From 96d04b8a6c49eca290a5cf089ee8e60040e3b0fd Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 25 Feb 2020 11:29:41 -0500 Subject: [PATCH 1/3] Update LAMMPS lexer for docs --- doc/utils/sphinx-config/LAMMPSLexer.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/utils/sphinx-config/LAMMPSLexer.py b/doc/utils/sphinx-config/LAMMPSLexer.py index 6436be410d..3ff23439de 100644 --- a/doc/utils/sphinx-config/LAMMPSLexer.py +++ b/doc/utils/sphinx-config/LAMMPSLexer.py @@ -35,7 +35,7 @@ class LAMMPSLexer(RegexLexer): (r'[\w_\.\[\]]+', Name), (r'\$[\w_]+', Name.Variable), (r'\s+', Whitespace), - (r'[\+\-\*\/&=<>]', Operator), + (r'[\+\-\*\^\|\/\!%&=<>]', Operator), ], 'variable' : [ ('[^\}]+', Name.Variable), From 8e1928aa65c4c7ff5fc69604334782287afce37e Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Tue, 25 Feb 2020 14:46:22 -0500 Subject: [PATCH 2/3] First batch of index cleanup and code-blocks --- doc/src/change_box.rst | 22 +++--- doc/src/comm_modify.rst | 14 ++-- doc/src/comm_style.rst | 10 +-- doc/src/compute_modify.rst | 10 +-- doc/src/compute_smd_ulsph_num_neighs.rst | 4 +- doc/src/compute_smd_ulsph_strain.rst | 4 +- doc/src/compute_smd_ulsph_strain_rate.rst | 4 +- doc/src/compute_smd_ulsph_stress.rst | 4 +- doc/src/create_atoms.rst | 14 ++-- doc/src/create_bonds.rst | 12 +-- doc/src/create_box.rst | 10 +-- doc/src/delete_atoms.rst | 10 +-- doc/src/delete_bonds.rst | 15 ++-- doc/src/dihedral_charmm.rst | 28 +++---- doc/src/dihedral_class2.rst | 44 +++++------ doc/src/dihedral_coeff.rst | 18 ++--- doc/src/dihedral_cosine_shift_exp.rst | 16 ++-- doc/src/dihedral_fourier.rst | 20 ++--- doc/src/dihedral_harmonic.rst | 24 +++--- doc/src/dihedral_helix.rst | 18 ++--- doc/src/dihedral_hybrid.rst | 12 +-- doc/src/dihedral_multi_harmonic.rst | 16 ++-- doc/src/dihedral_nharmonic.rst | 14 ++-- doc/src/dihedral_none.rst | 10 +-- doc/src/dihedral_opls.rst | 26 +++---- doc/src/dihedral_quadratic.rst | 16 ++-- doc/src/dihedral_spherical.rst | 18 ++--- doc/src/dihedral_style.rst | 10 +-- doc/src/dihedral_table.rst | 14 ++-- doc/src/dihedral_table_cut.rst | 15 ++-- doc/src/dihedral_zero.rst | 13 ++-- doc/src/displace_atoms.rst | 10 +-- doc/src/dump_modify.rst | 34 ++++---- doc/src/dynamical_matrix.rst | 10 +-- doc/src/fix_modify.rst | 12 +-- doc/src/fix_smd_adjust_dt.rst | 10 +-- doc/src/fix_smd_integrate_tlsph.rst | 10 +-- doc/src/fix_smd_integrate_ulsph.rst | 9 +-- doc/src/fix_smd_move_triangulated_surface.rst | 16 ++-- doc/src/fix_smd_wall_surface.rst | 10 +-- doc/src/improper_class2.rst | 30 +++---- doc/src/improper_coeff.rst | 18 ++--- doc/src/improper_cossq.rst | 16 ++-- doc/src/improper_cvff.rst | 18 ++--- doc/src/improper_distance.rst | 14 ++-- doc/src/improper_distharm.rst | 16 ++-- doc/src/improper_fourier.rst | 14 ++-- doc/src/improper_harmonic.rst | 24 +++--- doc/src/improper_hybrid.rst | 10 +-- doc/src/improper_inversion_harmonic.rst | 12 +-- doc/src/improper_none.rst | 10 +-- doc/src/improper_ring.rst | 14 ++-- doc/src/improper_sqdistharm.rst | 16 ++-- doc/src/improper_style.rst | 12 +-- doc/src/improper_umbrella.rst | 18 ++--- doc/src/improper_zero.rst | 14 ++-- doc/src/kim_commands.rst | 78 +++++++++---------- doc/src/kspace_modify.rst | 13 ++-- doc/src/kspace_style.rst | 26 +++---- doc/src/min_modify.rst | 24 +++--- doc/src/min_spin.rst | 24 +++--- doc/src/min_style.rst | 15 ++-- doc/src/neigh_modify.rst | 10 +-- doc/src/pair_awpmd.rst | 12 +-- doc/src/pair_bop.rst | 14 ++-- doc/src/pair_born.rst | 64 +++++++-------- doc/src/pair_brownian.rst | 22 +++--- doc/src/pair_buck.rst | 50 ++++++------ doc/src/pair_buck6d_coul_gauss.rst | 18 ++--- doc/src/pair_buck_long.rst | 12 +-- doc/src/pair_charmm.rst | 72 ++++++++--------- doc/src/pair_class2.rst | 54 ++++++------- doc/src/pair_coeff.rst | 12 +-- doc/src/pair_colloid.rst | 20 ++--- doc/src/pair_comb.rst | 33 ++++---- doc/src/pair_cosine_squared.rst | 12 +-- doc/src/pair_smd_ulsph.rst | 18 ++--- 77 files changed, 728 insertions(+), 717 deletions(-) diff --git a/doc/src/change_box.rst b/doc/src/change_box.rst index 02f06ac681..b9bed3a0d6 100644 --- a/doc/src/change_box.rst +++ b/doc/src/change_box.rst @@ -1,13 +1,13 @@ -.. index:: change\_box +.. index:: change_box -change\_box command -=================== +change_box command +================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS change_box group-ID parameter args ... keyword args ... @@ -58,7 +58,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box change_box all x scale 1.1 y volume z volume remap @@ -114,7 +114,7 @@ new owning processors. is non-periodic and atoms extend from 0 to 20 in all dimensions: -.. parsed-literal:: +.. code-block:: LAMMPS change_box all x final -10 20 create_atoms 1 single -5 5 5 # this will fail to insert an atom @@ -195,7 +195,7 @@ style, then both it and the current keyword apply to the keyword preceding "key". I.e. this sequence of keywords is allowed: -.. parsed-literal:: +.. code-block:: LAMMPS change_box all x scale 1.1 y volume z volume @@ -207,7 +207,7 @@ If the following command is used, then the z box length will shrink by the same 1.1 factor the x box length was increased by: -.. parsed-literal:: +.. code-block:: LAMMPS change_box all x scale 1.1 z volume @@ -217,16 +217,16 @@ y,z box lengths shrink so as to keep their relative aspect ratio constant: -.. parsed-literal:: +.. code-block:: LAMMPS - change_box all"x scale 1.1 y volume z volume + change_box all x scale 1.1 y volume z volume If the following command is used, then the final box will be a factor of 10% larger in x and y, and a factor of 21% smaller in z, so as to keep the volume constant: -.. parsed-literal:: +.. code-block:: LAMMPS change_box all x scale 1.1 z volume y scale 1.1 z volume diff --git a/doc/src/comm_modify.rst b/doc/src/comm_modify.rst index 67ce65e2a9..839b179e8b 100644 --- a/doc/src/comm_modify.rst +++ b/doc/src/comm_modify.rst @@ -1,13 +1,13 @@ -.. index:: comm\_modify +.. index:: comm_modify -comm\_modify command -==================== +comm_modify command +=================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS comm_modify keyword value ... @@ -30,14 +30,14 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS comm_modify mode multi comm_modify mode multi group solvent - comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2\*4 15.0 + comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0 comm_modify vel yes comm_modify mode single cutoff 5.0 vel yes - comm_modify cutoff/multi \* 0.0 + comm_modify cutoff/multi * 0.0 Description """"""""""" diff --git a/doc/src/comm_style.rst b/doc/src/comm_style.rst index bbafa21d62..37184794c1 100644 --- a/doc/src/comm_style.rst +++ b/doc/src/comm_style.rst @@ -1,13 +1,13 @@ -.. index:: comm\_style +.. index:: comm_style -comm\_style command -=================== +comm_style command +================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS comm_style style @@ -17,7 +17,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS comm_style brick comm_style tiled diff --git a/doc/src/compute_modify.rst b/doc/src/compute_modify.rst index 723f78df9f..d857472256 100644 --- a/doc/src/compute_modify.rst +++ b/doc/src/compute_modify.rst @@ -1,13 +1,13 @@ -.. index:: compute\_modify +.. index:: compute_modify -compute\_modify command -======================= +compute_modify command +====================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute_modify compute-ID keyword value ... @@ -30,7 +30,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute_modify myTemp extra/dof 0 compute_modify newtemp dynamic/dof yes extra/dof 600 diff --git a/doc/src/compute_smd_ulsph_num_neighs.rst b/doc/src/compute_smd_ulsph_num_neighs.rst index 7652d53915..baa53f4eda 100644 --- a/doc/src/compute_smd_ulsph_num_neighs.rst +++ b/doc/src/compute_smd_ulsph_num_neighs.rst @@ -7,7 +7,7 @@ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID smd/ulsph/num/neighs @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/ulsph/num/neighs diff --git a/doc/src/compute_smd_ulsph_strain.rst b/doc/src/compute_smd_ulsph_strain.rst index a335c7add9..9f5a952778 100644 --- a/doc/src/compute_smd_ulsph_strain.rst +++ b/doc/src/compute_smd_ulsph_strain.rst @@ -7,7 +7,7 @@ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID smd/ulsph/strain @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/ulsph/strain diff --git a/doc/src/compute_smd_ulsph_strain_rate.rst b/doc/src/compute_smd_ulsph_strain_rate.rst index b4485253b2..0145e86f7e 100644 --- a/doc/src/compute_smd_ulsph_strain_rate.rst +++ b/doc/src/compute_smd_ulsph_strain_rate.rst @@ -7,7 +7,7 @@ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID smd/ulsph/strain/rate @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/ulsph/strain/rate diff --git a/doc/src/compute_smd_ulsph_stress.rst b/doc/src/compute_smd_ulsph_stress.rst index 52d3e69ec4..9295112478 100644 --- a/doc/src/compute_smd_ulsph_stress.rst +++ b/doc/src/compute_smd_ulsph_stress.rst @@ -7,7 +7,7 @@ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS compute ID group-ID smd/ulsph/stress @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all smd/ulsph/stress diff --git a/doc/src/create_atoms.rst b/doc/src/create_atoms.rst index c54fd675dc..bb3e7ba775 100644 --- a/doc/src/create_atoms.rst +++ b/doc/src/create_atoms.rst @@ -1,13 +1,13 @@ -.. index:: create\_atoms +.. index:: create_atoms -create\_atoms command +create_atoms command ===================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS create_atoms type style args keyword values ... @@ -29,7 +29,7 @@ Syntax * zero or more keyword/value pairs may be appended * keyword = *mol* or *basis* or *ratio* or *subset* or *remap* or *var* or *set* or *rotate* or *units* - .. parsed-literal:: + .. code-block:: LAMMPS *mol* value = template-ID seed template-ID = ID of molecule template specified in a separate :doc:`molecule ` command @@ -61,7 +61,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS create_atoms 1 box create_atoms 3 region regsphere basis 2 3 @@ -269,7 +269,7 @@ converts lattice spacings to distance. Click on the image for a larger version. -.. parsed-literal:: +.. code-block:: LAMMPS dimension 2 variable x equal 100 @@ -280,7 +280,7 @@ larger version. variable xx internal 0.0 variable yy internal 0.0 - variable v equal "(0.2\*v_y\*ylat \* cos(v_xx/xlat \* 2.0\*PI\*4.0/v_x) + 0.5\*v_y\*ylat - v_yy) > 0.0" + variable v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0" create_atoms 1 box var v set x xx set y yy write_dump all atom sinusoid.lammpstrj diff --git a/doc/src/create_bonds.rst b/doc/src/create_bonds.rst index 332b0ad0df..04749f0289 100644 --- a/doc/src/create_bonds.rst +++ b/doc/src/create_bonds.rst @@ -1,13 +1,13 @@ -.. index:: create\_bonds +.. index:: create_bonds -create\_bonds command -===================== +create_bonds command +==================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS create_bonds style args ... keyword value ... @@ -48,7 +48,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS create_bonds many all all 1 1.0 1.2 create_bonds many surf solvent 3 2.0 2.4 @@ -198,7 +198,7 @@ to only trigger the internal list to be created once, after the last bond (or angle, or dihedral, or improper) is added: -.. parsed-literal:: +.. code-block:: LAMMPS create_bonds single/bond 5 52 98 special no create_bonds single/bond 5 73 74 special no diff --git a/doc/src/create_box.rst b/doc/src/create_box.rst