diff --git a/doc/src/pair_coul.rst b/doc/src/pair_coul.rst index be586a6510..a5d0a0f42f 100644 --- a/doc/src/pair_coul.rst +++ b/doc/src/pair_coul.rst @@ -1,88 +1,88 @@ -.. index:: pair\_style coul/cut +.. index:: pair_style coul/cut -pair\_style coul/cut command -============================ +pair_style coul/cut command +=========================== -pair\_style coul/cut/gpu command -================================ - -pair\_style coul/cut/kk command +pair_style coul/cut/gpu command =============================== -pair\_style coul/cut/omp command -================================ - -pair\_style coul/debye command +pair_style coul/cut/kk command ============================== -pair\_style coul/debye/gpu command -================================== - -pair\_style coul/debye/kk command -================================= - -pair\_style coul/debye/omp command -================================== - -pair\_style coul/dsf command -============================ - -pair\_style coul/dsf/gpu command -================================ - -pair\_style coul/dsf/kk command +pair_style coul/cut/omp command =============================== -pair\_style coul/dsf/omp command -================================ - -pair\_style coul/long command +pair_style coul/debye command ============================= -pair\_style coul/long/omp command +pair_style coul/debye/gpu command ================================= -pair\_style coul/long/gpu command +pair_style coul/debye/kk command +================================ + +pair_style coul/debye/omp command ================================= -pair\_style coul/long/kk command -================================ +pair_style coul/dsf command +=========================== -pair\_style coul/msm command -============================ +pair_style coul/dsf/gpu command +=============================== -pair\_style coul/msm/omp command -================================ - -pair\_style coul/streitz command -================================ - -pair\_style coul/wolf command -============================= - -pair\_style coul/wolf/kk command -================================ - -pair\_style coul/wolf/omp command -================================= - -pair\_style tip4p/cut command -============================= - -pair\_style tip4p/long command +pair_style coul/dsf/kk command ============================== -pair\_style tip4p/cut/omp command -================================= +pair_style coul/dsf/omp command +=============================== -pair\_style tip4p/long/omp command -================================== +pair_style coul/long command +============================ + +pair_style coul/long/omp command +================================ + +pair_style coul/long/gpu command +================================ + +pair_style coul/long/kk command +=============================== + +pair_style coul/msm command +=========================== + +pair_style coul/msm/omp command +=============================== + +pair_style coul/streitz command +=============================== + +pair_style coul/wolf command +============================ + +pair_style coul/wolf/kk command +=============================== + +pair_style coul/wolf/omp command +================================ + +pair_style tip4p/cut command +============================ + +pair_style tip4p/long command +============================= + +pair_style tip4p/cut/omp command +================================ + +pair_style tip4p/long/omp command +================================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style coul/cut cutoff pair_style coul/debye kappa cutoff @@ -102,37 +102,37 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style coul/cut 2.5 - pair_coeff \* \* + pair_coeff * * pair_coeff 2 2 3.5 pair_style coul/debye 1.4 3.0 - pair_coeff \* \* + pair_coeff * * pair_coeff 2 2 3.5 pair_style coul/dsf 0.05 10.0 - pair_coeff \* \* + pair_coeff * * pair_style coul/long 10.0 - pair_coeff \* \* + pair_coeff * * pair_style coul/msm 10.0 - pair_coeff \* \* + pair_coeff * * pair_style coul/wolf 0.2 9.0 - pair_coeff \* \* + pair_coeff * * pair_style coul/streitz 12.0 ewald pair_style coul/streitz 12.0 wolf 0.30 - pair_coeff \* \* AlO.streitz Al O + pair_coeff * * AlO.streitz Al O pair_style tip4p/cut 1 2 7 8 0.15 12.0 - pair_coeff \* \* + pair_coeff * * pair_style tip4p/long 1 2 7 8 0.15 10.0 - pair_coeff \* \* + pair_coeff * * Description """"""""""" @@ -142,7 +142,7 @@ potential given by .. math:: - E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c + E = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c where C is an energy-conversion constant, Qi and Qj are the charges on @@ -159,7 +159,7 @@ Coulombic term, given by .. math:: - E = \frac{C q_i q_j}{\epsilon r} \exp(- \kappa r) \qquad r < r_c + E = \frac{C q_i q_j}{\epsilon r} \exp(- \kappa r) \qquad r < r_c where :math:`\kappa` is the Debye length. This potential is another way to @@ -174,9 +174,8 @@ shifted force model described in :ref:`Fennell `, given by: .. math:: - E = - q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} + - \left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c + E = q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} + + \left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c where :math:`\alpha` is the damping parameter and erfc() is the @@ -194,10 +193,10 @@ summation method, described in :ref:`Wolf `, given by: .. math:: - E_i = \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} + - \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c + E_i = \frac{1}{2} \sum_{j \neq i} + \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} + + \frac{1}{2} \sum_{j \neq i} + \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c where :math:`\alpha` is the damping parameter, and erc() and erfc() are @@ -228,11 +227,11 @@ the :doc:`pair_style hybrid/overlay ` command. Likewise, charge equilibration must be performed via the :doc:`fix qeq/slater ` command. For example: -.. parsed-literal:: +.. code-block:: LAMMPS pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy - pair_coeff \* \* coul/streitz AlO.streitz Al O - pair_coeff \* \* eam/alloy AlO.eam.alloy Al O + pair_coeff * * coul/streitz AlO.streitz Al O + pair_coeff * * eam/alloy AlO.eam.alloy Al O fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz The keyword *wolf* in the coul/streitz command denotes computing @@ -242,7 +241,7 @@ coul/wolf potential above. Alternatively, Coulombic interactions can be computed via an Ewald summation. For example: -.. parsed-literal:: +.. code-block:: LAMMPS pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy kspace_style ewald 1e-6 diff --git a/doc/src/pair_coul_diel.rst b/doc/src/pair_coul_diel.rst index 361a33f568..47b93387d3 100644 --- a/doc/src/pair_coul_diel.rst +++ b/doc/src/pair_coul_diel.rst @@ -1,16 +1,16 @@ -.. index:: pair\_style coul/diel +.. index:: pair_style coul/diel -pair\_style coul/diel command -============================= +pair_style coul/diel command +============================ -pair\_style coul/diel/omp command -================================= +pair_style coul/diel/omp command +================================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style coul/diel cutoff @@ -20,7 +20,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style coul/diel 3.5 pair_coeff 1 4 78. 1.375 0.112 diff --git a/doc/src/pair_coul_shield.rst b/doc/src/pair_coul_shield.rst index 5e0cb11933..97df7d4a13 100644 --- a/doc/src/pair_coul_shield.rst +++ b/doc/src/pair_coul_shield.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style coul/shield +.. index:: pair_style coul/shield -pair\_style coul/shield command -=============================== +pair_style coul/shield command +============================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style coul/shield cutoff tap_flag @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style coul/shield 16.0 1 pair_coeff 1 2 0.70 @@ -41,9 +41,9 @@ the pair style :doc:`ilp/graphene/hbn ` .. math:: - E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} = & {\rm Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\ - {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - + E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ + V_{ij} = & {\rm Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\ + {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 diff --git a/doc/src/pair_cs.rst b/doc/src/pair_cs.rst index 20d94af432..ebbbdcaeca 100644 --- a/doc/src/pair_cs.rst +++ b/doc/src/pair_cs.rst @@ -1,40 +1,40 @@ -.. index:: pair\_style born/coul/dsf/cs +.. index:: pair_style born/coul/dsf/cs -pair\_style born/coul/dsf/cs command +pair_style born/coul/dsf/cs command ==================================== -pair\_style born/coul/long/cs command +pair_style born/coul/long/cs command ===================================== -pair\_style born/coul/long/cs/gpu command +pair_style born/coul/long/cs/gpu command ========================================= -pair\_style born/coul/wolf/cs command +pair_style born/coul/wolf/cs command ===================================== -pair\_style born/coul/wolf/cs/gpu command +pair_style born/coul/wolf/cs/gpu command ========================================= -pair\_style buck/coul/long/cs command +pair_style buck/coul/long/cs command ===================================== -pair\_style coul/long/cs command +pair_style coul/long/cs command ================================ -pair\_style coul/long/cs/gpu command +pair_style coul/long/cs/gpu command ==================================== -pair\_style coul/wolf/cs command +pair_style coul/wolf/cs command ================================ -pair\_style lj/cut/coul/long/cs command +pair_style lj/cut/coul/long/cs command ======================================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style args @@ -71,33 +71,33 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style born/coul/dsf/cs 0.1 10.0 12.0 - pair_coeff \* \* 0.0 1.00 0.00 0.00 0.00 + pair_coeff * * 0.0 1.00 0.00 0.00 0.00 pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 pair_style born/coul/long/cs 10.0 8.0 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 pair_style born/coul/wolf/cs 0.25 10.0 12.0 - pair_coeff \* \* 0.0 1.00 0.00 0.00 0.00 + pair_coeff * * 0.0 1.00 0.00 0.00 0.00 pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 pair_style buck/coul/long/cs 10.0 pair_style buck/coul/long/cs 10.0 8.0 - pair_coeff \* \* 100.0 1.5 200.0 + pair_coeff * * 100.0 1.5 200.0 pair_coeff 1 1 100.0 1.5 200.0 9.0 pair_style coul/long/cs 10.0 - pair_coeff \* \* + pair_coeff * * pair_style coul/wolf/cs 0.2 9.0 - pair_coeff \* \* + pair_coeff * * pair_style lj/cut/coul/long/cs 10.0 pair_style lj/cut/coul/long/cs 10.0 8.0 - pair_coeff \* \* 100.0 3.0 + pair_coeff * * 100.0 3.0 pair_coeff 1 1 100.0 3.5 9.0 Description diff --git a/doc/src/pair_dipole.rst b/doc/src/pair_dipole.rst index 3f1cbf664f..6d685f27c3 100644 --- a/doc/src/pair_dipole.rst +++ b/doc/src/pair_dipole.rst @@ -1,37 +1,37 @@ -.. index:: pair\_style lj/cut/dipole/cut +.. index:: pair_style lj/cut/dipole/cut -pair\_style lj/cut/dipole/cut command -===================================== +pair_style lj/cut/dipole/cut command +==================================== -pair\_style lj/cut/dipole/cut/gpu command -========================================= +pair_style lj/cut/dipole/cut/gpu command +======================================== -pair\_style lj/cut/dipole/cut/omp command -========================================= +pair_style lj/cut/dipole/cut/omp command +======================================== -pair\_style lj/sf/dipole/sf command -=================================== +pair_style lj/sf/dipole/sf command +================================== -pair\_style lj/sf/dipole/sf/gpu command -======================================= - -pair\_style lj/sf/dipole/sf/omp command -======================================= - -pair\_style lj/cut/dipole/long command +pair_style lj/sf/dipole/sf/gpu command ====================================== -pair\_style lj/cut/dipole/long/gpu command -========================================== +pair_style lj/sf/dipole/sf/omp command +====================================== -pair\_style lj/long/dipole/long command -======================================= +pair_style lj/cut/dipole/long command +===================================== + +pair_style lj/cut/dipole/long/gpu command +========================================= + +pair_style lj/long/dipole/long command +====================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/cut/dipole/cut cutoff (cutoff2) pair_style lj/sf/dipole/sf cutoff (cutoff2) @@ -61,23 +61,23 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/cut/dipole/cut 10.0 - pair_coeff \* \* 1.0 1.0 + pair_coeff * * 1.0 1.0 pair_coeff 2 3 1.0 1.0 2.5 4.0 pair_style lj/sf/dipole/sf 9.0 - pair_coeff \* \* 1.0 1.0 + pair_coeff * * 1.0 1.0 pair_coeff 2 3 1.0 1.0 2.5 4.0 scale 0.5 pair_coeff 2 3 1.0 1.0 2.5 4.0 pair_style lj/cut/dipole/long 10.0 - pair_coeff \* \* 1.0 1.0 + pair_coeff * * 1.0 1.0 pair_coeff 2 3 1.0 1.0 2.5 4.0 pair_style lj/long/dipole/long long long 3.5 10.0 - pair_coeff \* \* 1.0 1.0 + pair_coeff * * 1.0 1.0 pair_coeff 2 3 1.0 1.0 2.5 4.0 Description diff --git a/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst index bf537a1006..a827627870 100644 --- a/doc/src/pair_dpd.rst +++ b/doc/src/pair_dpd.rst @@ -1,31 +1,31 @@ -.. index:: pair\_style dpd +.. index:: pair_style dpd -pair\_style dpd command -======================= +pair_style dpd command +====================== -pair\_style dpd/gpu command -=========================== +pair_style dpd/gpu command +========================== -pair\_style dpd/intel command -============================= +pair_style dpd/intel command +============================ -pair\_style dpd/omp command -=========================== +pair_style dpd/omp command +========================== -pair\_style dpd/tstat command -============================= +pair_style dpd/tstat command +============================ -pair\_style dpd/tstat/gpu command -================================= +pair_style dpd/tstat/gpu command +================================ -pair\_style dpd/tstat/omp command -================================= +pair_style dpd/tstat/omp command +================================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style dpd T cutoff seed pair_style dpd/tstat Tstart Tstop cutoff seed @@ -39,14 +39,14 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style dpd 1.0 2.5 34387 - pair_coeff \* \* 3.0 1.0 + pair_coeff * * 3.0 1.0 pair_coeff 1 1 3.0 1.0 1.0 pair_style dpd/tstat 1.0 1.0 2.5 34387 - pair_coeff \* \* 1.0 + pair_coeff * * 1.0 pair_coeff 1 1 1.0 1.0 Description diff --git a/doc/src/pair_dpd_fdt.rst b/doc/src/pair_dpd_fdt.rst index dfde24a8e2..fecd602c50 100644 --- a/doc/src/pair_dpd_fdt.rst +++ b/doc/src/pair_dpd_fdt.rst @@ -1,19 +1,19 @@ -.. index:: pair\_style dpd/fdt +.. index:: pair_style dpd/fdt -pair\_style dpd/fdt command -=========================== +pair_style dpd/fdt command +========================== -pair\_style dpd/fdt/energy command -================================== +pair_style dpd/fdt/energy command +================================= -pair\_style dpd/fdt/energy/kk command -===================================== +pair_style dpd/fdt/energy/kk command +==================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style args @@ -35,13 +35,13 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style dpd/fdt 300.0 2.5 34387 - pair_coeff \* \* 3.0 1.0 2.5 + pair_coeff * * 3.0 1.0 2.5 pair_style dpd/fdt/energy 2.5 34387 - pair_coeff \* \* 3.0 1.0 0.1 2.5 + pair_coeff * * 3.0 1.0 0.1 2.5 Description """"""""""" @@ -107,18 +107,18 @@ energies are computed within style *dpd/fdt/energy* as: .. math:: du_{i}^{cond} = & \kappa_{ij}(\frac{1}{\theta_{i}}-\frac{1}{\theta_{j}})\omega_{ij}^{2} + \alpha_{ij}\omega_{ij}\zeta_{ij}^{q}(\Delta{t})^{-1/2} \\ - du_{i}^{mech} = & -\frac{1}{2}\gamma_{ij}\omega_{ij}^{2}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})^{2} - - \frac{\sigma^{2}_{ij}}{4}(\frac{1}{m_{i}}+\frac{1}{m_{j}})\omega_{ij}^{2} - - \frac{1}{2}\sigma_{ij}\omega_{ij}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})\zeta_{ij}(\Delta{t})^{-1/2} + du_{i}^{mech} = & -\frac{1}{2}\gamma_{ij}\omega_{ij}^{2}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})^{2} - + \frac{\sigma^{2}_{ij}}{4}(\frac{1}{m_{i}}+\frac{1}{m_{j}})\omega_{ij}^{2} - + \frac{1}{2}\sigma_{ij}\omega_{ij}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})\zeta_{ij}(\Delta{t})^{-1/2} where .. math:: - \alpha_{ij}^{2} = & 2k_{B}\kappa_{ij} \\ - \sigma^{2}_{ij} = & 2\gamma_{ij}k_{B}\Theta_{ij} \\ - \Theta_{ij}^{-1} = & \frac{1}{2}(\frac{1}{\theta_{i}}+\frac{1}{\theta_{j}}) + \alpha_{ij}^{2} = & 2k_{B}\kappa_{ij} \\ + \sigma^{2}_{ij} = & 2\gamma_{ij}k_{B}\Theta_{ij} \\ + \Theta_{ij}^{-1} = & \frac{1}{2}(\frac{1}{\theta_{i}}+\frac{1}{\theta_{j}}) :math:`\zeta_ij^q` is a second Gaussian random number with zero mean and unit diff --git a/doc/src/pair_drip.rst b/doc/src/pair_drip.rst index efff4ce25b..e2dc88648f 100644 --- a/doc/src/pair_drip.rst +++ b/doc/src/pair_drip.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style drip +.. index:: pair_style drip -pair\_style drip command -======================== +pair_style drip command +======================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style hybrid/overlay drip [styles ...] @@ -17,19 +17,19 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style hybrid/overlay drip - pair_coeff \* \* none - pair_coeff \* \* drip C.drip C + pair_coeff * * none + pair_coeff * * drip C.drip C pair_style hybrid/overlay drip rebo - pair_coeff \* \* drip C.drip C - pair_coeff \* \* rebo CH.airebo C + pair_coeff * * drip C.drip C + pair_coeff * * rebo CH.airebo C pair_style hybrid/overlay drip rebo - pair_coeff \* \* drip C.drip C NULL - pair_coeff \* \* rebo CH.airebo C H + pair_coeff * * drip C.drip C NULL + pair_coeff * * rebo CH.airebo C H Description """"""""""" @@ -46,7 +46,7 @@ The total potential energy of a system is \phi_{ij} = &f_\text{c}(x_r) \left[ e^{-\lambda(r_{ij} - z_0 )} \left[C+f(\rho_{ij})+ g(\rho_{ij}, \{\alpha_{ij}^{(m)}\}) \right]- A\left (\frac{z_0}{r_{ij}} \right)^6 \right] -where the *r\^-6* term models the attractive London dispersion, +where the :math:`r^{-6}` term models the attractive London dispersion, the exponential term is designed to capture the registry effect due to overlapping *pi* bonds, and *fc* is a cutoff function. @@ -85,9 +85,9 @@ types and you want all of them to be C, you would use the following pair\_coeff command: -.. parsed-literal:: +.. code-block:: LAMMPS - pair_coeff \* \* drip C.drip C C C + pair_coeff * * drip C.drip C C C If a mapping value is specified as NULL, the mapping is not performed. This could be useful when DRIP is used to model part of the system where other @@ -96,11 +96,11 @@ and H of atom type 2, you can use the following command to inform DRIP not to model H atoms: -.. parsed-literal:: +.. code-block:: LAMMPS pair_style hybrid/overlay drip rebo - pair_coeff \* \* drip C.drip C NULL - pair_coeff \* \* rebo CH.airebo C H + pair_coeff * * drip C.drip C NULL + pair_coeff * * rebo CH.airebo C H .. note:: diff --git a/doc/src/pair_dsmc.rst b/doc/src/pair_dsmc.rst index 7848486eac..c42e6e5b82 100644 --- a/doc/src/pair_dsmc.rst +++ b/doc/src/pair_dsmc.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style dsmc +.. index:: pair_style dsmc -pair\_style dsmc command -======================== +pair_style dsmc command +======================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style dsmc max_cell_size seed weighting Tref Nrecompute Nsample @@ -22,10 +22,10 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style dsmc 2.5 34387 10 1.0 100 20 - pair_coeff \* \* 1.0 + pair_coeff * * 1.0 pair_coeff 1 1 1.0 Description @@ -74,7 +74,7 @@ the "fix nve/noforce" time integration fix for the DSMC particles, e.g. -.. parsed-literal:: +.. code-block:: LAMMPS fix 1 all nve/noforce @@ -85,7 +85,7 @@ on the same processor. To ensure this occurs, you should use these commands: -.. parsed-literal:: +.. code-block:: LAMMPS neighbor 0.0 bin neigh_modify every 1 delay 0 check no @@ -105,7 +105,7 @@ uniform, which will not give good DSMC collision rates. Specify as in the following: -.. parsed-literal:: +.. code-block:: LAMMPS velocity all create 594.6 87287 loop geom dist gaussian diff --git a/doc/src/pair_e3b.rst b/doc/src/pair_e3b.rst index 468c306620..84c793d192 100644 --- a/doc/src/pair_e3b.rst +++ b/doc/src/pair_e3b.rst @@ -1,21 +1,21 @@ -.. index:: pair\_style e3b +.. index:: pair_style e3b -pair\_style e3b command -======================= +pair_style e3b command +====================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style e3b Otype * Otype = atom type for oxygen -.. parsed-literal:: +.. code-block:: LAMMPS - pair_coeff \* \* keyword + pair_coeff * * keyword * one or more keyword/value pairs must be appended. * keyword = *preset* or *Ea* or *Eb* or *Ec* or *E2* or *K3* or *K2* or *Rs* or *Rc3* or *Rc2* or *bondL* or *neigh* @@ -44,13 +44,13 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style e3b 1 - pair_coeff \* \* Ea 35.85 Eb -240.2 Ec 449.3 E2 108269.9 K3 1.907 K2 4.872 Rc3 5.2 Rc2 5.2 Rs 5.0 bondL 0.9572 + pair_coeff * * Ea 35.85 Eb -240.2 Ec 449.3 E2 108269.9 K3 1.907 K2 4.872 Rc3 5.2 Rc2 5.2 Rs 5.0 bondL 0.9572 pair_style hybrid/overlay e3b 1 lj/cut/tip4p/long 1 2 1 1 0.15 8.5 - pair_coeff \* \* e3b preset 2011 + pair_coeff * * e3b preset 2011 Description """"""""""" diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index 575980eb39..82da121a79 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -1,76 +1,76 @@ -.. index:: pair\_style eam +.. index:: pair_style eam -pair\_style eam command -======================= +pair_style eam command +====================== -pair\_style eam/gpu command -=========================== - -pair\_style eam/intel command -============================= - -pair\_style eam/kk command +pair_style eam/gpu command ========================== -pair\_style eam/omp command -=========================== +pair_style eam/intel command +============================ -pair\_style eam/opt command -=========================== +pair_style eam/kk command +========================= -pair\_style eam/alloy command -============================= +pair_style eam/omp command +========================== -pair\_style eam/alloy/gpu command -================================= +pair_style eam/opt command +========================== -pair\_style eam/alloy/intel command -=================================== +pair_style eam/alloy command +============================ -pair\_style eam/alloy/kk command +pair_style eam/alloy/gpu command ================================ -pair\_style eam/alloy/omp command -================================= - -pair\_style eam/alloy/opt command -================================= - -pair\_style eam/cd command -========================== - -pair\_style eam/cd/omp command -============================== - -pair\_style eam/cd/old command -============================== - -pair\_style eam/cd/old/omp command +pair_style eam/alloy/intel command ================================== -pair\_style eam/fs command -========================== +pair_style eam/alloy/kk command +=============================== -pair\_style eam/fs/gpu command -============================== - -pair\_style eam/fs/intel command +pair_style eam/alloy/omp command ================================ -pair\_style eam/fs/kk command +pair_style eam/alloy/opt command +================================ + +pair_style eam/cd command +========================= + +pair_style eam/cd/omp command ============================= -pair\_style eam/fs/omp command -============================== +pair_style eam/cd/old command +============================= -pair\_style eam/fs/opt command -============================== +pair_style eam/cd/old/omp command +================================= + +pair_style eam/fs command +========================= + +pair_style eam/fs/gpu command +============================= + +pair_style eam/fs/intel command +=============================== + +pair_style eam/fs/kk command +============================ + +pair_style eam/fs/omp command +============================= + +pair_style eam/fs/opt command +============================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style @@ -80,20 +80,20 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style eam - pair_coeff \* \* cuu3 - pair_coeff 1\*3 1\*3 niu3.eam + pair_coeff * * cuu3 + pair_coeff 1*3 1\*3 niu3.eam pair_style eam/alloy - pair_coeff \* \* ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni + pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni pair_style eam/cd - pair_coeff \* \* ../potentials/FeCr.cdeam Fe Cr + pair_coeff * * ../potentials/FeCr.cdeam Fe Cr pair_style eam/fs - pair_coeff \* \* NiAlH_jea.eam.fs Ni Al Ni Ni + pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni Description """"""""""" @@ -182,9 +182,9 @@ single argument: Thus the following command -.. parsed-literal:: +.. code-block:: LAMMPS - pair_coeff \*2 1\*2 cuu3.eam + pair_coeff *2 1*2 cuu3.eam will read the cuu3 potential file and use the tabulated Cu values for F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs @@ -233,9 +233,9 @@ by LAMMPS to compute the pair potential term in the EAM energy expression as r\*phi, in units of eV-Angstroms, via the formula -.. parsed-literal:: +.. math:: - r\*phi = 27.2 \* 0.529 \* Zi \* Zj + r \cdot \phi = 27.2 \cdot 0.529 \cdot Z_i \cdot Z_j where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms. @@ -277,9 +277,9 @@ be Ni, and the 4th to be Al, you would use the following pair\_coeff command: -.. parsed-literal:: +.. code-block:: LAMMPS - pair_coeff \* \* NiAlH_jea.eam.alloy Ni Ni Ni Al + pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types. The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni @@ -402,9 +402,9 @@ For style *eam/fs*\ , the form of the pair\_coeff command is exactly the same as for style *eam/alloy*\ , e.g. -.. parsed-literal:: +.. code-block:: LAMMPS - pair_coeff \* \* NiAlH_jea.eam.fs Ni Ni Ni Al + pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al where there are N additional arguments after the filename, where N is the number of LAMMPS atom types. See the :doc:`pair_coeff ` diff --git a/doc/src/pair_edip.rst b/doc/src/pair_edip.rst index 7b7f5742ec..5a054621ef 100644 --- a/doc/src/pair_edip.rst +++ b/doc/src/pair_edip.rst @@ -1,19 +1,19 @@ -.. index:: pair\_style edip +.. index:: pair_style edip -pair\_style edip command -======================== +pair_style edip command +======================= -pair\_style edip/omp command -============================ +pair_style edip/omp command +=========================== -pair\_style edip/multi command -============================== +pair_style edip/multi command +============================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style @@ -22,8 +22,10 @@ Syntax Examples """""""" -pair\_style edip -pair\_coeff \* \* Si.edip Si +.. code-block:: LAMMPS + + pair_style edip + pair_coeff * * Si.edip Si Description """"""""""" @@ -43,13 +45,13 @@ In EDIP, the energy E of a system of atoms is \phi_{2}(r, Z) = & A\left[\left(\frac{B}{r}\right)^{\rho} - e^{-\beta Z^2}\right]exp{\left(\frac{\sigma}{r-a}\right)} \\ \phi_{3}(R_{ij}, R_{ik}, Z_i) = & exp{\left(\frac{\gamma}{R_{ij}-a}\right)}exp{\left(\frac{\gamma}{R_{ik}-a}\right)}h(cos\theta_{ijk},Z_i) \\ Z_i = & \sum_{m \ne i} f(R_{im}) \qquad - f(r) = \begin{cases} - 1 & \quad ra - \end{cases} \\ - h(l,Z) = & \lambda [(1-e^{-Q(Z)(l+\tau(Z))^2}) + \eta Q(Z)(l+\tau(Z))^2 ] \\ - Q(Z) = & Q_0 e^{-\mu Z} \qquad \tau(Z) = u_1 + u_2 (u_3 e^{-u_4 Z} - e^{-2u_4 Z}) + f(r) = \begin{cases} + 1 & \quad ra + \end{cases} \\ + h(l,Z) = & \lambda [(1-e^{-Q(Z)(l+\tau(Z))^2}) + \eta Q(Z)(l+\tau(Z))^2 ] \\ + Q(Z) = & Q_0 e^{-\mu Z} \qquad \tau(Z) = u_1 + u_2 (u_3 e^{-u_4 Z} - e^{-2u_4 Z}) where :math:`\phi_2` is a two-body term and :math:`\phi_3` is a diff --git a/doc/src/pair_eff.rst b/doc/src/pair_eff.rst index baf8e9bf6e..9a902054da 100644 --- a/doc/src/pair_eff.rst +++ b/doc/src/pair_eff.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style eff/cut +.. index:: pair_style eff/cut -pair\_style eff/cut command -=========================== +pair_style eff/cut command +========================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style eff/cut cutoff keyword args ... @@ -29,13 +29,13 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style eff/cut 39.7 pair_style eff/cut 40.0 limit/eradius pair_style eff/cut 40.0 limit/eradius pressure/evirials pair_style eff/cut 40.0 ecp 1 Si 3 C - pair_coeff \* \* + pair_coeff * * pair_coeff 2 2 20.0 pair_coeff 1 s 0.320852 2.283269 0.814857 pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621 @@ -100,7 +100,7 @@ given as, .. math:: -U\left(R,r,s\right) = E_{NN} \left( R \right) + E_{Ne} \left( {R,r,s} \right) + E_{ee} \left( {r,s} \right) + E_{KE} \left( {r,s} \right) + E_{PR} \left( { \uparrow \downarrow ,S} \right) + U\left(R,r,s\right) = E_{NN} \left( R \right) + E_{Ne} \left( {R,r,s} \right) + E_{ee} \left( {r,s} \right) + E_{KE} \left( {r,s} \right) + E_{PR} \left( { \uparrow \downarrow ,S} \right) The individual terms are defined as follows: @@ -224,6 +224,7 @@ representations, after the "ecp" keyword. electrons (i.e. Pauli repulsion) with one of the functional forms: .. math:: + E_{Pauli(ECP_s)} = & p_1\exp\left(-\frac{p_2r^2}{p_3+s^2} \right) \\ E_{Pauli(ECP_p)} = & p_1\left( \frac{2}{p_2/s+s/p_2} \right)\left( r-p_3s\right)^2\exp \left[ -\frac{p_4\left( r-p_3s \right)^2}{p_5+s^2} \right] diff --git a/doc/src/pair_eim.rst b/doc/src/pair_eim.rst index 7c1b4eca85..a3fee3fb96 100644 --- a/doc/src/pair_eim.rst +++ b/doc/src/pair_eim.rst @@ -1,16 +1,16 @@ -.. index:: pair\_style eim +.. index:: pair_style eim -pair\_style eim command -======================= +pair_style eim command +====================== -pair\_style eim/omp command -=========================== +pair_style eim/omp command +========================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style @@ -20,12 +20,12 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style eim - pair_coeff \* \* Na Cl ../potentials/ffield.eim Na Cl - pair_coeff \* \* Na Cl ffield.eim Na Na Na Cl - pair_coeff \* \* Na Cl ../potentials/ffield.eim Cl NULL Na + pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl + pair_coeff * * Na Cl ffield.eim Na Na Na Cl + pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na Description """"""""""" @@ -118,9 +118,9 @@ types and you want the 1st 3 to be Na, and the 4th to be Cl, you would use the following pair\_coeff command: -.. parsed-literal:: +.. code-block:: LAMMPS - pair_coeff \* \* Na Cl ffield.eim Na Na Na Cl + pair_coeff * * Na Cl ffield.eim Na Na Na Cl The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types. The filename is the EIM potential file. The Na and Cl arguments diff --git a/doc/src/pair_exp6_rx.rst b/doc/src/pair_exp6_rx.rst index d5ec1e5dc1..453f6f9aa8 100644 --- a/doc/src/pair_exp6_rx.rst +++ b/doc/src/pair_exp6_rx.rst @@ -1,16 +1,16 @@ -.. index:: pair\_style exp6/rx +.. index:: pair_style exp6/rx -pair\_style exp6/rx command -=========================== +pair_style exp6/rx command +========================== -pair\_style exp6/rx/kk command -============================== +pair_style exp6/rx/kk command +============================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style exp6/rx cutoff ... @@ -21,16 +21,16 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style exp6/rx 10.0 pair_style exp6/rx 10.0 fractional pair_style exp6/rx 10.0 molecular - pair_coeff \* \* exp6.params h2o h2o exponent 1.0 1.0 10.0 - pair_coeff \* \* exp6.params h2o 1fluid exponent 1.0 1.0 10.0 - pair_coeff \* \* exp6.params 1fluid 1fluid exponent 1.0 1.0 10.0 - pair_coeff \* \* exp6.params 1fluid 1fluid none 10.0 - pair_coeff \* \* exp6.params 1fluid 1fluid polynomial filename 10.0 + pair_coeff * * exp6.params h2o h2o exponent 1.0 1.0 10.0 + pair_coeff * * exp6.params h2o 1fluid exponent 1.0 1.0 10.0 + pair_coeff * * exp6.params 1fluid 1fluid exponent 1.0 1.0 10.0 + pair_coeff * * exp6.params 1fluid 1fluid none 10.0 + pair_coeff * * exp6.params 1fluid 1fluid polynomial filename 10.0 Description """"""""""" diff --git a/doc/src/pair_extep.rst b/doc/src/pair_extep.rst index 4564bde074..4618c44804 100644 --- a/doc/src/pair_extep.rst +++ b/doc/src/pair_extep.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style extep +.. index:: pair_style extep -pair\_style extep command -========================= +pair_style extep command +======================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style extep @@ -15,10 +15,10 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style extep - pair_coeff \* \* BN.extep B N + pair_coeff * * BN.extep B N Description """"""""""" @@ -32,7 +32,7 @@ interactions as described in :ref:`(Los2017) `. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/pair_fep_soft.rst b/doc/src/pair_fep_soft.rst index 263b52cacf..2d81628c0d 100644 --- a/doc/src/pair_fep_soft.rst +++ b/doc/src/pair_fep_soft.rst @@ -1,70 +1,70 @@ -.. index:: pair\_style lj/cut/soft +.. index:: pair_style lj/cut/soft -pair\_style lj/cut/soft command -=============================== +pair_style lj/cut/soft command +============================== -pair\_style lj/cut/soft/omp command -=================================== - -pair\_style lj/cut/coul/cut/soft command -======================================== - -pair\_style lj/cut/coul/cut/soft/omp command -============================================ - -pair\_style lj/cut/coul/long/soft command -========================================= - -pair\_style lj/cut/coul/long/soft/omp command -============================================= - -pair\_style lj/cut/tip4p/long/soft command -========================================== - -pair\_style lj/cut/tip4p/long/soft/omp command -============================================== - -pair\_style lj/charmm/coul/long/soft command -============================================ - -pair\_style lj/charmm/coul/long/soft/omp command -================================================ - -pair\_style lj/class2/soft command +pair_style lj/cut/soft/omp command ================================== -pair\_style lj/class2/coul/cut/soft command -=========================================== - -pair\_style lj/class2/coul/long/soft command -============================================ - -pair\_style coul/cut/soft command -================================= - -pair\_style coul/cut/soft/omp command -===================================== - -pair\_style coul/long/soft command -================================== - -pair\_style coul/long/soft/omp command -====================================== - -pair\_style tip4p/long/soft command -=================================== - -pair\_style tip4p/long/soft/omp command +pair_style lj/cut/coul/cut/soft command ======================================= -pair\_style morse/soft command +pair_style lj/cut/coul/cut/soft/omp command +=========================================== + +pair_style lj/cut/coul/long/soft command +======================================== + +pair_style lj/cut/coul/long/soft/omp command +============================================ + +pair_style lj/cut/tip4p/long/soft command +========================================== + +pair_style lj/cut/tip4p/long/soft/omp command +============================================== + +pair_style lj/charmm/coul/long/soft command +============================================ + +pair_style lj/charmm/coul/long/soft/omp command +================================================ + +pair_style lj/class2/soft command +================================== + +pair_style lj/class2/coul/cut/soft command +=========================================== + +pair_style lj/class2/coul/long/soft command +============================================ + +pair_style coul/cut/soft command +================================= + +pair_style coul/cut/soft/omp command +===================================== + +pair_style coul/long/soft command +================================== + +pair_style coul/long/soft/omp command +====================================== + +pair_style tip4p/long/soft