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Simon Gravelle
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fixed error tutorial 7
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docs/sphinx/source/tutorial7/tutorial.rst

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@@ -35,7 +35,7 @@ Basic LAMMPS parameters
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To begin this tutorial, if you are using LAMMPS--GUI, select ``Start Tutorial 7``
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from the ``Tutorials`` menu and follow the instructions. Alternatively, if you are
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not using LAMMPS--GUI, create a new folder and add a file named
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**free-energy.lmp**. Open the file in a text editor and paste in the following
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**free-sampling.lmp**. Open the file in a text editor and paste in the following
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content:
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.. code-block:: lammps
@@ -66,7 +66,7 @@ System creation and settings
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----------------------------
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Let us define the simulation box and randomly add atoms by addying the
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following lines to **free-energy.lmp**:
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following lines to **free-sampling.lmp**:
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.. code-block:: lammps
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@@ -119,7 +119,7 @@ frequently overcome the energy barrier due to thermal agitation.
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We impose the force :math:`F(x)` to the atoms in the simulation
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using the ``fix addforce`` command. Add the following
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lines to **free-energy.lmp**:
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lines to **free-sampling.lmp**:
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.. code-block:: lammps
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@@ -161,7 +161,7 @@ VMD-compatible trajectory to a file:
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dump_modify viz1 backcolor white acolor 1 cyan adiam 1 3 boxcolor black
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# Option 2
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dump viz2 all atom 50000 free-energy.lammpstrj
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dump viz2 all atom 50000 free-sampling.lammpstrj
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Finally, let us perform an equilibration of 50000 steps,
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using a timestep of :math:`2\,\text{fs}`, corresponding to a total duration of :math:`100\,\text{ps}`:
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Once the system is equilibrated, we will record the density profile of
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the atoms along the :math:`x`-axis using the ``ave/chunk`` command.
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Add the following line to **free-energy.lmp**:
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Add the following line to **free-sampling.lmp**:
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.. code-block:: lammps
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undump viz1 # Use 'viz1' or 'viz2' depending on your previous choice
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reset_timestep 0
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thermo 200000
@@ -287,7 +288,7 @@ unbiased free energy profile.
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LAMMPS input script
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-------------------
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If you are using LAMMPS--GUI, open the file named **free-energy.lmp**.
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If you are using LAMMPS--GUI, open the file named **umbrella-sampling.lmp**.
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Alternatively, if you are not using LAMMPS--GUI, create a new input file
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and paste in the following content:
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@@ -355,7 +356,7 @@ umbrella sampling run:
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dump_modify viz1 backcolor white acolor 1 cyan acolor 2 red adiam 1 3 adiam 2 3 boxcolor black
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# Option 2
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dump viz2 all atom 50000 free-energy.lammpstrj
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dump viz2 all atom 50000 umbrella-sampling.lammpstrj
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timestep 2.0
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run 50000

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