index 67690207f9..ee58323ae9 100644 --- a/doc/src/create_box.rst +++ b/doc/src/create_box.rst @@ -1,13 +1,13 @@ -.. index:: create\_box +.. index:: create_box -create\_box command -=================== +create_box command +================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS create_box N region-ID keyword value ... @@ -34,7 +34,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS create_box 2 mybox create_box 2 mybox bond/types 2 extra/bond/per/atom 1 diff --git a/doc/src/delete_atoms.rst b/doc/src/delete_atoms.rst index 97f4700612..7ad9c75550 100644 --- a/doc/src/delete_atoms.rst +++ b/doc/src/delete_atoms.rst @@ -1,13 +1,13 @@ -.. index:: delete\_atoms +.. index:: delete_atoms -delete\_atoms command -===================== +delete_atoms command +==================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS delete_atoms style args keyword value ... @@ -41,7 +41,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS delete_atoms group edge delete_atoms region sphere compress no diff --git a/doc/src/delete_bonds.rst b/doc/src/delete_bonds.rst index 11d9954647..37c52f8aff 100644 --- a/doc/src/delete_bonds.rst +++ b/doc/src/delete_bonds.rst @@ -1,19 +1,18 @@ -.. index:: delete\_bonds +.. index:: delete_bonds -delete\_bonds command -===================== +delete_bonds command +==================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS delete_bonds group-ID style arg keyword ... * group-ID = group ID -* style = *multi* or *atom* or *bond* or *angle* or *dihedral* or - *improper* or *stats* +* style = *multi* or *atom* or *bond* or *angle* or *dihedral* or *improper* or *stats* .. parsed-literal:: @@ -33,11 +32,11 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS delete_bonds frozen multi remove delete_bonds all atom 4 special - delete_bonds all bond 0\*3 special + delete_bonds all bond 0*3 special delete_bonds all stats Description diff --git a/doc/src/dihedral_charmm.rst b/doc/src/dihedral_charmm.rst index edaa22fe91..56eba0fe02 100644 --- a/doc/src/dihedral_charmm.rst +++ b/doc/src/dihedral_charmm.rst @@ -1,25 +1,25 @@ -.. index:: dihedral\_style charmm +.. index:: dihedral_style charmm -dihedral\_style charmm command -============================== +dihedral_style charmm command +============================= -dihedral\_style charmm/intel command -==================================== +dihedral_style charmm/intel command +=================================== -dihedral\_style charmm/kk command +dihedral_style charmm/kk command +================================ + +dihedral_style charmm/omp command ================================= -dihedral\_style charmm/omp command -================================== - -dihedral\_style charmmfsw command -================================= +dihedral_style charmmfsw command +================================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style style @@ -29,7 +29,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style charmm dihedral_style charmmfsw @@ -44,7 +44,7 @@ The *charmm* and *charmmfsw* dihedral styles use the potential .. math:: - E = K [ 1 + \cos (n \phi - d) ] + E = K [ 1 + \cos (n \phi - d) ] See :ref:`(MacKerell) ` for a description of the CHARMM diff --git a/doc/src/dihedral_class2.rst b/doc/src/dihedral_class2.rst index b6afa130f0..f079314129 100644 --- a/doc/src/dihedral_class2.rst +++ b/doc/src/dihedral_class2.rst @@ -1,19 +1,19 @@ -.. index:: dihedral\_style class2 +.. index:: dihedral_style class2 -dihedral\_style class2 command -============================== +dihedral_style class2 command +============================= -dihedral\_style class2/omp command -================================== - -dihedral\_style class2/kk command +dihedral_style class2/omp command ================================= +dihedral_style class2/kk command +================================ + Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style class2 @@ -21,15 +21,15 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style class2 dihedral_coeff 1 100 75 100 70 80 60 - dihedral_coeff \* mbt 3.5945 0.1704 -0.5490 1.5228 - dihedral_coeff \* ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010 + dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228 + dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010 dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270 - dihedral_coeff \* aat -13.5271 110.2453 105.1270 - dihedral_coeff \* bb13 0.0 1.0119 1.1010 + dihedral_coeff * aat -13.5271 110.2453 105.1270 + dihedral_coeff * bb13 0.0 1.0119 1.1010 Description """"""""""" @@ -38,15 +38,15 @@ The *class2* dihedral style uses the potential .. math:: - E = & E_d + E_{mbt} + E_{ebt} + E_{at} + E_{aat} + E_{bb13} \\ - E_d = & \sum_{n=1}^{3} K_n [ 1 - \cos (n \phi - \phi_n) ] \\ - E_{mbt} = & (r_{jk} - r_2) [ A_1 \cos (\phi) + A_2 \cos (2\phi) + A_3 \cos (3\phi) ] \\ - E_{ebt} = & (r_{ij} - r_1) [ B_1 \cos (\phi) + B_2 \cos (2\phi) + B_3 \cos (3\phi) ] + \\ - & (r_{kl} - r_3) [ C_1 \cos (\phi) + C_2 \cos (2\phi) + C_3 \cos (3\phi) ] \\ - E_{at} = & (\theta_{ijk} - \theta_1) [ D_1 \cos (\phi) + D_2 \cos (2\phi) + D_3 \cos (3\phi) ] + \\ - & (\theta_{jkl} - \theta_2) [ E_1 \cos (\phi) + E_2 \cos (2\phi) + E_3 \cos (3\phi) ] \\ - E_{aat} = & M (\theta_{ijk} - \theta_1) (\theta_{jkl} - \theta_2) \cos (\phi) \\ - E_{bb13} = & N (r_{ij} - r_1) (r_{kl} - r_3) + E = & E_d + E_{mbt} + E_{ebt} + E_{at} + E_{aat} + E_{bb13} \\ + E_d = & \sum_{n=1}^{3} K_n [ 1 - \cos (n \phi - \phi_n) ] \\ + E_{mbt} = & (r_{jk} - r_2) [ A_1 \cos (\phi) + A_2 \cos (2\phi) + A_3 \cos (3\phi) ] \\ + E_{ebt} = & (r_{ij} - r_1) [ B_1 \cos (\phi) + B_2 \cos (2\phi) + B_3 \cos (3\phi) ] + \\ + & (r_{kl} - r_3) [ C_1 \cos (\phi) + C_2 \cos (2\phi) + C_3 \cos (3\phi) ] \\ + E_{at} = & (\theta_{ijk} - \theta_1) [ D_1 \cos (\phi) + D_2 \cos (2\phi) + D_3 \cos (3\phi) ] + \\ + & (\theta_{jkl} - \theta_2) [ E_1 \cos (\phi) + E_2 \cos (2\phi) + E_3 \cos (3\phi) ] \\ + E_{aat} = & M (\theta_{ijk} - \theta_1) (\theta_{jkl} - \theta_2) \cos (\phi) \\ + E_{bb13} = & N (r_{ij} - r_1) (r_{kl} - r_3) where :math:`E_d` is the dihedral term, :math:`E_{mbt}` is a middle-bond-torsion term, diff --git a/doc/src/dihedral_coeff.rst b/doc/src/dihedral_coeff.rst index be455b384b..491546d9e0 100644 --- a/doc/src/dihedral_coeff.rst +++ b/doc/src/dihedral_coeff.rst @@ -1,13 +1,13 @@ -.. index:: dihedral\_coeff +.. index:: dihedral_coeff -dihedral\_coeff command -======================= +dihedral_coeff command +====================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_coeff N args @@ -18,11 +18,11 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_coeff 1 80.0 1 3 - dihedral_coeff \* 80.0 1 3 0.5 - dihedral_coeff 2\* 80.0 1 3 0.5 + dihedral_coeff * 80.0 1 3 0.5 + dihedral_coeff 2* 80.0 1 3 0.5 Description """"""""""" @@ -46,9 +46,9 @@ for the same dihedral type. For example, these commands set the coeffs for all dihedral types, then overwrite the coeffs for just dihedral type 2: -.. parsed-literal:: +.. code-block:: LAMMPS - dihedral_coeff \* 80.0 1 3 + dihedral_coeff * 80.0 1 3 dihedral_coeff 2 200.0 1 3 A line in a data file that specifies dihedral coefficients uses the exact diff --git a/doc/src/dihedral_cosine_shift_exp.rst b/doc/src/dihedral_cosine_shift_exp.rst index bba7fc376f..e866b79170 100644 --- a/doc/src/dihedral_cosine_shift_exp.rst +++ b/doc/src/dihedral_cosine_shift_exp.rst @@ -1,16 +1,16 @@ -.. index:: dihedral\_style cosine/shift/exp +.. index:: dihedral_style cosine/shift/exp -dihedral\_style cosine/shift/exp command -======================================== +dihedral_style cosine/shift/exp command +======================================= -dihedral\_style cosine/shift/exp/omp command -============================================ +dihedral_style cosine/shift/exp/omp command +=========================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style cosine/shift/exp @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style cosine/shift/exp dihedral_coeff 1 10.0 45.0 2.0 @@ -30,7 +30,7 @@ The *cosine/shift/exp* dihedral style uses the potential .. math:: - E = -U_{min}\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1} \quad\mbox{with}\quad U(\theta,\theta_0)=-0.5 \left(1+\cos(\theta-\theta_0) \right) + E = -U_{min}\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1} \quad\mbox{with}\quad U(\theta,\theta_0)=-0.5 \left(1+\cos(\theta-\theta_0) \right) where :math:`U_{min}`, :math:`\theta`, and :math:`a` are defined for diff --git a/doc/src/dihedral_fourier.rst b/doc/src/dihedral_fourier.rst index 82afbb01d8..58f7ec9cb0 100644 --- a/doc/src/dihedral_fourier.rst +++ b/doc/src/dihedral_fourier.rst @@ -1,19 +1,19 @@ -.. index:: dihedral\_style fourier +.. index:: dihedral_style fourier -dihedral\_style fourier command -=============================== +dihedral_style fourier command +============================== -dihedral\_style fourier/intel command -===================================== +dihedral_style fourier/intel command +==================================== -dihedral\_style fourier/omp command -=================================== +dihedral_style fourier/omp command +================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style fourier @@ -21,7 +21,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style fourier dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0 @@ -33,7 +33,7 @@ The *fourier* dihedral style uses the potential: .. math:: - E = \sum_{i=1,m} K_i [ 1.0 + \cos ( n_i \phi - d_i ) ] + E = \sum_{i=1,m} K_i [ 1.0 + \cos ( n_i \phi - d_i ) ] The following coefficients must be defined for each dihedral type via the diff --git a/doc/src/dihedral_harmonic.rst b/doc/src/dihedral_harmonic.rst index 981b6dda4b..665d055269 100644 --- a/doc/src/dihedral_harmonic.rst +++ b/doc/src/dihedral_harmonic.rst @@ -1,22 +1,22 @@ -.. index:: dihedral\_style harmonic +.. index:: dihedral_style harmonic -dihedral\_style harmonic command -================================ +dihedral_style harmonic command +=============================== -dihedral\_style harmonic/intel command -====================================== +dihedral_style harmonic/intel command +===================================== -dihedral\_style harmonic/kk command +dihedral_style harmonic/kk command +================================== + +dihedral_style harmonic/omp command =================================== -dihedral\_style harmonic/omp command -==================================== - Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style harmonic @@ -24,7 +24,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style harmonic dihedral_coeff 1 80.0 1 2 @@ -36,7 +36,7 @@ The *harmonic* dihedral style uses the potential .. math:: - E = K [ 1 + d \cos (n \phi) ] + E = K [ 1 + d \cos (n \phi) ] The following coefficients must be defined for each dihedral type via the diff --git a/doc/src/dihedral_helix.rst b/doc/src/dihedral_helix.rst index 82df804a81..870331944d 100644 --- a/doc/src/dihedral_helix.rst +++ b/doc/src/dihedral_helix.rst @@ -1,16 +1,16 @@ -.. index:: dihedral\_style helix +.. index:: dihedral_style helix -dihedral\_style helix command -============================= +dihedral_style helix command +============================ -dihedral\_style helix/omp command -================================= +dihedral_style helix/omp command +================================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style helix @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style helix dihedral_coeff 1 80.0 100.0 40.0 @@ -30,8 +30,8 @@ The *helix* dihedral style uses the potential .. math:: - E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] + - C [1 + \cos(\theta + \frac{\pi}{4})] + E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] + + C [1 + \cos(\theta + \frac{\pi}{4})] This coarse-grain dihedral potential is described in :ref:`(Guo) `. diff --git a/doc/src/dihedral_hybrid.rst b/doc/src/dihedral_hybrid.rst index 0aecb24d20..a2c962fab3 100644 --- a/doc/src/dihedral_hybrid.rst +++ b/doc/src/dihedral_hybrid.rst @@ -1,13 +1,13 @@ -.. index:: dihedral\_style hybrid +.. index:: dihedral_style hybrid -dihedral\_style hybrid command -============================== +dihedral_style hybrid command +============================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style hybrid style1 style2 ... @@ -17,11 +17,11 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style hybrid harmonic helix dihedral_coeff 1 harmonic 6.0 1 3 - dihedral_coeff 2\* helix 10 10 10 + dihedral_coeff 2* helix 10 10 10 Description """"""""""" diff --git a/doc/src/dihedral_multi_harmonic.rst b/doc/src/dihedral_multi_harmonic.rst index 68a24f59d6..8edd7bcd26 100644 --- a/doc/src/dihedral_multi_harmonic.rst +++ b/doc/src/dihedral_multi_harmonic.rst @@ -1,16 +1,16 @@ -.. index:: dihedral\_style multi/harmonic +.. index:: dihedral_style multi/harmonic -dihedral\_style multi/harmonic command -====================================== +dihedral_style multi/harmonic command +===================================== -dihedral\_style multi/harmonic/omp command -========================================== +dihedral_style multi/harmonic/omp command +========================================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style multi/harmonic @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style multi/harmonic dihedral_coeff 1 20 20 20 20 20 @@ -30,7 +30,7 @@ The *multi/harmonic* dihedral style uses the potential .. math:: - E = \sum_{n=1,5} A_n \cos^{n-1}(\phi) + E = \sum_{n=1,5} A_n \cos^{n-1}(\phi) The following coefficients must be defined for each dihedral type via the diff --git a/doc/src/dihedral_nharmonic.rst b/doc/src/dihedral_nharmonic.rst index 97403a3368..c34c523368 100644 --- a/doc/src/dihedral_nharmonic.rst +++ b/doc/src/dihedral_nharmonic.rst @@ -1,16 +1,16 @@ -.. index:: dihedral\_style nharmonic +.. index:: dihedral_style nharmonic -dihedral\_style nharmonic command +dihedral_style nharmonic command ================================= -dihedral\_style nharmonic/omp command +dihedral_style nharmonic/omp command ===================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style nharmonic @@ -18,10 +18,10 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style nharmonic - dihedral_coeff \* 3 10.0 20.0 30.0 + dihedral_coeff * 3 10.0 20.0 30.0 Description """"""""""" @@ -30,7 +30,7 @@ The *nharmonic* dihedral style uses the potential: .. math:: - E = \sum_{n=1,n} A_n \cos^{n-1}(\phi) + E = \sum_{n=1,n} A_n \cos^{n-1}(\phi) The following coefficients must be defined for each dihedral type via the diff --git a/doc/src/dihedral_none.rst b/doc/src/dihedral_none.rst index 1edba31372..d4520595d4 100644 --- a/doc/src/dihedral_none.rst +++ b/doc/src/dihedral_none.rst @@ -1,13 +1,13 @@ -.. index:: dihedral\_style none +.. index:: dihedral_style none -dihedral\_style none command -============================ +dihedral_style none command +=========================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style none @@ -15,7 +15,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style none diff --git a/doc/src/dihedral_opls.rst b/doc/src/dihedral_opls.rst index ef431b92d2..a22bd8b8ab 100644 --- a/doc/src/dihedral_opls.rst +++ b/doc/src/dihedral_opls.rst @@ -1,22 +1,22 @@ -.. index:: dihedral\_style opls +.. index:: dihedral_style opls -dihedral\_style opls command -============================ +dihedral_style opls command +=========================== -dihedral\_style opls/intel command -================================== +dihedral_style opls/intel command +================================= -dihedral\_style opls/kk command +dihedral_style opls/kk command +============================== + +dihedral_style opls/omp command =============================== -dihedral\_style opls/omp command -================================ - Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style opls @@ -24,7 +24,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style opls dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT @@ -38,8 +38,8 @@ The *opls* dihedral style uses the potential .. math:: - E = & \frac{1}{2} K_1 [1 + \cos(\phi)] + \frac{1}{2} K_2 [1 - \cos(2 \phi)] + \\ - & \frac{1}{2} K_3 [1 + \cos(3 \phi)] + \frac{1}{2} K_4 [1 - \cos(4 \phi)] + E = & \frac{1}{2} K_1 [1 + \cos(\phi)] + \frac{1}{2} K_2 [1 - \cos(2 \phi)] + \\ + & \frac{1}{2} K_3 [1 + \cos(3 \phi)] + \frac{1}{2} K_4 [1 - \cos(4 \phi)] Note that the usual 1/2 factor is not included in the K values. diff --git a/doc/src/dihedral_quadratic.rst b/doc/src/dihedral_quadratic.rst index 4bd425ad71..07d7eb0634 100644 --- a/doc/src/dihedral_quadratic.rst +++ b/doc/src/dihedral_quadratic.rst @@ -1,16 +1,16 @@ -.. index:: dihedral\_style quadratic +.. index:: dihedral_style quadratic -dihedral\_style quadratic command -================================= +dihedral_style quadratic command +================================ -dihedral\_style quadratic/omp command -===================================== +dihedral_style quadratic/omp command +==================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style quadratic @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style quadratic dihedral_coeff 100.0 80.0 @@ -30,7 +30,7 @@ The *quadratic* dihedral style uses the potential: .. math:: - E = K (\phi - \phi_0)^2 + E = K (\phi - \phi_0)^2 This dihedral potential can be used to keep a dihedral in a predefined diff --git a/doc/src/dihedral_spherical.rst b/doc/src/dihedral_spherical.rst index 795bd5ad4d..784a12c65e 100644 --- a/doc/src/dihedral_spherical.rst +++ b/doc/src/dihedral_spherical.rst @@ -1,13 +1,13 @@ -.. index:: dihedral\_style spherical +.. index:: dihedral_style spherical -dihedral\_style spherical command -================================= +dihedral_style spherical command +================================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style spherical @@ -15,7 +15,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0 dihedral_coeff 1 3 69.3 1 93.9 1 1 90 0 1 90 0 & @@ -32,10 +32,10 @@ The *spherical* dihedral style uses the potential: .. math:: - E(\phi,\theta_1,\theta_2) & = \sum_{i=1}^N\nolimits\ C_i\ \Phi_i(\phi)\ \Theta_{1i}(\theta_1)\ \Theta_{2i}(\theta_2) \\ - \Phi_{i}(\phi) & = u_i - \mathrm{cos}((\phi - a_i)K_i) \\ - \Theta_{1i}(\theta_1) & = v_i - \mathrm{cos}((\theta_1-b_i)L_i) \\ - \Theta_{2i}(\theta_2) & = w_i - \mathrm{cos}((\theta_2-c_i)M_i) + E(\phi,\theta_1,\theta_2) & = \sum_{i=1}^N\nolimits\ C_i\ \Phi_i(\phi)\ \Theta_{1i}(\theta_1)\ \Theta_{2i}(\theta_2) \\ + \Phi_{i}(\phi) & = u_i - \mathrm{cos}((\phi - a_i)K_i) \\ + \Theta_{1i}(\theta_1) & = v_i - \mathrm{cos}((\theta_1-b_i)L_i) \\ + \Theta_{2i}(\theta_2) & = w_i - \mathrm{cos}((\theta_2-c_i)M_i) For this dihedral style, the energy can be any function that combines the diff --git a/doc/src/dihedral_style.rst b/doc/src/dihedral_style.rst index 9091008340..59a28d034c 100644 --- a/doc/src/dihedral_style.rst +++ b/doc/src/dihedral_style.rst @@ -1,13 +1,13 @@ -.. index:: dihedral\_style +.. index:: dihedral_style -dihedral\_style command -======================= +dihedral_style command +====================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style style @@ -17,7 +17,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style harmonic dihedral_style multi/harmonic diff --git a/doc/src/dihedral_table.rst b/doc/src/dihedral_table.rst index 02a618b23b..a29e784ef5 100644 --- a/doc/src/dihedral_table.rst +++ b/doc/src/dihedral_table.rst @@ -1,16 +1,16 @@ -.. index:: dihedral\_style table +.. index:: dihedral_style table -dihedral\_style table command -============================= +dihedral_style table command +============================ -dihedral\_style table/omp command -================================= +dihedral_style table/omp command +================================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style table style Ntable @@ -21,7 +21,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style table spline 400 dihedral_style table linear 1000 diff --git a/doc/src/dihedral_table_cut.rst b/doc/src/dihedral_table_cut.rst index 529a911e0b..81ebcacaef 100644 --- a/doc/src/dihedral_table_cut.rst +++ b/doc/src/dihedral_table_cut.rst @@ -1,13 +1,13 @@ -.. index:: dihedral\_style table/cut +.. index:: dihedral_style table/cut -dihedral\_style table/cut command -================================= +dihedral_style table/cut command +================================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style table/cut style Ntable @@ -17,8 +17,7 @@ Syntax Examples """""""" - -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style table/cut spline 400 dihedral_style table/cut linear 1000 @@ -68,8 +67,8 @@ cutoff function: .. math:: - f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\ - f(\theta) & = K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2 + f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\ + f(\theta) & = K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2 The cutoff specifies an prefactor to the cutoff function. While this value diff --git a/doc/src/dihedral_zero.rst b/doc/src/dihedral_zero.rst index 38712957e8..be900ef13d 100644 --- a/doc/src/dihedral_zero.rst +++ b/doc/src/dihedral_zero.rst @@ -1,25 +1,24 @@ -.. index:: dihedral\_style zero +.. index:: dihedral_style zero -dihedral\_style zero command +dihedral_style zero command ============================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS - dihedral_style zero *nocoeff* + dihedral_style zero [nocoeff] Examples """""""" - -.. parsed-literal:: +.. code-block:: LAMMPS dihedral_style zero dihedral_style zero nocoeff - dihedral_coeff \* + dihedral_coeff * Description """"""""""" diff --git a/doc/src/displace_atoms.rst b/doc/src/displace_atoms.rst index 5d714c9625..57e6ac9986 100644 --- a/doc/src/displace_atoms.rst +++ b/doc/src/displace_atoms.rst @@ -1,13 +1,13 @@ -.. index:: displace\_atoms +.. index:: displace_atoms -displace\_atoms command -======================= +displace_atoms command +====================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS displace_atoms group-ID style args keyword value ... @@ -45,7 +45,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS displace_atoms top move 0 -5 0 units box displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5 diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 259a30d1cc..c035ea57a3 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -1,13 +1,13 @@ -.. index:: dump\_modify +.. index:: dump_modify -dump\_modify command -==================== +dump_modify command +=================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dump_modify dump-ID keyword values ... @@ -121,7 +121,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dump_modify 1 format line "%d %d %20.15g %g %g" scale yes dump_modify 1 format float %20.15g scale