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docs/sphinx/source/tutorial3/tutorial.rst

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@@ -408,7 +408,6 @@ constraints using the following commands:
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.. code-block:: lammps
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compute rgyr PEG gyration
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compute prop PEG property/local dtype
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compute dphi PEG dihedral/local phi
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The radius of gyration can be directly printed with the ``thermo_style`` command:
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thermo_style custom step temp etotal c_rgyr
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thermo 250
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dump mydmp all local 100 pull.dat index c_dphi c_prop
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dump mydmp all local 100 pull.dat index c_dphi
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By contrast with the radius of gyration (compute ``rgyr``), the dihedral angle
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:math:`\phi` (compute ``dphi``) is returned as a vector by the ``compute dihedral/local``
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.. admonition:: Note
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:class: non-title-info
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Since the trajectory dump file does not contain information about
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Since the default trajectory dump file does not contain information about
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topology and elements, it is usually preferred to first write out a
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data file and import it directly (in the case of OVITO) or convert it
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to a PSF file (for VMD). This allows the topology to be loaded before
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*adding* the trajectory file to it. When using LAMMPS--GUI,
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this process can be automated through the ``View in OVITO`` or
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``View in VMD`` options in the ``Run`` menu. Afterwards
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only the trajectory dump needs to be added.
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only the trajectory dump needs to be added. Alternatively, the
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``dump custom`` command can be combined with ``dump`` command to
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include element names in the dump file and simplify visualization.

docs/sphinx/source/tutorial4/tutorial.rst

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@@ -35,6 +35,10 @@ These lines are used to define the most basic parameters, including the
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atom, bond, and angle styles, as well as interaction
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potential. Here, ``lj/cut/tip4p/long`` imposes a Lennard-Jones potential with
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a cut-off at :math:`12\,\text{Å}` and a long-range Coulomb potential.
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The parameters ``O``, ``H``, ``O-H``, and ``H-O-H`` correspond
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respectively to the oxygens, hydrogens, O-H bonds, and H-O-H angle constraints of
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the water molecules; their definitions, provided by the ``labelmap`` commands,
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will be clarified below.
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.. include:: ../shared/needhelp.rst
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@@ -189,10 +193,10 @@ types. By default, LAMMPS calculates the pair coefficients for the
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interactions between atoms of different types (i and j) by using
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geometric average: :math:`\epsilon_{ij} = \sqrt{\epsilon_{ii} \epsilon_{jj}}`,
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:math:`\sigma_{ij} = \sqrt{\sigma_{ii} \sigma_{jj}}`. However, if the default
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value of :math:`1.472\,\text{kcal/mol}` was used for :math:`\epsilon_\text{1-5}`,
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value of :math:`1.472\,\text{kcal/mol}` was used for :math:`\epsilon_\text{O-WALL}`,
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the solid walls would be extremely hydrophilic, causing the water
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molecules to form dense layers. As a comparison, the water-water energy
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:math:`\epsilon_\text{1-1}` is only :math:`0.185199\,\text{kcal/mol}`. Therefore,
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:math:`\epsilon_\text{O-O}` is only :math:`0.185199\,\text{kcal/mol}`. Therefore,
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to make the walls less hydrophilic, the value of
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:math:`\epsilon_\text{O-WALL}` was reduced.
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docs/sphinx/source/tutorial5/tutorial.rst

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@@ -62,7 +62,10 @@ allocation issues, which sometimes can trigger segmentation faults and
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file, which should have been downloaded during the tutorial set up. Finally, the
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``fix qeq/reaxff`` is used to perform charge equilibration :cite:`rappe1991charge`,
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which occurs at every step. The values 0.0 and 10.0 represent the
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low and the high cutoffs, respectively, and :math:`1.0 \text{e} -6` is the tolerance.
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low and the high cutoffs, respectively, and :math:`1.0 \text{e} -6` is the tolerance,
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i.e., the precision to which the atomic charges are equilibrated during the
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charge equilibration process.
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The ``maxiter`` sets an upper limit to the number of attempts to
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equilibrate the charge.
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docs/sphinx/source/tutorial6/tutorial.rst

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@@ -387,8 +387,8 @@ following lines into **gcmc.lmp**:
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.. code-block:: lammps
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compute ctH2O H2O temp
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compute_modify thermo_temp dynamic yes
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compute_modify ctH2O dynamic yes
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compute_modify thermo_temp dynamic/dof yes
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compute_modify ctH2O dynamic/dof yes
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fix mynvt1 H2O nvt temp 300 300 0.1
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fix_modify mynvt1 temp ctH2O
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fix mynvt2 SiO nvt temp 300 300 0.1
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respectively. Using separate thermostats is usually better when the system contains
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two separate species, such as a solid and a liquid. It is particularly important
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to use two thermostats here because the number of water molecules will fluctuate
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with time. The ``compute_modify`` command with the ``dynamic yes``
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with time. The ``compute_modify`` command with the ``dynamic/dof yes``
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option for water is used to specify that the number of molecules will not be constant.
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Finally, let us use the ``fix gcmc`` and perform the grand canonical Monte

docs/sphinx/source/tutorial7/tutorial.rst

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@@ -48,20 +48,26 @@ content:
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units real
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atom_style atomic
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pair_style lj/cut 3.822
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pair_style lj/cut $(2^(1/6)*v_sigma)
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pair_modify shift yes
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boundary p p p
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Here, we begin by defining variables for the Lennard-Jones interaction
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:math:`\sigma` and :math:`\epsilon` and for the repulsive potential
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:math:`U`, which are :math:`U_0`, :math:`\delta`, and
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:math:`x_0` [see Eqs. :eq:`eq_U`-:eq:`eq_F` below]. The cut-off value of
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3.822 Å was chosen to create a Weeks-Chandler-Andersen (WCA) potential,
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which is a truncated and purely repulsive LJ
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potential :cite:`weeks1971role`. It was calculated as :math:`2^{1/6} \sigma`.
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:\math:`2^{1/6} \sigma = 3.822` was chosen to create a Weeks-Chandler-Andersen
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(WCA) potential, which is a truncated and purely repulsive LJ potential :cite:`weeks1971role`.
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The potential is also shifted to be equal to 0 at the cut-off
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using the ``pair_modify`` command.
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.. admonition:: Note
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:class: non-title-info
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The syntax ``$(...)``, where a dollar sign is followed by parentheses, allows
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you to evaluate a numeric formula immediately, without having to assign it
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to a named variable first.
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System creation and settings
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----------------------------
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units real
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atom_style atomic
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pair_style lj/cut 3.822
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pair_style lj/cut $(2^(1/6)*v_sigma)
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pair_modify shift yes
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boundary p p p
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