command +=================================== + +pair_style tip4p/long/soft/omp command +======================================= + +pair_style morse/soft command ============================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style args @@ -128,50 +128,50 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/cut/soft 2.0 0.5 9.5 - pair_coeff \* \* 0.28 3.1 1.0 + pair_coeff * * 0.28 3.1 1.0 pair_coeff 1 1 0.28 3.1 1.0 9.5 pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 9.5 - pair_coeff \* \* 0.28 3.1 1.0 + pair_coeff * * 0.28 3.1 1.0 pair_coeff 1 1 0.28 3.1 0.5 10.0 pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5 pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 9.5 - pair_coeff \* \* 0.28 3.1 1.0 + pair_coeff * * 0.28 3.1 1.0 pair_coeff 1 1 0.28 3.1 0.0 10.0 pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5 pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5 - pair_coeff \* \* 0.155 3.1536 1.0 + pair_coeff * * 0.155 3.1536 1.0 pair_coeff 1 1 0.155 3.1536 1.0 9.5 pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0 - pair_coeff \* \* 0.28 3.1 1.0 + pair_coeff * * 0.28 3.1 1.0 pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1 pair_style lj/class2/coul/long/soft 2.0 0.5 10.0 9.5 pair_style lj/class2/coul/long/soft 2.0 0.5 10.0 9.5 9.5 - pair_coeff \* \* 0.28 3.1 1.0 + pair_coeff * * 0.28 3.1 1.0 pair_coeff 1 1 0.28 3.1 0.0 10.0 pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5 pair_style coul/long/soft 1.0 10.0 9.5 - pair_coeff \* \* 1.0 + pair_coeff * * 1.0 pair_coeff 1 1 1.0 9.5 pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 - pair_coeff \* \* 1.0 + pair_coeff * * 1.0 pair_coeff 1 1 1.0 9.5 pair_style morse/soft 4 0.9 10.0 - pair_coeff \* \* 100.0 2.0 1.5 1.0 + pair_coeff * * 100.0 2.0 1.5 1.0 pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 Description diff --git a/doc/src/pair_gauss.rst b/doc/src/pair_gauss.rst index 383a69d188..911b1c1504 100644 --- a/doc/src/pair_gauss.rst +++ b/doc/src/pair_gauss.rst @@ -1,25 +1,25 @@ -.. index:: pair\_style gauss +.. index:: pair_style gauss -pair\_style gauss command -========================= +pair_style gauss command +======================== -pair\_style gauss/gpu command -============================= +pair_style gauss/gpu command +============================ -pair\_style gauss/omp command -============================= +pair_style gauss/omp command +============================ -pair\_style gauss/cut command -============================= +pair_style gauss/cut command +============================ -pair\_style gauss/cut/omp command -================================= +pair_style gauss/cut/omp command +================================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style gauss cutoff pair_style gauss/cut cutoff @@ -30,10 +30,10 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style gauss 12.0 - pair_coeff \* \* 1.0 0.9 + pair_coeff * * 1.0 0.9 pair_coeff 1 4 1.0 0.9 10.0 pair_style gauss/cut 3.5 @@ -175,7 +175,7 @@ To print this quantity to the log file (with a descriptive column heading) the following commands could be included in an input script: -.. parsed-literal:: +.. code-block:: LAMMPS compute gauss all pair gauss variable occ equal c_gauss[1] diff --git a/doc/src/pair_gayberne.rst b/doc/src/pair_gayberne.rst index b4eff81f68..e69d30a834 100644 --- a/doc/src/pair_gayberne.rst +++ b/doc/src/pair_gayberne.rst @@ -1,22 +1,22 @@ -.. index:: pair\_style gayberne +.. index:: pair_style gayberne -pair\_style gayberne command -============================ +pair_style gayberne command +=========================== -pair\_style gayberne/gpu command -================================ +pair_style gayberne/gpu command +=============================== -pair\_style gayberne/intel command -================================== +pair_style gayberne/intel command +================================= -pair\_style gayberne/omp command -================================ +pair_style gayberne/omp command +=============================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style gayberne gamma upsilon mu cutoff @@ -29,10 +29,10 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style gayberne 1.0 1.0 1.0 10.0 - pair_coeff \* \* 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0 + pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0 Description """"""""""" diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index 2a02d221c9..3a75a410b1 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -1,31 +1,31 @@ -.. index:: pair\_style gran/hooke +.. index:: pair_style gran/hooke -pair\_style gran/hooke command -============================== +pair_style gran/hooke command +============================= -pair\_style gran/hooke/omp command -================================== +pair_style gran/hooke/omp command +================================= -pair\_style gran/hooke/history command -====================================== +pair_style gran/hooke/history command +===================================== -pair\_style gran/hooke/history/omp command -========================================== - -pair\_style gran/hooke/history/kk command +pair_style gran/hooke/history/omp command ========================================= -pair\_style gran/hertz/history command -====================================== +pair_style gran/hooke/history/kk command +======================================== -pair\_style gran/hertz/history/omp command -========================================== +pair_style gran/hertz/history command +===================================== + +pair_style gran/hertz/history/omp command +========================================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style Kn Kt gamma_n gamma_t xmu dampflag @@ -53,7 +53,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 1 pair_style gran/hooke 200000.0 70000.0 50.0 30.0 0.5 0 @@ -204,9 +204,9 @@ However you must still use the :doc:`pair_coeff ` for all pairs of granular atom types. For example the command -.. parsed-literal:: +.. code-block:: LAMMPS - pair_coeff \* \* + pair_coeff * * should be used if all atoms in the simulation interact via a granular potential (i.e. one of the pair styles above is used). If a granular diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index d8404c6e3c..6d5dfbdba8 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style granular +.. index:: pair_style granular -pair\_style granular command -============================ +pair_style granular command +=========================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style granular cutoff @@ -17,22 +17,22 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style granular - pair_coeff \* \* hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping mass_velocity + pair_coeff * * hooke 1000.0 50.0 tangential linear_nohistory 1.0 0.4 damping mass_velocity pair_style granular - pair_coeff \* \* hooke 1000.0 50.0 tangential linear_history 500.0 1.0 0.4 damping mass_velocity + pair_coeff * * hooke 1000.0 50.0 tangential linear_history 500.0 1.0 0.4 damping mass_velocity pair_style granular - pair_coeff \* \* hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4 + pair_coeff * * hertz 1000.0 50.0 tangential mindlin 1000.0 1.0 0.4 pair_style granular - pair_coeff \* \* hertz/material 1e8 0.3 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji + pair_coeff * * hertz/material 1e8 0.3 0.3 tangential mindlin_rescale NULL 1.0 0.4 damping tsuji pair_style granular - pair_coeff 1 \* jkr 1000.0 500.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall + pair_coeff 1 * jkr 1000.0 500.0 0.3 10 tangential mindlin 800.0 1.0 0.5 rolling sds 500.0 200.0 0.5 twisting marshall pair_coeff 2 2 hertz 200.0 100.0 tangential linear_history 300.0 1.0 0.1 rolling sds 200.0 100.0 0.1 twisting marshall pair_style granular diff --git a/doc/src/pair_gromacs.rst b/doc/src/pair_gromacs.rst index 723d8c6792..fd309c25a0 100644 --- a/doc/src/pair_gromacs.rst +++ b/doc/src/pair_gromacs.rst @@ -1,31 +1,31 @@ -.. index:: pair\_style lj/gromacs +.. index:: pair_style lj/gromacs -pair\_style lj/gromacs command -============================== +pair_style lj/gromacs command +============================= -pair\_style lj/gromacs/gpu command -================================== - -pair\_style lj/gromacs/kk command +pair_style lj/gromacs/gpu command ================================= -pair\_style lj/gromacs/omp command -================================== +pair_style lj/gromacs/kk command +================================ -pair\_style lj/gromacs/coul/gromacs command -=========================================== +pair_style lj/gromacs/omp command +================================= -pair\_style lj/gromacs/coul/gromacs/kk command +pair_style lj/gromacs/coul/gromacs command +========================================== + +pair_style lj/gromacs/coul/gromacs/kk command +============================================= + +pair_style lj/gromacs/coul/gromacs/omp command ============================================== -pair\_style lj/gromacs/coul/gromacs/omp command -=============================================== - Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style args @@ -45,15 +45,15 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/gromacs 9.0 12.0 - pair_coeff \* \* 100.0 2.0 + pair_coeff * * 100.0 2.0 pair_coeff 2 2 100.0 2.0 8.0 10.0 pair_style lj/gromacs/coul/gromacs 9.0 12.0 pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0 - pair_coeff \* \* 100.0 2.0 + pair_coeff * * 100.0 2.0 Description """"""""""" diff --git a/doc/src/pair_gw.rst b/doc/src/pair_gw.rst index 08d689cf27..06dfd240b3 100644 --- a/doc/src/pair_gw.rst +++ b/doc/src/pair_gw.rst @@ -1,16 +1,16 @@ -.. index:: pair\_style gw +.. index:: pair_style gw -pair\_style gw command -====================== +pair_style gw command +===================== -pair\_style gw/zbl command -========================== +pair_style gw/zbl command +========================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style @@ -19,14 +19,13 @@ Syntax Examples """""""" -pair\_style gw -pair\_coeff \* \* SiC.gw Si C C +.. code-block:: LAMMPS - -.. parsed-literal:: + pair_style gw + pair_coeff * * SiC.gw Si C C pair_style gw/zbl - pair_coeff \* \* SiC.gw.zbl C Si + pair_coeff * * SiC.gw.zbl C Si Description """"""""""" @@ -60,9 +59,9 @@ If your LAMMPS simulation has 4 atoms types and you want the first 3 to be Si, and the 4th to be C, you would use the following pair\_coeff command: -.. parsed-literal:: +.. code-block:: LAMMPS - pair_coeff \* \* SiC.gw Si Si Si C + pair_coeff * * SiC.gw Si Si Si C The first 2 arguments must be \* \* so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si diff --git a/doc/src/pair_hbond_dreiding.rst b/doc/src/pair_hbond_dreiding.rst index 5a0e2657f2..1deaf35c39 100644 --- a/doc/src/pair_hbond_dreiding.rst +++ b/doc/src/pair_hbond_dreiding.rst @@ -1,22 +1,22 @@ -.. index:: pair\_style hbond/dreiding/lj +.. index:: pair_style hbond/dreiding/lj -pair\_style hbond/dreiding/lj command -===================================== +pair_style hbond/dreiding/lj command +==================================== -pair\_style hbond/dreiding/lj/omp command -========================================= - -pair\_style hbond/dreiding/morse command +pair_style hbond/dreiding/lj/omp command ======================================== -pair\_style hbond/dreiding/morse/omp command -============================================ +pair_style hbond/dreiding/morse command +======================================= + +pair_style hbond/dreiding/morse/omp command +=========================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof @@ -31,7 +31,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90 pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0 @@ -253,7 +253,7 @@ To print these quantities to the log file (with a descriptive column heading) the following commands could be included in an input script: -.. parsed-literal:: +.. code-block:: LAMMPS compute hb all pair hbond/dreiding/lj variable n_hbond equal c_hb[1] #number hbonds diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index 