yes @@ -265,7 +265,7 @@ For example, the following commands will write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc: -.. parsed-literal:: +.. code-block:: LAMMPS variable s equal logfreq(10,3,10) dump 1 all atom 100 tmp.dump @@ -275,7 +275,7 @@ The following commands would write snapshots at the timesteps listed in file tmp.times: -.. parsed-literal:: +.. code-block:: LAMMPS variable f file tmp.times variable s equal next(f) @@ -372,7 +372,7 @@ settings, reverting all values to their default format. example, these commands: -.. parsed-literal:: +.. code-block:: LAMMPS compute 1 all property/local batom1 batom2 dump 1 all local 100 tmp.bonds index c_1[1] c_1[2] @@ -535,7 +535,7 @@ last snapshot. This can be accomplished with something the following commands: -.. parsed-literal:: +.. code-block:: LAMMPS variable Dhop equal 0.6 variable check atom "c_dsp[4] > v_Dhop" @@ -678,7 +678,7 @@ only dump atoms whose attribute has changed (or not changed). Three examples follow. -.. parsed-literal:: +.. code-block:: LAMMPS dump_modify ... thresh ix != LAST @@ -688,20 +688,20 @@ once and then crossed back between the two dump timesteps would not be included.) -.. parsed-literal:: +.. code-block:: LAMMPS region foo sphere 10 20 10 15 variable inregion atom rmask(foo) - dump_modify ... thresh v_inregion \|\^ LAST + dump_modify ... thresh v_inregion |^ LAST This will dump atoms which crossed the boundary of the spherical region since the last dump. -.. parsed-literal:: +.. code-block:: LAMMPS - variable charge atom "(q > 0.5) \|\| (q < -0.5)" - dump_modify ... thresh v_charge \|\^ LAST + variable charge atom "(q > 0.5) || (q < -0.5)" + dump_modify ... thresh v_charge |^ LAST This will dump atoms whose charge has changed from an absolute value less than 1/2 to greater than 1/2 (or vice versa) since the last dump. @@ -935,13 +935,13 @@ examples/pour/in.pour.2d.molecule input script for an example of how this is used. -.. parsed-literal:: +.. code-block:: LAMMPS variable colors string & "red green blue yellow white & purple pink orange lime gray" variable mol atom mol%10 - dump 1 all image 250 image.\*.jpg v_mol type & + dump 1 all image 250 image.*.jpg v_mol type & zoom 1.6 adiam 1.5 dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors} diff --git a/doc/src/dynamical_matrix.rst b/doc/src/dynamical_matrix.rst index 623ab4b4f1..b5ba6f2bf4 100644 --- a/doc/src/dynamical_matrix.rst +++ b/doc/src/dynamical_matrix.rst @@ -1,13 +1,13 @@ -.. index:: dynamical\_matrix +.. index:: dynamical_matrix -dynamical\_matrix command -========================= +dynamical_matrix command +======================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS dynamical_matrix group-ID style gamma args keyword value ... @@ -28,7 +28,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS dynamical_matrix 1 regular 0.000001 dynamical_matrix 1 eskm 0.000001 diff --git a/doc/src/fix_modify.rst b/doc/src/fix_modify.rst index 4ac460952f..02b0de3a7a 100644 --- a/doc/src/fix_modify.rst +++ b/doc/src/fix_modify.rst @@ -1,13 +1,13 @@ -.. index:: fix\_modify +.. index:: fix_modify -fix\_modify command -=================== +fix_modify command +================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS fix_modify fix-ID keyword value ... @@ -33,7 +33,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS fix_modify 3 temp myTemp press myPress fix_modify 1 energy yes @@ -154,7 +154,7 @@ will give a warning if that is the case. Restrictions """""""""""" - none +none Related commands """""""""""""""" diff --git a/doc/src/fix_smd_adjust_dt.rst b/doc/src/fix_smd_adjust_dt.rst index 4677c455f3..87e7d303b3 100644 --- a/doc/src/fix_smd_adjust_dt.rst +++ b/doc/src/fix_smd_adjust_dt.rst @@ -1,13 +1,13 @@ -.. index:: fix smd/adjust\_dt +.. index:: fix smd/adjust_dt -fix smd/adjust\_dt command -========================== +fix smd/adjust_dt command +========================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS fix ID group-ID smd/adjust_dt arg @@ -25,7 +25,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS fix 1 all smd/adjust_dt 0.1 diff --git a/doc/src/fix_smd_integrate_tlsph.rst b/doc/src/fix_smd_integrate_tlsph.rst index e153fec089..f2f10121e5 100644 --- a/doc/src/fix_smd_integrate_tlsph.rst +++ b/doc/src/fix_smd_integrate_tlsph.rst @@ -1,13 +1,13 @@ -.. index:: fix smd/integrate\_tlsph +.. index:: fix smd/integrate_tlsph -fix smd/integrate\_tlsph command -================================ +fix smd/integrate_tlsph command +=============================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS fix ID group-ID smd/integrate_tlsph keyword values @@ -26,7 +26,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS fix 1 all smd/integrate_tlsph fix 1 all smd/integrate_tlsph limit_velocity 1000 diff --git a/doc/src/fix_smd_integrate_ulsph.rst b/doc/src/fix_smd_integrate_ulsph.rst index d0fe508e4e..1bea4bfb15 100644 --- a/doc/src/fix_smd_integrate_ulsph.rst +++ b/doc/src/fix_smd_integrate_ulsph.rst @@ -1,13 +1,13 @@ -.. index:: fix smd/integrate\_ulsph +.. index:: fix smd/integrate_ulsph -fix smd/integrate\_ulsph command +fix smd/integrate_ulsph command ================================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS fix ID group-ID smd/integrate_ulsph keyword @@ -26,8 +26,7 @@ limit\_velocity values = max\_velocity Examples """""""" - -.. parsed-literal:: +.. code-block:: LAMMPS fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50 fix 1 all smd/integrate_ulsph limit_velocity 1000 diff --git a/doc/src/fix_smd_move_triangulated_surface.rst b/doc/src/fix_smd_move_triangulated_surface.rst index 56fbccf2a6..d5796e0c99 100644 --- a/doc/src/fix_smd_move_triangulated_surface.rst +++ b/doc/src/fix_smd_move_triangulated_surface.rst @@ -1,13 +1,13 @@ -.. index:: fix smd/move\_tri\_surf +.. index:: fix smd/move_tri_surf -fix smd/move\_tri\_surf command -=============================== +fix smd/move_tri_surf command +============================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS fix ID group-ID smd/move_tri_surf keyword @@ -33,11 +33,11 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS - fix 1 tool smd/move_tri_surf \*LINEAR 20 20 10 - fix 2 tool smd/move_tri_surf \*WIGGLE 20 20 10 - fix 2 tool smd/move_tri_surf \*ROTATE 0 0 0 5 2 1 + fix 1 tool smd/move_tri_surf *LINEAR 20 20 10 + fix 2 tool smd/move_tri_surf *WIGGLE 20 20 10 + fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1 Description """"""""""" diff --git a/doc/src/fix_smd_wall_surface.rst b/doc/src/fix_smd_wall_surface.rst index 713569b372..a75a75ab27 100644 --- a/doc/src/fix_smd_wall_surface.rst +++ b/doc/src/fix_smd_wall_surface.rst @@ -1,13 +1,13 @@ -.. index:: fix smd/wall\_surface +.. index:: fix smd/wall_surface -fix smd/wall\_surface command -============================= +fix smd/wall_surface command +============================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS fix ID group-ID smd/wall_surface arg type mol-ID @@ -26,7 +26,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS fix stl_surf all smd/wall_surface tool.stl 2 65535 diff --git a/doc/src/improper_class2.rst b/doc/src/improper_class2.rst index 260348a668..e2bcc3829b 100644 --- a/doc/src/improper_class2.rst +++ b/doc/src/improper_class2.rst @@ -1,19 +1,19 @@ -.. index:: improper\_style class2 +.. index:: improper_style class2 -improper\_style class2 command -============================== +improper_style class2 command +============================= -improper\_style class2/omp command -================================== - -improper\_style class2/kk command +improper_style class2/omp command ================================= +improper_style class2/kk command +================================ + Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style class2 @@ -21,11 +21,11 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style class2 improper_coeff 1 100.0 0 - improper_coeff \* aa 0.0 0.0 0.0 115.06 130.01 115.06 + improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06 Description """"""""""" @@ -34,11 +34,11 @@ The *class2* improper style uses the potential .. math:: - E = & E_i + E_{aa} \\ - E_i = & K [ \frac{\chi_{ijkl} + \chi_{kjli} + \chi_{ljik}}{3} - \chi_0 ]^2 \\ - E_{aa} = & M_1 (\theta_{ijk} - \theta_1) (\theta_{kjl} - \theta_3) + \\ - & M_2 (\theta_{ijk} - \theta_1) (\theta_{ijl} - \theta_2) + \\ - & M_3 (\theta_{ijl} - \theta_2) (\theta_{kjl} - \theta_3) + E = & E_i + E_{aa} \\ + E_i = & K [ \frac{\chi_{ijkl} + \chi_{kjli} + \chi_{ljik}}{3} - \chi_0 ]^2 \\ + E_{aa} = & M_1 (\theta_{ijk} - \theta_1) (\theta_{kjl} - \theta_3) + \\ + & M_2 (\theta_{ijk} - \theta_1) (\theta_{ijl} - \theta_2) + \\ + & M_3 (\theta_{ijl} - \theta_2) (\theta_{kjl} - \theta_3) where :math:`E_i` is the improper term and :math:`E_{aa}` is an diff --git a/doc/src/improper_coeff.rst b/doc/src/improper_coeff.rst index 6415d9d3f4..d8974a6494 100644 --- a/doc/src/improper_coeff.rst +++ b/doc/src/improper_coeff.rst @@ -1,13 +1,13 @@ -.. index:: improper\_coeff +.. index:: improper_coeff -improper\_coeff command -======================= +improper_coeff command +====================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_coeff N args @@ -18,11 +18,11 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_coeff 1 300.0 0.0 - improper_coeff \* 80.2 -1 2 - improper_coeff \*4 80.2 -1 2 + improper_coeff * 80.2 -1 2 + improper_coeff *4 80.2 -1 2 Description """"""""""" @@ -48,9 +48,9 @@ the coeffs for all improper types, then overwrite the coeffs for just improper type 2: -.. parsed-literal:: +.. code-block:: LAMMPS - improper_coeff \* 300.0 0.0 + improper_coeff * 300.0 0.0 improper_coeff 2 50.0 0.0 A line in a data file that specifies improper coefficients uses the diff --git a/doc/src/improper_cossq.rst b/doc/src/improper_cossq.rst index e8f2032d80..39a1c014dc 100644 --- a/doc/src/improper_cossq.rst +++ b/doc/src/improper_cossq.rst @@ -1,16 +1,16 @@ -.. index:: improper\_style cossq +.. index:: improper_style cossq -improper\_style cossq command -============================= +improper_style cossq command +============================ -improper\_style cossq/omp command -================================= +improper_style cossq/omp command +================================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style cossq @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style cossq improper_coeff 1 4.0 0.0 @@ -30,7 +30,7 @@ The *cossq* improper style uses the potential .. math:: - E = \frac{1}{2} K \cos^2{\left(\chi - \chi_0\right)} + E = \frac{1}{2} K \cos^2{\left(\chi - \chi_0\right)} where :math:`\chi` is the improper angle, :math:`\chi_0` is its diff --git a/doc/src/improper_cvff.rst b/doc/src/improper_cvff.rst index c1086797e2..4d1e0be059 100644 --- a/doc/src/improper_cvff.rst +++ b/doc/src/improper_cvff.rst @@ -1,19 +1,19 @@ -.. index:: improper\_style cvff +.. index:: improper_style cvff -improper\_style cvff command -============================ +improper_style cvff command +=========================== -improper\_style cvff/intel command -================================== +improper_style cvff/intel command +================================= -improper\_style cvff/omp command -================================ +improper_style cvff/omp command +=============================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style cvff @@ -21,7 +21,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style