunk all com/chunk cc1
		fix 1 all ave/time 100 1 100 c_myChunk[\*] file tmp.out mode vector
		fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector

		(4) Total force on each molecule and ave/max across all molecules:


		.. parsed-literal::
		.. code-block:: LAMMPS

		compute cc1 all chunk/atom molecule
		fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
		@@ -190,7 +190,7 @@ velocity:
		(5) Histogram of cluster sizes:


		.. parsed-literal::
		.. code-block:: LAMMPS

		compute cluster all cluster/atom 1.0
		compute cc1 all chunk/atom c_cluster compress yes

doc/src/Howto_client_server.rst

+2 −2

Original line number	Diff line number	Diff line
		@@ -135,7 +135,7 @@ together to exchange MPI messages between them.
		For message exchange in file\ , zmq\ , or mpi/two modes:


		.. parsed-literal::
		.. code-block:: bash

		% mpirun -np 1 lmp_mpi -log log.client < in.client &
		% mpirun -np 2 lmp_mpi -log log.server < in.server
		@@ -151,7 +151,7 @@ For message exchange in mpi/one mode:
		Launch both codes in a single mpirun command:


		.. parsed-literal::
		.. code-block:: bash

		mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server

Admin message