747a865049..d8abec1f4a 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -1,22 +1,22 @@ -.. index:: pair\_style hybrid +.. index:: pair_style hybrid -pair\_style hybrid command -========================== +pair_style hybrid command +========================= -pair\_style hybrid/kk command -============================= +pair_style hybrid/kk command +============================ -pair\_style hybrid/overlay command -================================== +pair_style hybrid/overlay command +================================= -pair\_style hybrid/overlay/kk command -===================================== +pair_style hybrid/overlay/kk command +==================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style hybrid style1 args style2 args ... pair_style hybrid/overlay style1 args style2 args ... @@ -27,16 +27,16 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style hybrid lj/cut/coul/cut 10.0 eam lj/cut 5.0 - pair_coeff 1\*2 1\*2 eam niu3 + pair_coeff 1*2 1*2 eam niu3 pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0 - pair_coeff 1\*2 3 lj/cut 0.5 1.2 + pair_coeff 1*2 3 lj/cut 0.5 1.2 pair_style hybrid/overlay lj/cut 2.5 coul/long 2.0 - pair_coeff \* \* lj/cut 1.0 1.0 - pair_coeff \* \* coul/long + pair_coeff * * lj/cut 1.0 1.0 + pair_coeff * * coul/long Description """"""""""" @@ -101,12 +101,12 @@ are Ni atoms, type 3 are LJ atoms with charges. The following commands would set up a hybrid simulation: -.. parsed-literal:: +.. code-block:: LAMMPS pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0 - pair_coeff \* \* eam/alloy nialhjea Ni Ni NULL + pair_coeff * * eam/alloy nialhjea Ni Ni NULL pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0 - pair_coeff 1\*2 3 lj/cut 0.8 1.3 + pair_coeff 1*2 3 lj/cut 0.8 1.3 As an example of using the same pair style multiple times, consider a simulation with 2 atom types. Type 1 is Si, type 2 is C. The @@ -114,11 +114,11 @@ following commands would model the Si atoms with Tersoff, the C atoms with Tersoff, and the cross-interactions with Lennard-Jones: -.. parsed-literal:: +.. code-block:: LAMMPS pair_style hybrid lj/cut 2.5 tersoff tersoff - pair_coeff \* \* tersoff 1 Si.tersoff Si NULL - pair_coeff \* \* tersoff 2 C.tersoff NULL C + pair_coeff * * tersoff 1 Si.tersoff Si NULL + pair_coeff * * tersoff 2 C.tersoff NULL C pair_coeff 1 2 lj/cut 1.0 1.5 If pair coefficients are specified in the data file read via the @@ -159,14 +159,14 @@ normal usage of the pair\_coeff command. E.g. these two sets of commands are the same: -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/cut 2.5 - pair_coeff \* \* 1.0 1.0 + pair_coeff * * 1.0 1.0 pair_coeff 2 2 1.5 0.8 pair_style hybrid/overlay lj/cut 2.5 - pair_coeff \* \* lj/cut 1.0 1.0 + pair_coeff * * lj/cut 1.0 1.0 pair_coeff 2 2 lj/cut 1.5 0.8 Coefficients must be defined for each pair of atoms types via the @@ -190,7 +190,7 @@ LJ potential). Or, for *hybrid* and *hybrid/overlay* simulations, you can use this form of the pair\_coeff command in your input script: -.. parsed-literal:: +.. code-block:: LAMMPS pair_coeff 2 3 none @@ -230,7 +230,7 @@ setting sets the 1-4 interactions to non-zero scaling factors and then overrides them with 0.0 only for CHARMM: -.. parsed-literal:: +.. code-block:: LAMMPS special_bonds amber pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0 @@ -239,7 +239,7 @@ then overrides them with 0.0 only for CHARMM: The this input achieves the same effect: -.. parsed-literal:: +.. code-block:: LAMMPS special_bonds 0.0 0.0 0.1 pair_hybrid lj/charmm/coul/long 8.0 10.0 lj/cut/coul/long 10.0 @@ -254,7 +254,7 @@ interactions have been set to 0. Note the global settings are effectively *lj/coul 0.0 0.0 0.5* as required for OPLS/AA: -.. parsed-literal:: +.. code-block:: LAMMPS special_bonds lj/coul 1e-20 1e-20 0.5 pair_hybrid tersoff lj/cut/coul/long 12.0 @@ -323,14 +323,14 @@ surface, but not between surfaces. Then either of these two command sequences would implement that model: -.. parsed-literal:: +.. code-block:: LAMMPS pair_style hybrid tersoff - pair_coeff \* \* tersoff SiC.tersoff C C + pair_coeff * * tersoff SiC.tersoff C C pair_coeff 1 2 none pair_style tersoff - pair_coeff \* \* SiC.tersoff C C + pair_coeff * * SiC.tersoff C C neigh_modify exclude type 1 2 Either way, only neighbor lists with 1-1 or 2-2 interactions would be @@ -344,11 +344,11 @@ interactions, and AIREBO for C/C interactions. Si atoms are type 1; C atoms are type 2. Something like this will work: -.. parsed-literal:: +.. code-block:: LAMMPS pair_style hybrid/overlay tersoff airebo 3.0 - pair_coeff \* \* tersoff SiC.tersoff.custom Si C - pair_coeff \* \* airebo CH.airebo NULL C + pair_coeff * * tersoff SiC.tersoff.custom Si C + pair_coeff * * airebo CH.airebo NULL C Note that to prevent the Tersoff potential from computing C/C interactions, you would need to modify the SiC.tersoff file to turn @@ -436,4 +436,5 @@ Related commands :doc:`pair_coeff ` -**Default:** none +**Default:** +none diff --git a/doc/src/pair_ilp_graphene_hbn.rst b/doc/src/pair_ilp_graphene_hbn.rst index 5383d47573..a727d87eb6 100644 --- a/doc/src/pair_ilp_graphene_hbn.rst +++ b/doc/src/pair_ilp_graphene_hbn.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style ilp/graphene/hbn +.. index:: pair_style ilp/graphene/hbn -pair\_style ilp/graphene/hbn command -==================================== +pair_style ilp/graphene/hbn command +=================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style [hybrid/overlay ...] ilp/graphene/hbn cutoff tap_flag @@ -18,15 +18,15 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style hybrid/overlay ilp/graphene/hbn 16.0 1 - pair_coeff \* \* ilp/graphene/hbn BNCH.ILP B N C + pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0 - pair_coeff \* \* rebo CH.rebo NULL NULL C - pair_coeff \* \* tersoff BNC.tersoff B N NULL - pair_coeff \* \* ilp/graphene/hbn BNCH.ILP B N C + pair_coeff * * rebo CH.rebo NULL NULL C + pair_coeff * * tersoff BNC.tersoff B N NULL + pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C pair_coeff 1 1 coul/shield 0.70 pair_coeff 1 2 coul/shield 0.695 pair_coeff 2 2 coul/shield 0.69 @@ -42,18 +42,18 @@ in :ref:`(Kolmogorov) `. .. math:: - E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} - \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - - \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}} - \cdot \frac{C_6}{r^6_{ij}} \right \}\\ - \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\ - \rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\ - f(\rho) = & C e^{ -( \rho / \delta )^2 } \\ - {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - - 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + - 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - - 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 + E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ + V_{ij} = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} + \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - + \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}} + \cdot \frac{C_6}{r^6_{ij}} \right \}\\ + \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\ + \rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\ + f(\rho) = & C e^{ -( \rho / \delta )^2 } \\ + {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 - + 70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 + + 84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 - + 35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1 Where :math:`\mathrm{Tap}(r_{ij})` is the taper function which provides @@ -120,7 +120,7 @@ To print these quantities to the log file (with descriptive column headings) the following commands could be included in an input script: -.. parsed-literal:: +.. code-block:: LAMMPS compute 0 all pair ilp/graphene/hbn variable Evdw equal c_0[1] diff --git a/doc/src/pair_kim.rst b/doc/src/pair_kim.rst index 88a47f900a..72f4908b53 100644 --- a/doc/src/pair_kim.rst +++ b/doc/src/pair_kim.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style kim +.. index:: pair_style kim -pair\_style kim command -======================= +pair_style kim command +====================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style kim model @@ -17,10 +17,10 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005 - pair_coeff \* \* Si + pair_coeff * * Si Description """"""""""" @@ -68,9 +68,9 @@ If the LAMMPS simulation has four atom types, where the first three are Si, and the fourth is C, the following *pair\_coeff* command would be used: -.. parsed-literal:: +.. code-block:: LAMMPS - pair_coeff \* \* Si Si Si C + pair_coeff * * Si Si Si C The first two arguments must be \* \* so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1, 2, and 3 to Si as diff --git a/doc/src/pair_kolmogorov_crespi_full.rst b/doc/src/pair_kolmogorov_crespi_full.rst index 23d699a36f..d8b1f6db12 100644 --- a/doc/src/pair_kolmogorov_crespi_full.rst +++ b/doc/src/pair_kolmogorov_crespi_full.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style kolmogorov/crespi/full +.. index:: pair_style kolmogorov/crespi/full -pair\_style kolmogorov/crespi/full command -========================================== +pair_style kolmogorov/crespi/full command +========================================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag @@ -18,15 +18,15 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style hybrid/overlay kolmogorov/crespi/full 20.0 0 - pair_coeff \* \* none - pair_coeff \* \* kolmogorov/crespi/full CH.KC C C + pair_coeff * * none + pair_coeff * * kolmogorov/crespi/full CH.KC C C pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1 - pair_coeff \* \* rebo CH.rebo C H - pair_coeff \* \* kolmogorov/crespi/full CH_taper.KC C H + pair_coeff * * rebo CH.rebo C H + pair_coeff * * kolmogorov/crespi/full CH_taper.KC C H Description """"""""""" @@ -100,7 +100,7 @@ To print these quantities to the log file (with descriptive column headings) the following commands could be included in an input script: -.. parsed-literal:: +.. code-block:: LAMMPS compute 0 all pair kolmogorov/crespi/full variable Evdw equal c_0[1] diff --git a/doc/src/pair_kolmogorov_crespi_z.rst b/doc/src/pair_kolmogorov_crespi_z.rst index ea29d98e26..c697226504 100644 --- a/doc/src/pair_kolmogorov_crespi_z.rst +++ b/doc/src/pair_kolmogorov_crespi_z.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style kolmogorov/crespi/z +.. index:: pair_style kolmogorov/crespi/z -pair\_style kolmogorov/crespi/z command -======================================= +pair_style kolmogorov/crespi/z command +====================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style [hybrid/overlay ...] kolmogorov/crespi/z cutoff @@ -15,14 +15,14 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style hybrid/overlay kolmogorov/crespi/z 20.0 - pair_coeff \* \* none + pair_coeff * * none pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C pair_style hybrid/overlay rebo kolmogorov/crespi/z 14.0 - pair_coeff \* \* rebo CH.rebo C C + pair_coeff * * rebo CH.rebo C C pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C Description @@ -34,10 +34,10 @@ which is to take all normals along the z-axis. .. math:: - E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ - V_{ij} = & e^{-\lambda(r_{ij} -z_0}) \left[ C + f(\rho_{ij}) + f(\rho_{ji}) \right] - A \left( \frac{r_{ij}}{z_0}\right)^{-6} + A \left( \frac{\textrm{cutoff}}{z_0}\right)^{-6} \\ - \rho_{ij}^2 = & \rho_{ji}^2 = x_{ij}^2 + y_{ij}^2 \qquad \qquad (\mathbf{n}_i \equiv \mathbf{\hat{z}}) \\ - f(\rho) = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} \left( \rho/\delta \right)^{2n} + E = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\ + V_{ij} = & e^{-\lambda(r_{ij} -z_0}) \left[ C + f(\rho_{ij}) + f(\rho_{ji}) \right] - A \left( \frac{r_{ij}}{z_0}\right)^{-6} + A \left( \frac{\textrm{cutoff}}{z_0}\right)^{-6} \\ + \rho_{ij}^2 = & \rho_{ji}^2 = x_{ij}^2 + y_{ij}^2 \qquad \qquad (\mathbf{n}_i \equiv \mathbf{\hat{z}}) \\ + f(\rho) = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} \left( \rho/\delta \right)^{2n} diff --git a/doc/src/pair_lcbop.rst b/doc/src/pair_lcbop.rst index 5430b2dd23..f492b79919 100644 --- a/doc/src/pair_lcbop.rst +++ b/doc/src/pair_lcbop.