cvff improper_coeff 1 80.0 -1 4 diff --git a/doc/src/improper_distance.rst b/doc/src/improper_distance.rst index c29386e010..8917b6ed22 100644 --- a/doc/src/improper_distance.rst +++ b/doc/src/improper_distance.rst @@ -1,18 +1,20 @@ -.. index:: improper\_style distance +.. index:: improper_style distance -improper\_style distance command -================================ +improper_style distance command +=============================== Syntax """""" -improper\_style distance +.. code-block:: LAMMPS + + improper_style distance Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style distance improper_coeff 1 80.0 100.0 @@ -27,7 +29,7 @@ The *distance* improper style uses the potential E = K_2 d^2 + K_4 d^4 -where d is the distance between the central atom and the plane formed +where :math:`d` is the distance between the central atom and the plane formed by the other three atoms. If the 4 atoms in an improper quadruplet (listed in the data file read by the :doc:`read_data ` command) are ordered I,J,K,L then the I-atom is assumed to be the diff --git a/doc/src/improper_distharm.rst b/doc/src/improper_distharm.rst index 585285b88e..49c64ae133 100644 --- a/doc/src/improper_distharm.rst +++ b/doc/src/improper_distharm.rst @@ -1,18 +1,20 @@ -.. index:: improper\_style distharm +.. index:: improper_style distharm -improper\_style distharm command -================================ +improper_style distharm command +=============================== Syntax """""" -improper\_style distharm +.. code-block:: LAMMPS + + improper_style distharm Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style distharm improper_coeff 1 25.0 0.5 @@ -24,10 +26,10 @@ The *distharm* improper style uses the potential .. math:: - E = K (d - d_0)^2 + E = K (d - d_0)^2 -where d is the oriented distance between the central atom and the plane formed +where :math:`d` is the oriented distance between the central atom and the plane formed by the other three atoms. If the 4 atoms in an improper quadruplet (listed in the data file read by the :doc:`read_data ` command) are ordered I,J,K,L then the L-atom is assumed to be the diff --git a/doc/src/improper_fourier.rst b/doc/src/improper_fourier.rst index 734aa75eb9..18876e69c6 100644 --- a/doc/src/improper_fourier.rst +++ b/doc/src/improper_fourier.rst @@ -1,16 +1,16 @@ -.. index:: improper\_style fourier +.. index:: improper_style fourier -improper\_style fourier command -=============================== +improper_style fourier command +============================== -improper\_style fourier/omp command -=================================== +improper_style fourier/omp command +================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style fourier @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style fourier improper_coeff 1 100.0 0.0 1.0 0.5 1 diff --git a/doc/src/improper_harmonic.rst b/doc/src/improper_harmonic.rst index 666bd425e8..1fcaa181be 100644 --- a/doc/src/improper_harmonic.rst +++ b/doc/src/improper_harmonic.rst @@ -1,22 +1,22 @@ -.. index:: improper\_style harmonic +.. index:: improper_style harmonic -improper\_style harmonic command -================================ +improper_style harmonic command +=============================== -improper\_style harmonic/intel command -====================================== +improper_style harmonic/intel command +===================================== -improper\_style harmonic/kk command +improper_style harmonic/kk command +================================== + +improper_style harmonic/omp command =================================== -improper\_style harmonic/omp command -==================================== - Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style harmonic @@ -24,7 +24,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style harmonic improper_coeff 1 100.0 0 @@ -36,7 +36,7 @@ The *harmonic* improper style uses the potential .. math:: - E = K (\chi - \chi_0)^2 + E = K (\chi - \chi_0)^2 where :math:`\chi` is the improper angle, :math:`\chi_0` is its equilibrium diff --git a/doc/src/improper_hybrid.rst b/doc/src/improper_hybrid.rst index aac53bbb66..4696296ff5 100644 --- a/doc/src/improper_hybrid.rst +++ b/doc/src/improper_hybrid.rst @@ -1,13 +1,13 @@ -.. index:: improper\_style hybrid +.. index:: improper_style hybrid -improper\_style hybrid command -============================== +improper_style hybrid command +============================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style hybrid style1 style2 ... @@ -17,7 +17,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style hybrid harmonic helix improper_coeff 1 harmonic 120.0 30 diff --git a/doc/src/improper_inversion_harmonic.rst b/doc/src/improper_inversion_harmonic.rst index 86cdbc7c8f..f74ac78e07 100644 --- a/doc/src/improper_inversion_harmonic.rst +++ b/doc/src/improper_inversion_harmonic.rst @@ -1,13 +1,13 @@ -.. index:: improper\_style inversion/harmonic +.. index:: improper_style inversion/harmonic -improper\_style inversion/harmonic command -========================================== +improper_style inversion/harmonic command +========================================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style inversion/harmonic @@ -15,7 +15,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style inversion/harmonic improper_coeff 1 18.776340 0.000000 @@ -28,7 +28,7 @@ out-of-plane angle definition and uses an harmonic potential: .. math:: - E = K \left(\omega - \omega_0\right)^2 + E = K \left(\omega - \omega_0\right)^2 where :math:`K` is the force constant and :math:`\omega` is the angle diff --git a/doc/src/improper_none.rst b/doc/src/improper_none.rst index c194eebd0f..9037ba9892 100644 --- a/doc/src/improper_none.rst +++ b/doc/src/improper_none.rst @@ -1,13 +1,13 @@ -.. index:: improper\_style none +.. index:: improper_style none -improper\_style none command -============================ +improper_style none command +=========================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style none @@ -15,7 +15,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style none diff --git a/doc/src/improper_ring.rst b/doc/src/improper_ring.rst index 1554439380..b09e353fd1 100644 --- a/doc/src/improper_ring.rst +++ b/doc/src/improper_ring.rst @@ -1,16 +1,16 @@ -.. index:: improper\_style ring +.. index:: improper_style ring -improper\_style ring command -============================ +improper_style ring command +=========================== -improper\_style ring/omp command -================================ +improper_style ring/omp command +=============================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style ring @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style ring improper_coeff 1 8000 70.5 diff --git a/doc/src/improper_sqdistharm.rst b/doc/src/improper_sqdistharm.rst index b9bf53ba34..b883d5e4f0 100644 --- a/doc/src/improper_sqdistharm.rst +++ b/doc/src/improper_sqdistharm.rst @@ -1,18 +1,19 @@ -.. index:: improper\_style sqdistharm +.. index:: improper_style sqdistharm -improper\_style sqdistharm command -================================== +improper_style sqdistharm command +================================= Syntax """""" -improper\_style sqdistharm +.. code-block:: LAMMPS + + improper_style sqdistharm Examples """""""" - -.. parsed-literal:: +.. code-block:: LAMMPS improper_style sqdistharm improper_coeff 1 50.0 0.1 @@ -24,8 +25,7 @@ The *sqdistharm* improper style uses the potential .. math:: - E = K (d^2 - {d_0}^2)^2 - + E = K (d^2 - {d_0}^2)^2 where :math:`d` is the distance between the central atom and the plane formed by the other three atoms. If the 4 atoms in an improper quadruplet diff --git a/doc/src/improper_style.rst b/doc/src/improper_style.rst index 463e66704b..4035f763df 100644 --- a/doc/src/improper_style.rst +++ b/doc/src/improper_style.rst @@ -1,13 +1,13 @@ -.. index:: improper\_style +.. index:: improper_style -improper\_style command -======================= +improper_style command +====================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style style @@ -17,7 +17,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style harmonic improper_style cvff @@ -118,6 +118,6 @@ Default """"""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style none diff --git a/doc/src/improper_umbrella.rst b/doc/src/improper_umbrella.rst index 33f549ffc8..cc690dc3b4 100644 --- a/doc/src/improper_umbrella.rst +++ b/doc/src/improper_umbrella.rst @@ -1,16 +1,16 @@ -.. index:: improper\_style umbrella +.. index:: improper_style umbrella -improper\_style umbrella command -================================ +improper_style umbrella command +=============================== -improper\_style umbrella/omp command -==================================== +improper_style umbrella/omp command +=================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style umbrella @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style umbrella improper_coeff 1 100.0 180.0 @@ -32,8 +32,8 @@ commonly referred to as a classic inversion and used in the .. math:: - E = & \frac{1}{2}K\left( \frac{1}{\sin\omega_0}\right) ^2 \left( \cos\omega - \cos\omega_0\right) ^2 \qquad \omega_0 \neq 0^o \\ - E = & K\left( 1-cos\omega\right) \qquad \omega_0 = 0^o + E = & \frac{1}{2}K\left( \frac{1}{\sin\omega_0}\right) ^2 \left( \cos\omega - \cos\omega_0\right) ^2 \qquad \omega_0 \neq 0^o \\ + E = & K\left( 1-cos\omega\right) \qquad \omega_0 = 0^o where :math:`K` is the force constant and :math:`\omega` is the angle between the IL diff --git a/doc/src/improper_zero.rst b/doc/src/improper_zero.rst index c745b69013..d1419f7618 100644 --- a/doc/src/improper_zero.rst +++ b/doc/src/improper_zero.rst @@ -1,25 +1,25 @@ -.. index:: improper\_style zero +.. index:: improper_style zero -improper\_style zero command -============================ +improper_style zero command +=========================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS - improper_style zero *nocoeff* + improper_style zero [nocoeff] Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS improper_style zero improper_style zero nocoeff - improper_coeff \* + improper_coeff * Description """"""""""" diff --git a/doc/src/kim_commands.rst b/doc/src/kim_commands.rst index 704657bb68..aeab9fae56 100644 --- a/doc/src/kim_commands.rst +++ b/doc/src/kim_commands.rst @@ -1,22 +1,22 @@ -.. index:: kim\_init +.. index:: kim_init, kim_interactions, kim_query, kim_param -kim\_init command +kim_init command ================= -kim\_interactions command +kim_interactions command ========================= -kim\_query command +kim_query command ================== -kim\_param command +kim_param command ================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS kim_init model user_units unitarg kim_interactions typeargs @@ -56,7 +56,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal kim_interactions Si @@ -238,7 +238,7 @@ of a face-centered cubic (fcc) lattice for the Ercolessi and Adams (1994) potential for Al: -.. parsed-literal:: +.. code-block:: LAMMPS kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal boundary p p p @@ -293,15 +293,15 @@ meters, computes the total energy, and prints the cohesive energy in Joules regardless of the units of the IM. -.. parsed-literal:: +.. code-block:: LAMMPS kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 si unit_conversion_mode boundary p p p - lattice fcc 4.032e-10\*${_u_distance} + lattice fcc 4.032e-10*${_u_distance} region simbox block 0 1 0 1 0 1 units lattice create_box 1 simbox create_atoms 1 box - mass 1 4.480134e-26\*${_u_mass} + mass 1 4.480134e-26*${_u_mass} kim_interactions Al run 0 variable Ec_in_J equal (pe/count(all))/${_u_energy} @@ -320,11 +320,11 @@ dump file using the :doc:`read_dump ` command, the following can be done to convert the box and all atomic positions to the correct units: -.. parsed-literal:: +.. code-block:: LAMMPS - variable xyfinal equal xy\*${_u_distance} - variable xzfinal equal xz\*${_u_distance} - variable yzfinal equal yz\*${_u_distance} + variable xyfinal equal xy*${_u_distance} + variable xzfinal equal xz*${_u_distance} + variable yzfinal equal yz*${_u_distance} change_box all x scale ${_u_distance} & y scale ${_u_distance} & z scale ${_u_distance} & @@ -360,14 +360,14 @@ If the LAMMPS simulation has four atom types, where the first three are Si, and the fourth is C, the following *kim\_interactions* command would be used: -.. parsed-literal:: +.. code-block:: LAMMPS kim_interactions Si Si Si C Alternatively, for a model with a fixed mapping the command would be: -.. parsed-literal:: +.. code-block:: LAMMPS kim_interactions fixed_types @@ -379,7 +379,7 @@ the appropriate *pair\_coeff* command. For example, for the Ercolessi and Adams (1994) KIM PM for Al set by the following commands: -.. parsed-literal:: +.. code-block:: LAMMPS kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal ... @@ -390,10 +390,10 @@ Ercolessi and Adams (1994) KIM PM for Al set by the following commands: the *kim\_interactions* command executes the following LAMMPS input commands: -.. parsed-literal:: +.. code-block:: LAMMPS pair_style kim EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 - pair_coeff \* \* Al + pair_coeff * * Al For a KIM SM, the generated input commands may be more complex and require that LAMMPS is built with the required packages included @@ -403,7 +403,7 @@ For example, for the Strachan et al. (2003) ReaxFF SM set by the following commands: -.. parsed-literal:: +.. code-block:: LAMMPS kim_init Sim_LAMMPS_ReaxFF_StrachanVanDuinChakraborty_2003_CHNO__SM_107643900657_000 real ... @@ -414,10 +414,10 @@ set by the following commands: the *kim\_interactions* command executes the following LAMMPS input commands: -.. parsed-literal:: +.. code-block:: LAMMPS pair_style reax/c lmp_control safezone 2.0 mincap 100 - pair_coeff \* \* ffield.reax.rdx C H N O + pair_coeff * * ffield.reax.rdx C H N O fix reaxqeq all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq Note that the files *lmp\_control*, *ffield.reax.rdx* and *param.qeq* @@ -449,7 +449,7 @@ of an IM set by *kim\_init* for material properties archived in The syntax for the *kim\_query* command is as follows: -.. parsed-literal:: +.. code-block:: LAMMPS kim_query variable formatarg query_function queryargs @@ -509,7 +509,7 @@ or analysis phases of LAMMPS simulations. Some examples are given below. **Define an equilibrium fcc crystal** -.. parsed-literal:: +.. code-block:: LAMMPS kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal boundary p p p @@ -533,7 +533,7 @@ changed to: "lattice fcc ${a0}\*${\_u_distance}". **Define an equilibrium hcp crystal** -.. parsed-literal:: +.. code-block:: LAMMPS kim_init EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000 metal boundary p p p @@ -556,14 +556,14 @@ input script more readable. **Define a crystal at finite temperature accounting for thermal expansion** -.. parsed-literal:: +.. code-block:: LAMMPS kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal boundary p p p kim_query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Al"] units=["angstrom"] kim_query alpha get_linear_thermal_expansion_coefficient_cubic crystal=["fcc"] species=["Al"] units=["1/K"] temperature=[293.15] temperature_units=["K"] variable DeltaT equal 300 - lattice fcc ${a0}\*${alpha}\*${DeltaT} + lattice fcc ${a0}*${alpha}*${DeltaT} ... As in the previous example, the equilibrium lattice constant is obtained @@ -587,7 +587,7 @@ potential. **Compute defect formation energy** -.. parsed-literal:: +.. code-block:: LAMMPS kim_init EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005 metal ... @@ -595,7 +595,7 @@ potential. ... which is stored in the variable *Etot* ... kim_query Ec get_cohesive_energy_cubic crystal=["fcc"] species=["Al"] units=["eV"] - variable Eform equal ${Etot} - count(all)\*${Ec} + variable Eform equal ${Etot} - count(all)*${Ec} ... The defect formation energy *Eform* is computed by subtracting from *Etot* the @@ -654,7 +654,7 @@ for details). The syntax for the *kim\_param* command is as follows: -.. parsed-literal:: +.. code-block:: LAMMPS kim_param get param_name index_range variable formatarg kim_param set param_name index_range values @@ -715,7 +715,7 @@ clarifications are provided below. **Getting a scalar parameter** -.. parsed-literal:: +.. code-block:: LAMMPS kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal ... @@ -729,7 +729,7 @@ LAMMPS variable. **Getting multiple scalar parameters with a single call** -.. parsed-literal:: +.. code-block:: LAMMPS kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal ... @@ -744,7 +744,7 @@ There are several options when getting a range of values from a parameter determined by the *formatarg* argument. -.. parsed-literal:: +.. code-block:: LAMMPS kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal ... @@ -767,7 +767,7 @@ lambda retrieved by the *get* operation are placed in the LAMMPS variables is provided at the top of the model page. -.. parsed-literal:: +.. code-block:: LAMMPS kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal ... @@ -789,7 +789,7 @@ as shown in the example. At each iteration of the loop *LAM\_VALUE* contains the current value of lambda. -.. parsed-literal:: +.. code-block:: LAMMPS kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal ... @@ -804,7 +804,7 @@ the lambda array is appended to create the variable names. **Setting a scalar parameter** -.. parsed-literal:: +.. code-block:: LAMMPS kim_init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal ... @@ -816,7 +816,7 @@ and *set* commands work together, so that a *get* following a *set* operation will return the new value that was set. For example: -.. parsed-literal:: +.. code-block:: LAMMPS ... kim_interactions Si @@ -849,7 +849,7 @@ be used when setting parameters. **Setting a range of values of a parameter** -.. parsed-literal:: +.. code-block:: LAMMPS kim_init SW_ZhouWardMartin_2013_CdTeZnSeHgS__MO_503261197030_002 metal ... diff --git a/doc/src/kspace_modify.rst b/doc/src/kspace_modify.rst index 087466a9e1..9c692997c9 100644 --- a/doc/src/kspace_modify.rst +++ b/doc/src/kspace_modify.rst @@ -1,13 +1,13 @@ -.. index:: kspace\_modify +.. index:: kspace_modify -kspace\_modify command -====================== +kspace_modify command +===================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS kspace_modify keyword value ... @@ -62,7 +62,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS kspace_modify mesh 24 24 30 order 6 kspace_modify slab 3.0 @@ -483,7 +483,8 @@ parameters, see the :doc:`Howto dispersion ` doc page. Restrictions """""""""""" - none + +none Related commands """""""""""""""" diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst index 41a66078ae..921600a3e8 100644 --- a/doc/src/kspace_style.rst +++ b/doc/src/kspace_style.rst @@ -1,13 +1,13 @@ -.. index:: kspace\_style +.. index:: kspace_style -kspace\_style command -===================== +kspace_style command +==================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS kspace_style style value @@ -82,7 +82,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS kspace_style pppm 1.0e-4 kspace_style pppm/cg 1.0e-5 1.0e-6 @@ -94,12 +94,12 @@ Description """"""""""" Define a long-range solver for LAMMPS to use each timestep to compute -long-range Coulombic interactions or long-range 1/r\^6 interactions. +long-range Coulombic interactions or long-range :math:`1/r^6` interactions. Most of the long-range solvers perform their computation in K-space, hence the name of this command. When such a solver is used in conjunction with an appropriate pair -style, the cutoff for Coulombic or 1/r\^N interactions is effectively +style, the cutoff for Coulombic or :math:`1/r^N` interactions is effectively infinite. If the Coulombic case, this means each charge in the system interacts with charges in an infinite array of periodic images of the simulation domain. @@ -128,9 +128,9 @@ The *ewald* style performs a standard Ewald summation as described in any solid-state physics text. The *ewald/disp* style adds a long-range dispersion sum option for -1/r\^6 potentials and is useful for simulation of interfaces +:math:`1/r^6` potentials and is useful for simulation of interfaces :ref:`(Veld) `. It also performs standard Coulombic Ewald summations, -but in a more efficient manner than the *ewald* style. The 1/r\^6 +but in a more efficient manner than the *ewald* style. The :math:`1/r^6` capability means that Lennard-Jones or Buckingham potentials can be used without a cutoff, i.e. they become full long-range potentials. The *ewald/disp* style can also be used with point-dipoles, see @@ -153,8 +153,8 @@ to solve Poisson's equation on the mesh, then interpolates electric fields on the mesh points back to the atoms. It is closely related to the particle-mesh Ewald technique (PME) :ref:`(Darden) ` used in AMBER and CHARMM. The cost of traditional Ewald summation scales as -N\^(3/2) where N is the number of atoms in the system. The PPPM solver -scales as Nlog(N) due to the FFTs, so it is almost always a faster +:math:`N^{\frac{3}{2}}` where :math:`N` is the number of atoms in the system. The PPPM solver +scales as :math:`N \log{N}` due to the FFTs, so it is almost always a faster choice :ref:`(Pollock) `. The *pppm/cg* style is identical to the *pppm* style except that it @@ -244,7 +244,7 @@ The *msm* style invokes a multi-level summation method MSM solver, :ref:`(Hardy) ` or :ref:`(Hardy2) `, which maps atom charge to a 3d mesh, and uses a multi-level hierarchy of coarser and coarser meshes on which direct Coulomb solvers are done. This method does not -use FFTs and scales as N. It may therefore be faster than the other +use FFTs and scales as :math:`N`. It may therefore be faster than the other K-space solvers for relatively large problems when running on large core counts. MSM can also be used for non-periodic boundary conditions and for mixed periodic and non-periodic boundaries. @@ -466,7 +466,7 @@ Default """"""" -.. parsed-literal:: +.. code-block:: LAMMPS kspace_style none diff --git a/doc/src/min_modify.rst b/doc/src/min_modify.rst index 4714b17aa1..5628c65710 100644 --- a/doc/src/min_modify.rst +++ b/doc/src/min_modify.rst @@ -1,13 +1,13 @@ -.. index:: min\_modify +.. index:: min_modify -min\_modify command -=================== +min_modify command +================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS min_modify keyword values ... @@ -39,7 +39,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS min_modify dmax 0.2 min_modify integrator verlet tmax 4 @@ -91,20 +91,23 @@ The choice of a norm can be modified for the min styles *cg*\ , *sd*\ the 2-norm (Euclidean length) of the global force vector: .. math:: - || \vec{F} ||_{2} = \sqrt{\vec{F}_1+ \cdots + \vec{F}_N} + + || \vec{F} ||_{2} = \sqrt{\vec{F}_1+ \cdots + \vec{F}_N} The *max* norm computes the length of the 3-vector force for each atom (2-norm), and takes the maximum value of those across all atoms .. math:: - || \vec{F} ||_{max} = {\rm max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right) + + || \vec{F} ||_{max} = {\rm max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right) The *inf* norm takes the maximum component across the forces of all atoms in the system: .. math:: - || \vec{F} ||_{inf} = {\rm max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, |F_N^1|, |F_N^2|, |F_N^3|\right) + + || \vec{F} ||_{inf} = {\rm max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, |F_N^1|, |F_N^2|, |F_N^3|\right) For the min styles *spin*\ , *spin/cg* and *spin/lbfgs*\ , the force norm is replaced by the spin-torque norm. @@ -155,8 +158,9 @@ The :doc:`min_style ` *fire* is an optimized implementation of :doc:`min_style ` *fire/old*. It can however behave similarly to the *fire/old* style by using the following set of parameters: -.. parsed-literal:: - min_modify integrator eulerexplicit tmax 10.0 tmin 0.0 delaystep 5 & +.. code-block:: LAMMPS + + min_modify integrator eulerexplicit tmax 10.0 tmin 0.0 delaystep 5 & dtgrow 1.1 dtshrink 0.5 alpha0 0.1 alphashrink 0.99 & vdfmax 100000 halfstepback no initialdelay no diff --git a/doc/src/min_spin.rst b/doc/src/min_spin.rst index 7071d7e864..49db5c783a 100644 --- a/doc/src/min_spin.rst +++ b/doc/src/min_spin.rst @@ -1,19 +1,19 @@ -.. index:: min\_style spin +.. index:: min_style spin -min\_style spin command -======================= +min_style spin command +====================== -min\_style spin/cg command -========================== +min_style spin/cg command +========================= -min\_style spin/lbfgs command -============================= +min_style spin/lbfgs command +============================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS min_style spin min_style spin/cg @@ -23,7 +23,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS min_style spin/lbfgs min_modify line spin_cubic discrete_factor 10.0 @@ -38,7 +38,8 @@ Style *spin* defines a damped spin dynamics with an adaptive timestep, according to: .. math:: - \frac{d \vec{s}_{i}}{dt} = \lambda\, \vec{s}_{i} \times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right) + + \frac{d \vec{s}_{i}}{dt} = \lambda\, \vec{s}_{i} \times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right) with :math:`\lambda` a damping coefficient (similar to a Gilbert damping). :math:`\lambda` can be defined by setting the @@ -50,7 +51,8 @@ by the largest precession frequency that has to be solved in the system: .. math:: - {\Delta t}_{\rm max} = \frac{2\pi}{\kappa \left|\vec{\omega}_{\rm max} \right|} + + {\Delta t}_{\rm max} = \frac{2\pi}{\kappa \left|\vec{\omega}_{\rm max} \right|} with :math:`\left|\vec{\omega}_{\rm max}\right|` the norm of the largest precession frequency in the system (across all processes, and across all replicas if a diff --git a/doc/src/min_style.rst b/doc/src/min_style.rst index dffacab8a5..0382f0d075 100644 --- a/doc/src/min_style.rst +++ b/doc/src/min_style.rst @@ -1,13 +1,13 @@ -.. index:: min\_style +.. index:: min_style -min\_style command -================== +min_style command +================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS min_style style @@ -17,7 +17,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS min_style cg min_style spin @@ -148,7 +148,8 @@ instructions on how to use the accelerated styles effectively. Restrictions """""""""""" - none + +none Related commands """""""""""""""" @@ -159,7 +160,7 @@ Default """"""" -.. parsed-literal:: +.. code-block:: LAMMPS min_style cg diff --git a/doc/src/neigh_modify.rst b/doc/src/neigh_modify.rst index b01554402f..dbf08d6726 100644 --- a/doc/src/neigh_modify.rst +++ b/doc/src/neigh_modify.rst @@ -1,13 +1,13 @@ -.. index:: neigh\_modify +.. index:: neigh_modify -neigh\_modify command -===================== +neigh_modify command +==================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS neigh_modify keyword values ... @@ -55,7 +55,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS neigh_modify every 2 delay 10 check yes page 100000 neigh_modify exclude type 2 3 diff --git a/doc/src/pair_awpmd.rst b/doc/src/pair_awpmd.rst index baef5d7209..8e353960f0 100644 --- a/doc/src/pair_awpmd.rst +++ b/doc/src/pair_awpmd.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style awpmd/cut +.. index:: pair_style awpmd/cut -pair\_style awpmd/cut command -============================= +pair_style awpmd/cut command +============================ Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style awpmd/cut Rc keyword value ... @@ -37,11 +37,11 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style awpmd/cut -1 pair_style awpmd/cut 40.0 uhf free - pair_coeff \* \* + pair_coeff * * pair_coeff 2 2 20.0 Description diff --git a/doc/src/pair_bop.rst b/doc/src/pair_bop.rst index 08c9188a69..5cf3bbb4a8 100644 --- a/doc/src/pair_bop.rst +++ b/doc/src/pair_bop.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style bop +.. index:: pair_style bop -pair\_style bop command -======================= +pair_style bop command +====================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style bop keyword ... @@ -24,12 +24,12 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style bop - pair_coeff \* \* ../potentials/CdTe_bop Cd Te + pair_coeff * * ../potentials/CdTe_bop Cd Te pair_style bop save - pair_coeff \* \* ../potentials/CdTe.bop.table Cd Te Te + pair_coeff * * ../potentials/CdTe.bop.table Cd Te Te comm_modify cutoff 14.70 Description diff --git a/doc/src/pair_born.rst b/doc/src/pair_born.rst index c753f47b10..1e0dfc5611 100644 --- a/doc/src/pair_born.rst +++ b/doc/src/pair_born.rst @@ -1,46 +1,46 @@ -.. index:: pair\_style born +.. index:: pair_style born -pair\_style born command -======================== +pair_style born command +======================= -pair\_style born/omp command -============================ +pair_style born/omp command +=========================== -pair\_style born/gpu command -============================ +pair_style born/gpu command +=========================== -pair\_style born/coul/long command -================================== - -pair\_style born/coul/long/gpu command -====================================== - -pair\_style born/coul/long/omp command -====================================== - -pair\_style born/coul/msm command +pair_style born/coul/long command ================================= -pair\_style born/coul/msm/omp command +pair_style born/coul/long/gpu command ===================================== -pair\_style born/coul/wolf command -================================== +pair_style born/coul/long/omp command +===================================== -pair\_style born/coul/wolf/gpu command -====================================== +pair_style born/coul/msm command +================================ -pair\_style born/coul/wolf/omp command -====================================== +pair_style born/coul/msm/omp command +==================================== -pair\_style born/coul/dsf command +pair_style born/coul/wolf command ================================= +pair_style born/coul/wolf/gpu command +===================================== + +pair_style born/coul/wolf/omp command +===================================== + +pair_style born/coul/dsf command +================================ + Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style args @@ -71,29 +71,29 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style born 10.0 - pair_coeff \* \* 6.08 0.317 2.340 24.18 11.51 + pair_coeff * * 6.08 0.317 2.340 24.18 11.51 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 pair_style born/coul/long 10.0 pair_style born/coul/long 10.0 8. - pair_coeff \* \* 6.08 0.317 2.340 24.18 11.51 + pair_coeff * * 6.08 0.317 2.340 24.18 11.51 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 pair_style born/coul/msm 10.0 pair_style born/coul/msm 10.0 8.0 - pair_coeff \* \* 6.08 0.317 2.340 24.18 11.51 + pair_coeff * * 6.08 0.317 2.340 24.18 11.51 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 pair_style born/coul/wolf 0.25 10.0 pair_style born/coul/wolf 0.25 10.0 9.0 - pair_coeff \* \* 6.08 0.317 2.340 24.18 11.51 + pair_coeff * * 6.08 0.317 2.340 24.18 11.51 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 pair_style born/coul/dsf 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 Description diff --git a/doc/src/pair_brownian.rst b/doc/src/pair_brownian.rst index 3f66365fb2..24c93551cf 100644 --- a/doc/src/pair_brownian.rst +++ b/doc/src/pair_brownian.rst @@ -1,22 +1,22 @@ -.. index:: pair\_style brownian +.. index:: pair_style brownian -pair\_style brownian command -============================ +pair_style brownian command +=========================== -pair\_style brownian/omp command +pair_style brownian/omp command ================================ -pair\_style brownian/poly command -================================= +pair_style brownian/poly command +================================ -pair\_style brownian/poly/omp command -===================================== +pair_style brownian/poly/omp command +==================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style mu flaglog flagfld cutinner cutoff t_target seed flagHI flagVF @@ -35,11 +35,11 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style brownian 1.5 1 1 2.01 2.5 2.0 5878567 (assuming radius = 1) pair_coeff 1 1 2.05 2.8 - pair_coeff \* \* + pair_coeff * * Description """"""""""" diff --git a/doc/src/pair_buck.rst b/doc/src/pair_buck.rst index 127d05ccf8..7c09e7a0ed 100644 --- a/doc/src/pair_buck.rst +++ b/doc/src/pair_buck.rst @@ -1,61 +1,61 @@ -.. index:: pair\_style buck +.. index:: pair_style buck -pair\_style buck command +pair_style buck command ======================== -pair\_style buck/gpu command +pair_style buck/gpu command ============================ -pair\_style buck/intel command +pair_style buck/intel command ============================== -pair\_style buck/kk command +pair_style buck/kk command =========================== -pair\_style buck/omp command +pair_style buck/omp command ============================ -pair\_style buck/coul/cut command +pair_style buck/coul/cut command ================================= -pair\_style buck/coul/cut/gpu command +pair_style buck/coul/cut/gpu command ===================================== -pair\_style buck/coul/cut/intel command +pair_style buck/coul/cut/intel command ======================================= -pair\_style buck/coul/cut/kk command +pair_style buck/coul/cut/kk command ==================================== -pair\_style buck/coul/cut/omp command +pair_style buck/coul/cut/omp command ===================================== -pair\_style buck/coul/long command +pair_style buck/coul/long command ================================== -pair\_style buck/coul/long/gpu command +pair_style buck/coul/long/gpu command ====================================== -pair\_style buck/coul/long/intel command +pair_style buck/coul/long/intel command ======================================== -pair\_style buck/coul/long/kk command +pair_style buck/coul/long/kk command ===================================== -pair\_style buck/coul/long/omp command +pair_style buck/coul/long/omp command ====================================== -pair\_style buck/coul/msm command +pair_style buck/coul/msm command ================================= -pair\_style buck/coul/msm/omp command +pair_style buck/coul/msm/omp command ===================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style args @@ -81,26 +81,26 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style buck 2.5 - pair_coeff \* \* 100.0 1.5 200.0 - pair_coeff \* \* 100.0 1.5 200.0 3.0 + pair_coeff * * 100.0 1.5 200.0 + pair_coeff * * 100.0 1.5 200.0 3.0 pair_style buck/coul/cut 10.0 pair_style buck/coul/cut 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_coeff 1 1 100.0 1.5 200.0 9.0 8.0 pair_style buck/coul/long 10.0 pair_style buck/coul/long 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 buck/coul/msm 10.0 pair_style buck/coul/msm 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 Description diff --git a/doc/src/pair_buck6d_coul_gauss.rst b/doc/src/pair_buck6d_coul_gauss.rst index 823e615784..797f2a8cec 100644 --- a/doc/src/pair_buck6d_coul_gauss.rst +++ b/doc/src/pair_buck6d_coul_gauss.rst @@ -1,16 +1,16 @@ -.. index:: pair\_style buck6d/coul/gauss/dsf +.. index:: pair_style buck6d/coul/gauss/dsf -pair\_style buck6d/coul/gauss/dsf command +pair_style buck6d/coul/gauss/dsf command +======================================== + +pair_style buck6d/coul/gauss/long command ========================================= -pair\_style buck6d/coul/gauss/long command -========================================== - Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style args @@ -34,7 +34,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style buck6d/coul/gauss/dsf 0.9000 12.0000 pair_coeff 1 1 1030. 