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style lcbop +.. index:: pair_style lcbop -pair\_style lcbop command -========================= +pair_style lcbop command +======================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lcbop @@ -15,10 +15,10 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lcbop - pair_coeff \* \* ../potentials/C.lcbop C + pair_coeff * * ../potentials/C.lcbop C Description """"""""""" @@ -43,9 +43,9 @@ As an example, if your LAMMPS simulation has 4 atom types and you want the 1st 3 to be C you would use the following pair\_coeff command: -.. parsed-literal:: +.. code-block:: LAMMPS - pair_coeff \* \* C.lcbop C C C NULL + pair_coeff * * C.lcbop C C C NULL The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types. The first C argument maps LAMMPS atom type 1 to the C element in the diff --git a/doc/src/pair_lebedeva_z.rst b/doc/src/pair_lebedeva_z.rst index 20b8462825..b78a29fb54 100644 --- a/doc/src/pair_lebedeva_z.rst +++ b/doc/src/pair_lebedeva_z.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style lebedeva/z +.. index:: pair_style lebedeva/z -pair\_style lebedeva/z command -============================== +pair_style lebedeva/z command +============================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style [hybrid/overlay ...] lebedeva/z cutoff @@ -15,14 +15,14 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style hybrid/overlay lebedeva/z 20.0 - pair_coeff \* \* none + pair_coeff * * none pair_coeff 1 2 lebedeva/z CC.Lebedeva C C pair_style hybrid/overlay rebo lebedeva/z 14.0 - pair_coeff \* \* rebo CH.rebo C C + pair_coeff * * rebo CH.rebo C C pair_coeff 1 2 lebedeva/z CC.Lebedeva C C Description diff --git a/doc/src/pair_line_lj.rst b/doc/src/pair_line_lj.rst index 4c52e82b42..3840158fbc 100644 --- a/doc/src/pair_line_lj.rst +++ b/doc/src/pair_line_lj.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style line/lj +.. index:: pair_style line/lj -pair\_style line/lj command -=========================== +pair_style line/lj command +========================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style line/lj cutoff @@ -17,10 +17,10 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style line/lj 3.0 - pair_coeff \* \* 1.0 1.0 1.0 0.8 1.12 + pair_coeff * * 1.0 1.0 1.0 0.8 1.12 pair_coeff 1 2 1.0 2.0 1.0 1.5 1.12 5.0 pair_coeff 1 2 1.0 0.0 1.0 1.0 2.5 diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst index 8a719c40a4..ff1b841223 100644 --- a/doc/src/pair_lj.rst +++ b/doc/src/pair_lj.rst @@ -1,115 +1,115 @@ -.. index:: pair\_style lj/cut +.. index:: pair_style lj/cut -pair\_style lj/cut command -========================== +pair_style lj/cut command +========================= -pair\_style lj/cut/gpu command -============================== - -pair\_style lj/cut/intel command -================================ - -pair\_style lj/cut/kk command +pair_style lj/cut/gpu command ============================= -pair\_style lj/cut/opt command -============================== +pair_style lj/cut/intel command +=============================== -pair\_style lj/cut/omp command -============================== +pair_style lj/cut/kk command +============================ -pair\_style lj/cut/coul/cut command -=================================== +pair_style lj/cut/opt command +============================= -pair\_style lj/cut/coul/cut/gpu command -======================================= +pair_style lj/cut/omp command +============================= -pair\_style lj/cut/coul/cut/kk command +pair_style lj/cut/coul/cut command +================================== + +pair_style lj/cut/coul/cut/gpu command ====================================== -pair\_style lj/cut/coul/cut/omp command -======================================= - -pair\_style lj/cut/coul/debye command +pair_style lj/cut/coul/cut/kk command ===================================== -pair\_style lj/cut/coul/debye/gpu command -========================================= - -pair\_style lj/cut/coul/debye/kk command -======================================== - -pair\_style lj/cut/coul/debye/omp command -========================================= - -pair\_style lj/cut/coul/dsf command -=================================== - -pair\_style lj/cut/coul/dsf/gpu command -======================================= - -pair\_style lj/cut/coul/dsf/kk command +pair_style lj/cut/coul/cut/omp command ====================================== -pair\_style lj/cut/coul/dsf/omp command -======================================= - -pair\_style lj/cut/coul/long command +pair_style lj/cut/coul/debye command ==================================== -pair\_style lj/cut/coul/long/gpu command +pair_style lj/cut/coul/debye/gpu command ======================================== -pair\_style lj/cut/coul/long/kk command +pair_style lj/cut/coul/debye/kk command ======================================= -pair\_style lj/cut/coul/long/intel command -========================================== - -pair\_style lj/cut/coul/long/opt command +pair_style lj/cut/coul/debye/omp command ======================================== -pair\_style lj/cut/coul/long/omp command -======================================== +pair_style lj/cut/coul/dsf command +================================== -pair\_style lj/cut/coul/msm command -=================================== +pair_style lj/cut/coul/dsf/gpu command +====================================== -pair\_style lj/cut/coul/msm/gpu command -======================================= - -pair\_style lj/cut/coul/msm/omp command -======================================= - -pair\_style lj/cut/coul/wolf command -==================================== - -pair\_style lj/cut/coul/wolf/omp command -======================================== - -pair\_style lj/cut/tip4p/cut command -==================================== - -pair\_style lj/cut/tip4p/cut/omp command -======================================== - -pair\_style lj/cut/tip4p/long command +pair_style lj/cut/coul/dsf/kk command ===================================== -pair\_style lj/cut/tip4p/long/gpu command +pair_style lj/cut/coul/dsf/omp command +====================================== + +pair_style lj/cut/coul/long command +=================================== + +pair_style lj/cut/coul/long/gpu command +======================================= + +pair_style lj/cut/coul/long/kk command +====================================== + +pair_style lj/cut/coul/long/intel command ========================================= -pair\_style lj/cut/tip4p/long/omp command -========================================= +pair_style lj/cut/coul/long/opt command +======================================= -pair\_style lj/cut/tip4p/long/opt command -========================================= +pair_style lj/cut/coul/long/omp command +======================================= + +pair_style lj/cut/coul/msm command +================================== + +pair_style lj/cut/coul/msm/gpu command +====================================== + +pair_style lj/cut/coul/msm/omp command +====================================== + +pair_style lj/cut/coul/wolf command +=================================== + +pair_style lj/cut/coul/wolf/omp command +======================================= + +pair_style lj/cut/tip4p/cut command +=================================== + +pair_style lj/cut/tip4p/cut/omp command +======================================= + +pair_style lj/cut/tip4p/long command +==================================== + +pair_style lj/cut/tip4p/long/gpu command +======================================== + +pair_style lj/cut/tip4p/long/omp command +======================================== + +pair_style lj/cut/tip4p/long/opt command +======================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style args @@ -159,50 +159,50 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/cut 2.5 - pair_coeff \* \* 1 1 + pair_coeff * * 1 1 pair_coeff 1 1 1 1.1 2.8 pair_style lj/cut/coul/cut 10.0 pair_style lj/cut/coul/cut 10.0 8.0 - pair_coeff \* \* 100.0 3.0 + pair_coeff * * 100.0 3.0 pair_coeff 1 1 100.0 3.5 9.0 pair_coeff 1 1 100.0 3.5 9.0 9.0 pair_style lj/cut/coul/debye 1.5 3.0 pair_style lj/cut/coul/debye 1.5 2.5 5.0 - pair_coeff \* \* 1.0 1.0 + pair_coeff * * 1.0 1.0 pair_coeff 1 1 1.0 1.5 2.5 pair_coeff 1 1 1.0 1.5 2.5 5.0 pair_style lj/cut/coul/dsf 0.05 2.5 10.0 - pair_coeff \* \* 1.0 1.0 + pair_coeff * * 1.0 1.0 pair_coeff 1 1 1.0 1.0 2.5 pair_style lj/cut/coul/long 10.0 pair_style lj/cut/coul/long 10.0 8.0 - pair_coeff \* \* 100.0 3.0 + pair_coeff * * 100.0 3.0 pair_coeff 1 1 100.0 3.5 9.0 pair_style lj/cut/coul/msm 10.0 pair_style lj/cut/coul/msm 10.0 8.0 - pair_coeff \* \* 100.0 3.0 + pair_coeff * * 100.0 3.0 pair_coeff 1 1 100.0 3.5 9.0 pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0 - pair_coeff \* \* 100.0 3.0 + pair_coeff * * 100.0 3.0 pair_coeff 1 1 100.0 3.5 9.0 pair_style lj/cut/coul/wolf 0.2 5. 10.0 - pair_coeff \* \* 1.0 1.0 + pair_coeff * * 1.0 1.0 pair_coeff 1 1 1.0 1.0 2.5 pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0 - pair_coeff \* \* 100.0 3.0 + pair_coeff * * 100.0 3.0 pair_coeff 1 1 100.0 3.5 9.0 Description @@ -250,9 +250,9 @@ shifted force model described in :ref:`Fennell `, given by: .. math:: - E = - q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} + - \left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c + E = + q_iq_j \left[ \frac{\mbox{erfc} (\alpha r)}{r} - \frac{\mbox{erfc} (\alpha r_c)}{r_c} + + \left( \frac{\mbox{erfc} (\alpha r_c)}{r_c^2} + \frac{2\alpha}{\sqrt{\pi}}\frac{\exp (-\alpha^2 r^2_c)}{r_c} \right)(r-r_c) \right] \qquad r < r_c where :math:`\alpha` is the damping parameter and erfc() is the complementary @@ -281,10 +281,10 @@ summation method, described in :ref:`Wolf `, given by: .. math:: - E_i = \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} + - \frac{1}{2} \sum_{j \neq i} - \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c + E_i = \frac{1}{2} \sum_{j \neq i} + \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} + + \frac{1}{2} \sum_{j \neq i} + \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c where :math:`\alpha` is the damping parameter, and erfc() is the diff --git a/doc/src/pair_lj96.rst b/doc/src/pair_lj96.rst index 4874225006..2f2dcc76e4 100644 --- a/doc/src/pair_lj96.rst +++ b/doc/src/pair_lj96.rst @@ -1,19 +1,19 @@ -.. index:: pair\_style lj96/cut +.. index:: pair_style lj96/cut -pair\_style lj96/cut command -============================ +pair_style lj96/cut command +=========================== -pair\_style lj96/cut/gpu command -================================ +pair_style lj96/cut/gpu command +=============================== -pair\_style lj96/cut/omp command -================================ +pair_style lj96/cut/omp command +=============================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj96/cut cutoff @@ -23,10 +23,10 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj96/cut 2.5 - pair_coeff \* \* 1.0 1.0 4.0 + pair_coeff * * 1.0 1.0 4.0 pair_coeff 1 1 1.0 1.0 Description @@ -115,7 +115,7 @@ details. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/pair_lj_cubic.rst b/doc/src/pair_lj_cubic.rst index ea2827532b..f975a65524 100644 --- a/doc/src/pair_lj_cubic.rst +++ b/doc/src/pair_lj_cubic.rst @@ -1,19 +1,19 @@ -.. index:: pair\_style lj/cubic +.. index:: pair_style lj/cubic -pair\_style lj/cubic command -============================ +pair_style lj/cubic command +=========================== -pair\_style lj/cubic/gpu command -================================ +pair_style lj/cubic/gpu command +=============================== -pair\_style lj/cubic/omp command -================================ +pair_style lj/cubic/omp command +=============================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/cubic @@ -21,10 +21,10 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/cubic - pair_coeff \* \* 1.0 0.8908987 + pair_coeff * * 1.0 0.8908987 Description """"""""""" diff --git a/doc/src/pair_lj_expand.rst b/doc/src/pair_lj_expand.rst index 92bb1e6512..8d69c760ad 100644 --- a/doc/src/pair_lj_expand.rst +++ b/doc/src/pair_lj_expand.rst @@ -1,28 +1,28 @@ -.. index:: pair\_style lj/expand +.. index:: pair_style lj/expand -pair\_style lj/expand command -============================= +pair_style lj/expand command +============================ -pair\_style lj/expand/gpu command -================================= - -pair\_style lj/expand/kk command +pair_style lj/expand/gpu command ================================ -pair\_style lj/expand/omp command -================================= +pair_style lj/expand/kk command +=============================== -pair\_style lj/expand/coul/long command -======================================= +pair_style lj/expand/omp command +================================ -pair\_style lj/expand/coul/long/gpu command -=========================================== +pair_style lj/expand/coul/long command +====================================== + +pair_style lj/expand/coul/long/gpu command +========================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/expand cutoff @@ -32,15 +32,15 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/expand 2.5 - pair_coeff \* \* 1.0 1.0 0.5 + pair_coeff * * 1.0 1.0 0.5 pair_coeff 1 1 1.0 1.0 -0.2 2.0 pair_style lj/expand/coul/long 2.5 pair_style lj/expand/coul/long 2.5 4.0 - pair_coeff \* \* 1.0 1.0 0.5 + pair_coeff * * 1.0 1.0 0.5 pair_coeff 1 1 1.0 1.0 -0.2 3.0 Description @@ -53,9 +53,9 @@ formula: .. math:: - E = 4 \epsilon \left[ \left(\frac{\sigma}{r - \Delta}\right)^{12} - - \left(\frac{\sigma}{r - \Delta}\right)^6 \right] - \qquad r < r_c + \Delta + E = 4 \epsilon \left[ \left(\frac{\sigma}{r - \Delta}\right)^{12} - + \left(\frac{\sigma}{r - \Delta}\right)^6 \right] + \qquad r < r_c + \Delta :math:`r_c` is the cutoff which does not include the :math:`\Delta` @@ -139,7 +139,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/pair_lj_long.rst b/doc/src/pair_lj_long.rst index 748e03d559..628eb40664 100644 --- a/doc/src/pair_lj_long.rst +++ b/doc/src/pair_lj_long.rst @@ -1,28 +1,28 @@ -.. index:: pair\_style lj/long/coul/long +.. index:: pair_style lj/long/coul/long -pair\_style lj/long/coul/long command +pair_style lj/long/coul/long command +==================================== + +pair_style lj/long/coul/long/intel command +========================================== + +pair_style lj/long/coul/long/omp command +======================================== + +pair_style lj/long/coul/long/opt command +======================================== + +pair_style lj/long/tip4p/long command ===================================== -pair\_style lj/long/coul/long/intel command -=========================================== - -pair\_style lj/long/coul/long/omp command +pair_style lj/long/tip4p/long/omp command ========================================= -pair\_style lj/long/coul/long/opt command -========================================= - -pair\_style lj/long/tip4p/long command -====================================== - -pair\_style lj/long/tip4p/long/omp command -========================================== - Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style args @@ -59,17 +59,17 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/long/coul/long cut off 2.5 pair_style lj/long/coul/long cut long 2.5 4.0 pair_style lj/long/coul/long long long 2.5 4.0 - pair_coeff \* \* 1 1 + pair_coeff * * 1 1 pair_coeff 1 1 1 3 4 pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 10.0 - pair_coeff \* \* 100.0 3.0 + pair_coeff * * 100.0 3.0 pair_coeff 1 1 100.0 3.5 9.0 Description diff --git a/doc/src/pair_lj_smooth.rst b/doc/src/pair_lj_smooth.rst index c8fa9f6a6f..d4be64fcc1 100644 --- a/doc/src/pair_lj_smooth.rst +++ b/doc/src/pair_lj_smooth.rst @@ -1,16 +1,16 @@ -.. index:: pair\_style lj/smooth +.. index:: pair_style lj/smooth -pair\_style lj/smooth command -============================= +pair_style lj/smooth command +============================ -pair\_style lj/smooth/omp command -================================= +pair_style lj/smooth/omp command +================================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/smooth Rin Rc @@ -21,10 +21,10 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/smooth 8.0 10.0 - pair_coeff \* \* 10.0 1.5 + pair_coeff * * 10.0 1.5 pair_coeff 1 1 20.0 1.3 7.0 9.0 Description @@ -35,10 +35,10 @@ applied between the inner and outer cutoff. .. math:: - E & = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^6 \right] - \qquad r < r_{in} \\ - F & = C_1 + C_2 (r - r_{in}) + C_3 (r - r_{in})^2 + C_4 (r - r_{in})^3 + E & = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - + \left(\frac{\sigma}{r}\right)^6 \right] + \qquad r < r_{in} \\ + F & = C_1 + C_2 (r - r_{in}) + C_3 (r - r_{in})^2 + C_4 (r - r_{in})^3 \qquad r_{in} < r < r_c @@ -131,7 +131,7 @@ This pair style can only be used via the *pair* keyword of the Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/pair_lj_smooth_linear.rst b/doc/src/pair_lj_smooth_linear.rst index 5085199ff7..42da051b57 100644 --- a/doc/src/pair_lj_smooth_linear.rst +++ b/doc/src/pair_lj_smooth_linear.rst @@ -1,16 +1,16 @@ -.. index:: pair\_style lj/smooth/linear +.. index:: pair_style lj/smooth/linear -pair\_style lj/smooth/linear command -==================================== +pair_style lj/smooth/linear command +=================================== -pair\_style lj/smooth/linear/omp command -======================================== +pair_style lj/smooth/linear/omp command +======================================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/smooth/linear cutoff @@ -20,10 +20,10 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/smooth/linear 2.5 - pair_coeff \* \* 1.0 1.0 + pair_coeff * * 1.0 1.0 pair_coeff 1 1 0.3 3.0 9.0 Description diff --git a/doc/src/pair_lj_switch3_coulgauss_long.rst b/doc/src/pair_lj_switch3_coulgauss_long.rst index 816d6b4427..5f3a797040 100644 --- a/doc/src/pair_lj_switch3_coulgauss_long.rst +++ b/doc/src/pair_lj_switch3_coulgauss_long.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style lj/switch3/coulgauss/long +.. index:: pair_style lj/switch3/coulgauss/long -pair\_style lj/switch3/coulgauss/long command -============================================= +pair_style lj/switch3/coulgauss/long command +============================================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style args @@ -26,7 +26,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/switch3/coulgauss/long 12.0 3.0 pair_coeff 1 0.2 2.5 1.2 diff --git a/doc/src/pair_local_density.rst b/doc/src/pair_local_density.rst index 805b569ec5..ed99d03c6f 100644 --- a/doc/src/pair_local_density.rst +++ b/doc/src/pair_local_density.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style local/density +.. index:: pair_style local/density -pair\_style local/density command -================================= +pair_style local/density command +================================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style arg @@ -18,12 +18,12 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style local/density benzene_water.localdensity.table pair_style hybrid/overlay table spline 500 local/density - pair_coeff \* \* local/density benzene_water.localdensity.table + pair_coeff * * local/density benzene_water.localdensity.table Description """"""""""" diff --git a/doc/src/pair_lubricate.rst b/doc/src/pair_lubricate.rst index 496cb34610..6e2cefd091 100644 --- a/doc/src/pair_lubricate.rst +++ b/doc/src/pair_lubricate.rst @@ -1,22 +1,22 @@ -.. index:: pair\_style lubricate +.. index:: pair_style lubricate -pair\_style lubricate command -============================= +pair_style lubricate command +============================ -pair\_style lubricate/omp command +pair_style lubricate/omp command +================================ + +pair_style lubricate/poly command ================================= -pair\_style lubricate/poly command -================================== - -pair\_style lubricate/poly/omp command -====================================== +pair_style lubricate/poly/omp command +===================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style mu flaglog flagfld cutinner cutoff flagHI flagVF @@ -32,16 +32,16 @@ Syntax **Examples:** (all assume radius = 1) -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lubricate 1.5 1 1 2.01 2.5 pair_coeff 1 1 2.05 2.8 - pair_coeff \* \* + pair_coeff * * pair_style lubricate 1.5 1 1 2.01 2.5 - pair_coeff \* \* + pair_coeff * * variable mu equal ramp(1,2) - fix 1 all adapt 1 pair lubricate mu \* \* v_mu + fix 1 all adapt 1 pair lubricate mu * * v_mu Description """"""""""" diff --git a/doc/src/pair_lubricateU.rst b/doc/src/pair_lubricateU.rst index 40a1fa2a74..44eff99158 100644 --- a/doc/src/pair_lubricateU.rst +++ b/doc/src/pair_lubricateU.rst @@ -1,16 +1,16 @@ -.. index:: pair\_style lubricateU +.. index:: pair_style lubricateU -pair\_style lubricateU command -============================== +pair_style lubricateU command +============================= -pair\_style lubricateU/poly command -=================================== +pair_style lubricateU/poly command +================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style mu flaglog cutinner cutoff gdot flagHI flagVF @@ -26,11 +26,11 @@ Syntax **Examples:** (all assume radius = 1) -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lubricateU 1.5 1 2.01 2.5 0.01 1 1 pair_coeff 1 1 2.05 2.8 - pair_coeff \* \* + pair_coeff * * Description """"""""""" diff --git a/doc/src/pair_mdf.rst b/doc/src/pair_mdf.rst index 3dd336adf8..2ec6cfc0af 100644 --- a/doc/src/pair_mdf.rst +++ b/doc/src/pair_mdf.rst @@ -1,19 +1,19 @@ -.. index:: pair\_style lj/mdf +.. index:: pair_style lj/mdf -pair\_style lj/mdf command -========================== +pair_style lj/mdf command +========================= -pair\_style buck/mdf command -============================ +pair_style buck/mdf command +=========================== -pair\_style lennard/mdf command -=============================== +pair_style lennard/mdf command +============================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style args @@ -38,18 +38,18 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/mdf 2.5 3.0 - pair_coeff \* \* 1.0 1.0 + pair_coeff * * 1.0 1.0 pair_coeff 1 1 1.1 2.8 3.0 3.2 pair_style buck 2.5 3.0 - pair_coeff \* \* 100.0 1.5 200.0 - pair_coeff \* \* 100.0 1.5 200.0 3.0 3.5 + pair_coeff * * 100.0 1.5 200.0 + pair_coeff * * 100.0 1.5 200.0 3.0 3.5 pair_style lennard/mdf 2.5 3.0 - pair_coeff \* \* 1.0 1.0 + pair_coeff * * 1.0 1.0 pair_coeff 1 1 1021760.3664 2120.317338 3.0 3.2 Description diff --git a/doc/src/pair_meam_spline.rst b/doc/src/pair_meam_spline.rst index 1bbd8b2d20..7e91d6185a 100644 --- a/doc/src/pair_meam_spline.rst +++ b/doc/src/pair_meam_spline.rst @@ -1,16 +1,16 @@ -.. index:: pair\_style meam/spline +.. index:: pair_style meam/spline -pair\_style meam/spline command -=============================== +pair_style meam/spline command +============================== -pair\_style meam/spline/omp command -=================================== +pair_style meam/spline/omp command +================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style meam/spline @@ -18,11 +18,11 @@ Examples """""""" -.. parsed-literal:: +.. code:: LAMMPS pair_style meam/spline - pair_coeff \* \* Ti.meam.spline Ti - pair_coeff \* \* Ti.meam.spline Ti Ti Ti + pair_coeff * * Ti.meam.spline Ti + pair_coeff * * Ti.meam.spline Ti Ti Ti Description """"""""""" @@ -92,9 +92,9 @@ treated with this potentials, you would use the following pair\_coeff command: -.. parsed-literal:: +.. code-block:: LAMMPS - pair_coeff \* \* Ti.meam.spline Ti Ti Ti + pair_coeff * * Ti.meam.spline Ti Ti Ti The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types. The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element @@ -109,9 +109,9 @@ An example with a two component spline (new style) is TiO.meam.spline, where the command -.. parsed-literal:: +.. code-block:: LAMMPS - pair_coeff \* \* TiO.meam.spline Ti O + pair_coeff * * TiO.meam.spline Ti O will map the 1st atom type to Ti and the second atom type to O. Note in this case that the species names need to match exactly with the diff --git a/doc/src/pair_meam_sw_spline.rst b/doc/src/pair_meam_sw_spline.rst index a217d03e62..827497e1a0 100644 --- a/doc/src/pair_meam_sw_spline.rst +++ b/doc/src/pair_meam_sw_spline.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style meam/sw/spline +.. index:: pair_style meam/sw/spline -pair\_style meam/sw/spline command -================================== +pair_style meam/sw/spline command +================================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style meam/sw/spline @@ -15,11 +15,11 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style meam/sw/spline - pair_coeff \* \* Ti.meam.sw.spline Ti - pair_coeff \* \* Ti.meam.sw.spline Ti Ti Ti + pair_coeff * * Ti.meam.sw.spline Ti + pair_coeff * * Ti.meam.sw.spline Ti Ti Ti Description """"""""""" diff --git a/doc/src/pair_meamc.rst b/doc/src/pair_meamc.rst index a3def2dd68..60a6585e5b 100644 --- a/doc/src/pair_meamc.rst +++ b/doc/src/pair_meamc.rst @@ -1,27 +1,24 @@ -.. index:: pair\_style meam/c +.. index:: pair_style meam/c -pair\_style meam/c command -========================== +pair_style meam/c command +========================= Syntax """""" +.. code-block:: LAMMPS -.. parsed-literal:: - - pair_style style - -style = *meam/c* + pair_style meam/c Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style meam/c - pair_coeff \* \* ../potentials/library.meam Si ../potentials/si.meam Si - pair_coeff \* \* ../potentials/library.meam Ni Al NULL Ni Al Ni Ni + pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si + pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni Description """"""""""" @@ -48,8 +45,8 @@ given by: .. math:: - E = \sum_i \left\{ F_i(\bar{\rho}_i) - + \frac{1}{2} \sum_{i \neq j} \phi_{ij} (r_{ij}) \right\} + E = \sum_i \left\{ F_i(\bar{\rho}_i) + + \frac{1}{2} \sum_{i \neq j} \phi_{ij} (r_{ij}) \right\} where *F* is the embedding energy which is a function of the atomic @@ -94,9 +91,9 @@ LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair\_coeff command: -.. parsed-literal:: +.. code-block:: LAMMPS - pair_coeff \* \* library.meam Si C sic.meam Si Si Si C + pair_coeff * * library.meam Si C sic.meam Si Si Si C The 1st 2 arguments must be \* \* so as to span all LAMMPS atom types. The two filenames are for the library and parameter file respectively. @@ -204,9 +201,9 @@ MEAM library file numbered in the order of how those elements were selected starting from 1. Thus for the example given below -.. parsed-literal:: +.. code-block:: LAMMPS - pair_coeff \* \* library.meam Si C sic.meam Si Si Si C + pair_coeff * * library.meam Si C sic.meam Si Si Si C an index of 1 would refer to Si and an index of 2 to C. diff --git a/doc/src/pair_meso.rst b/doc/src/pair_meso.rst index 08c2d0a337..a40ae3db10 100644 --- a/doc/src/pair_meso.rst +++ b/doc/src/pair_meso.rst @@ -1,22 +1,22 @@ -.. index:: pair\_style edpd +.. index:: pair_style edpd -pair\_style edpd command -======================== +pair_style edpd command +======================= -pair\_style mdpd command -======================== +pair_style mdpd command +======================= -pair\_style mdpd/rhosum command -=============================== +pair_style mdpd/rhosum command +============================== -pair\_style tdpd command -======================== +pair_style tdpd command +======================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style args @@ -44,10 +44,10 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style edpd 1.58 9872598 - pair_coeff \* \* 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 + pair_coeff * * 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 pair_coeff 1 1 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 pair_coeff 1 1 18.75 4.5 0.41 1.58 1.42E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00 @@ -56,7 +56,7 @@ Examples pair_coeff 1 1 mdpd -40.0 25.0 18.0 1.0 0.75 pair_style tdpd 1.0 1.58 935662 - pair_coeff \* \* 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 + pair_coeff * * 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0 Description @@ -207,10 +207,10 @@ by .. math:: - Q_{ij}^D & = -\kappa_{ij} w_{DC}(r_{ij}) \left( C_i - C_j \right) \\ - Q_{ij}^R & = \epsilon_{ij}\left( C_i + C_j \right) w_{RC}(r_{ij}) \xi_{ij} \\ - w_{DC}(r_{ij}) & =w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^{\rm power\_{cc}} \\ - \epsilon_{ij}^2 & = m_s^2\kappa_{ij}\rho + Q_{ij}^D & = -\kappa_{ij} w_{DC}(r_{ij}) \left( C_i - C_j \right) \\ + Q_{ij}^R & = \epsilon_{ij}\left( C_i + C_j \right) w_{RC}(r_{ij}) \xi_{ij} \\ + w_{DC}(r_{ij}) & =w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^{\rm power\_{cc}} \\ + \epsilon_{ij}^2 & = m_s^2\kappa_{ij}\rho where the parameters kappa and epsilon determine the strength of the Fickian and random fluxes. :math:`m_s` is the mass of a single solute diff --git a/doc/src/pair_mesocnt.rst b/doc/src/pair_mesocnt.rst index 41c47fc957..4aea500e79 100644 --- a/doc/src/pair_mesocnt.rst +++ b/doc/src/pair_mesocnt.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style mesocnt +.. index:: pair_style mesocnt -pair\_style mesocnt command -=========================== +pair_style mesocnt command +========================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style mesocnt @@ -15,10 +15,10 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style mesocnt - pair_coeff \* \* 10_10.cnt + pair_coeff * * 10_10.cnt Description """"""""""" diff --git a/doc/src/pair_mgpt.rst b/doc/src/pair_mgpt.rst index 53531289e3..3d33d7da26 100644 --- a/doc/src/pair_mgpt.rst +++ b/doc/src/pair_mgpt.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style mgpt +.. index:: pair_style mgpt -pair\_style mgpt command -======================== +pair_style mgpt command +======================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style mgpt @@ -15,14 +15,14 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style mgpt - pair_coeff \* \* Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega + pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin - pair_coeff \* \* parmin potin Omega volpress yes nbody 1234 precision double - pair_coeff \* \* parmin potin Omega volpress yes nbody 12 + pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double + pair_coeff * * parmin potin Omega volpress yes nbody 12 Description """"""""""" diff --git a/doc/src/pair_mie.rst b/doc/src/pair_mie.rst index ec037b8d1a..17018ddf97 100644 --- a/doc/src/pair_mie.rst +++ b/doc/src/pair_mie.rst @@ -1,16 +1,16 @@ -.. index:: pair\_style mie/cut +.. index:: pair_style mie/cut -pair\_style mie/cut command -=========================== +pair_style mie/cut command +========================== -pair\_style mie/cut/gpu command -=============================== +pair_style mie/cut/gpu command +============================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style mie/cut cutoff @@ -20,7 +20,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style mie/cut 10.0 pair_coeff 1 1 0.72 3.40 23.00 6.66 @@ -34,8 +34,8 @@ The *mie/cut* style computes the Mie potential, given by .. math:: - E = C \epsilon \left[ \left(\frac{\sigma}{r}\right)^{\gamma_{rep}} - \left(\frac{\sigma}{r}\right)^{\gamma_{att}} \right] - \qquad r < r_c + E = C \epsilon \left[ \left(\frac{\sigma}{r}\right)^{\gamma_{rep}} - \left(\frac{\sigma}{r}\right)^{\gamma_{att}} \right] + \qquad r < r_c Rc is the cutoff and C is a function that depends on the repulsive and @@ -43,7 +43,7 @@ attractive exponents, given by: .. math:: - C = \left(\frac{\gamma_{rep}}{\gamma_{rep}-\gamma_{att}}\right) \left(\frac{\gamma_{rep}}{\gamma_{att}}\right)^{\left(\frac{\gamma_{att}}{\gamma_{rep}-\gamma_{att}}\right)} + C = \left(\frac{\gamma_{rep}}{\gamma_{rep}-\gamma_{att}}\right) \left(\frac{\gamma_{rep}}{\gamma_{att}}\right)^{\left(\frac{\gamma_{att}}{\gamma_{rep}-\gamma_{att}}\right)} Note that for 12/6 exponents, C is equal to 4 and the formula is the @@ -99,7 +99,7 @@ details. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/pair_mm3_switch3_coulgauss_long.rst b/doc/src/pair_mm3_switch3_coulgauss_long.rst index da78fbad76..2b294574b1 100644 --- a/doc/src/pair_mm3_switch3_coulgauss_long.rst +++ b/doc/src/pair_mm3_switch3_coulgauss_long.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style mm3/switch3/coulgauss/long +.. index:: pair_style mm3/switch3/coulgauss/long -pair\_style mm3/switch3/coulgauss/long command +pair_style mm3/switch3/coulgauss/long command ============================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style args @@ -26,7 +26,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style mm3/switch3/coulgauss/long 12.0 3.0 pair_coeff 1 0.2 2.5 1.2 @@ -42,9 +42,9 @@ vdW potential :ref:`(Allinger) ` .. math:: - E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\ - r_{v,ij} & = r_{v,i} + r_{v,j} \\ - \epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j} + E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\ + r_{v,ij} & = r_{v,i} + r_{v,j} \\ + \epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j} , which goes smoothly to zero at the cutoff r\_c as defined @@ -52,11 +52,11 @@ by the switching function .. math:: - S_3(r) = \left\lbrace \begin{array}{ll} - 1 & \quad\mathrm{if}\quad r < r_\mathrm{c} - w \\ - 3x^2 - 2x^3 & \quad\mathrm{if}\quad r < r_\mathrm{c} \quad\mathrm{with\quad} x=\frac{r_\mathrm{c} - r}{w} \\ - 0 & \quad\mathrm{if}\quad r >= r_\mathrm{c} - \end{array} \right. + S_3(r) = \left\lbrace \begin{array}{ll} + 1 & \quad\mathrm{if}\quad r < r_\mathrm{c} - w \\ + 3x^2 - 2x^3 & \quad\mathrm{if}\quad r < r_\mathrm{c} \quad\mathrm{with\quad} x=\frac{r_\mathrm{c} - r}{w} \\ + 0 & \quad\mathrm{if}\quad r >= r_\mathrm{c} + \end{array} \right. where w is the width defined in the arguments. This potential @@ -64,7 +64,7 @@ is combined with Coulomb interaction between Gaussian charge densities: .. math:: - E = \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}} + E = \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}} where :math:`q_i` and :math:`q_j` are the charges on the 2 atoms, diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst index 68ab45457c..7a7923c0cc 100644 --- a/doc/src/pair_modify.rst +++ b/doc/src/pair_modify.rst @@ -1,13 +1,13 @@ -.. index:: pair\_modify +.. index:: pair_modify -pair\_modify command -==================== +pair_modify command +=================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_modify keyword values ... @@ -44,7 +44,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_modify shift yes mix geometric pair_modify tail yes @@ -63,12 +63,12 @@ specified parameters are by default modified for all the hybrid sub-styles. .. note:: - The behavior for hybrid pair styles can be changed by using the *pair* - keyword, which allows selection of a specific sub-style to apply all - remaining keywords to. - The *special* and *compute/tally* keywords can **only** be - used in conjunction with the *pair* keyword. See further details about - these 3 keywords below. + The behavior for hybrid pair styles can be changed by using the *pair* + keyword, which allows selection of a specific sub-style to apply all + remaining keywords to. + The *special* and *compute/tally* keywords can **only** be + used in conjunction with the *pair* keyword. See further details about + these 3 keywords below. The *mix* keyword affects pair coefficients for interactions between atoms of type I and J, when I != J and the coefficients are not diff --git a/doc/src/pair_momb.rst b/doc/src/pair_momb.rst index 7a4dff52cc..81a3eb3320 100644 --- a/doc/src/pair_momb.rst +++ b/doc/src/pair_momb.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style momb +.. index:: pair_style momb -pair\_style momb command -======================== +pair_style momb command +======================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style momb cutoff s6 d @@ -19,7 +19,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style momb 12.0 0.75 20.0 pair_style hybrid/overlay eam/fs lj/charmm/coul/long 10.0 12.0 momb 12.0 0.75 20.0 morse 5.5