3.061 457.179 4.521 0.608 @@ -52,7 +52,7 @@ computes a dispersion damped Buckingham potential: .. math:: - E = A e^{-\kappa r} - \frac{C}{r^6} \cdot \frac{1}{1 + D r^{14}} \qquad r < r_c \\ + E = A e^{-\kappa r} - \frac{C}{r^6} \cdot \frac{1}{1 + D r^{14}} \qquad r < r_c \\ where A and C are a force constant, :math:`\kappa` is an ionic-pair dependent @@ -82,7 +82,7 @@ is thus evaluated as: .. math:: - E = \frac{C_{q_i q_j}}{\epsilon r_{ij}}\,\, \textrm{erf}\left(\alpha_{ij} r_{ij}\right)\quad\quad\quad r < r_c + E = \frac{C_{q_i q_j}}{\epsilon r_{ij}}\,\, \textrm{erf}\left(\alpha_{ij} r_{ij}\right)\quad\quad\quad r < r_c where C is an energy-conversion constant, :math:`q_i` and :math:`q_j` diff --git a/doc/src/pair_buck_long.rst b/doc/src/pair_buck_long.rst index fb4fa2cace..1c6701463b 100644 --- a/doc/src/pair_buck_long.rst +++ b/doc/src/pair_buck_long.rst @@ -1,16 +1,16 @@ -.. index:: pair\_style buck/long/coul/long +.. index:: pair_style buck/long/coul/long -pair\_style buck/long/coul/long command +pair_style buck/long/coul/long command ======================================= -pair\_style buck/long/coul/long/omp command +pair_style buck/long/coul/long/omp command =========================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style buck/long/coul/long flag_buck flag_coul cutoff (cutoff2) @@ -36,12 +36,12 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style buck/long/coul/long cut off 2.5 pair_style buck/long/coul/long cut long 2.5 4.0 pair_style buck/long/coul/long long long 4.0 - pair_coeff \* \* 1 1 + pair_coeff * * 1 1 pair_coeff 1 1 1 3 4 Description diff --git a/doc/src/pair_charmm.rst b/doc/src/pair_charmm.rst index f10d7a8d08..78de46d23f 100644 --- a/doc/src/pair_charmm.rst +++ b/doc/src/pair_charmm.rst @@ -1,61 +1,61 @@ -.. index:: pair\_style lj/charmm/coul/charmm +.. index:: pair_style lj/charmm/coul/charmm -pair\_style lj/charmm/coul/charmm command +pair_style lj/charmm/coul/charmm command ========================================= -pair\_style lj/charmm/coul/charmm/intel command +pair_style lj/charmm/coul/charmm/intel command =============================================== -pair\_style lj/charmm/coul/charmm/kk command +pair_style lj/charmm/coul/charmm/kk command ============================================ -pair\_style lj/charmm/coul/charmm/omp command +pair_style lj/charmm/coul/charmm/omp command ============================================= -pair\_style lj/charmm/coul/charmm/implicit command +pair_style lj/charmm/coul/charmm/implicit command ================================================== -pair\_style lj/charmm/coul/charmm/implicit/kk command +pair_style lj/charmm/coul/charmm/implicit/kk command ===================================================== -pair\_style lj/charmm/coul/charmm/implicit/omp command +pair_style lj/charmm/coul/charmm/implicit/omp command ====================================================== -pair\_style lj/charmm/coul/long command +pair_style lj/charmm/coul/long command ======================================= -pair\_style lj/charmm/coul/long/gpu command +pair_style lj/charmm/coul/long/gpu command =========================================== -pair\_style lj/charmm/coul/long/intel command +pair_style lj/charmm/coul/long/intel command ============================================= -pair\_style lj/charmm/coul/long/kk command +pair_style lj/charmm/coul/long/kk command ========================================== -pair\_style lj/charmm/coul/long/opt command +pair_style lj/charmm/coul/long/opt command =========================================== -pair\_style lj/charmm/coul/long/omp command +pair_style lj/charmm/coul/long/omp command =========================================== -pair\_style lj/charmm/coul/msm command +pair_style lj/charmm/coul/msm command ====================================== -pair\_style lj/charmm/coul/msm/omp command +pair_style lj/charmm/coul/msm/omp command ========================================== -pair\_style lj/charmmfsw/coul/charmmfsh command +pair_style lj/charmmfsw/coul/charmmfsh command =============================================== -pair\_style lj/charmmfsw/coul/long command +pair_style lj/charmmfsw/coul/long command ========================================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style args @@ -88,30 +88,30 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/charmm/coul/charmm 8.0 10.0 pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0 pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0 pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0 9.0 - pair_coeff \* \* 100.0 2.0 + pair_coeff * * 100.0 2.0 pair_coeff 1 1 100.0 2.0 150.0 3.5 pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0 - pair_coeff \* \* 100.0 2.0 + pair_coeff * * 100.0 2.0 pair_coeff 1 1 100.0 2.0 150.0 3.5 pair_style lj/charmm/coul/long 8.0 10.0 pair_style lj/charmm/coul/long 8.0 10.0 9.0 pair_style lj/charmmfsw/coul/long 8.0 10.0 pair_style lj/charmmfsw/coul/long 8.0 10.0 9.0 - pair_coeff \* \* 100.0 2.0 + pair_coeff * * 100.0 2.0 pair_coeff 1 1 100.0 2.0 150.0 3.5 pair_style lj/charmm/coul/msm 8.0 10.0 pair_style lj/charmm/coul/msm 8.0 10.0 9.0 - pair_coeff \* \* 100.0 2.0 + pair_coeff * * 100.0 2.0 pair_coeff 1 1 100.0 2.0 150.0 3.5 Description @@ -162,18 +162,18 @@ artifacts. .. math:: - E = & LJ(r) \qquad \qquad \qquad r < r_{\rm in} \\ - = & S(r) * LJ(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\ - = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\ - E = & C(r) \qquad \qquad \qquad r < r_{\rm in} \\ - = & S(r) * C(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\ - = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\ - LJ(r) = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - - \left(\frac{\sigma}{r}\right)^6 \right] \\ - C(r) = & \frac{C q_i q_j}{ \epsilon r} \\ - S(r) = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2 - \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]} - { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 } + E = & LJ(r) \qquad \qquad \qquad r < r_{\rm in} \\ + = & S(r) * LJ(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\ + = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\ + E = & C(r) \qquad \qquad \qquad r < r_{\rm in} \\ + = & S(r) * C(r) \qquad \qquad r_{\rm in} < r < r_{\rm out} \\ + = & 0 \qquad \qquad \qquad \qquad r > r_{\rm out} \\ + LJ(r) = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - + \left(\frac{\sigma}{r}\right)^6 \right] \\ + C(r) = & \frac{C q_i q_j}{ \epsilon r} \\ + S(r) = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2 + \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]} + { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 } where S(r) is the energy switching function mentioned above for the diff --git a/doc/src/pair_class2.rst b/doc/src/pair_class2.rst index b2bd1e10be..3b005ed517 100644 --- a/doc/src/pair_class2.rst +++ b/doc/src/pair_class2.rst @@ -1,43 +1,43 @@ -.. index:: pair\_style lj/class2 +.. index:: pair_style lj/class2 -pair\_style lj/class2 command -============================= +pair_style lj/class2 command +============================ -pair\_style lj/class2/gpu command -================================= - -pair\_style lj/class2/kk command +pair_style lj/class2/gpu command ================================ -pair\_style lj/class2/omp command -================================= +pair_style lj/class2/kk command +=============================== -pair\_style lj/class2/coul/cut command -====================================== +pair_style lj/class2/omp command +================================ -pair\_style lj/class2/coul/cut/kk command +pair_style lj/class2/coul/cut command +===================================== + +pair_style lj/class2/coul/cut/kk command +======================================== + +pair_style lj/class2/coul/cut/omp command ========================================= -pair\_style lj/class2/coul/cut/omp command +pair_style lj/class2/coul/long command +====================================== + +pair_style lj/class2/coul/long/gpu command ========================================== -pair\_style lj/class2/coul/long command -======================================= +pair_style lj/class2/coul/long/kk command +========================================= -pair\_style lj/class2/coul/long/gpu command -=========================================== - -pair\_style lj/class2/coul/long/kk command +pair_style lj/class2/coul/long/omp command ========================================== -pair\_style lj/class2/coul/long/omp command -=========================================== - Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style style args @@ -60,7 +60,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style lj/class2 10.0 pair_coeff \* \* 100.0 2.5 @@ -84,9 +84,9 @@ The *lj/class2* styles compute a 6/9 Lennard-Jones potential given by .. math:: - E = \epsilon \left[ 2 \left(\frac{\sigma}{r}\right)^9 - - 3 \left(\frac{\sigma}{r}\right)^6 \right] - \qquad r < r_c + E = \epsilon \left[ 2 \left(\frac{\sigma}{r}\right)^9 - + 3 \left(\frac{\sigma}{r}\right)^6 \right] + \qquad r < r_c :math:`r_c` is the cutoff. diff --git a/doc/src/pair_coeff.rst b/doc/src/pair_coeff.rst index dec45a5f11..3b8b93e3ff 100644 --- a/doc/src/pair_coeff.rst +++ b/doc/src/pair_coeff.rst @@ -1,13 +1,13 @@ -.. index:: pair\_coeff +.. index:: pair_coeff -pair\_coeff command -=================== +pair_coeff command +================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_coeff I J args @@ -18,7 +18,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_coeff 1 2 1.0 1.0 2.5 pair_coeff 2 \* 1.0 1.0 @@ -56,7 +56,7 @@ same I,J pair. For example, these commands set the coeffs for all I,J pairs, then overwrite the coeffs for just the I,J = 2,3 pair: -.. parsed-literal:: +.. code-block:: LAMMPS pair_coeff \* \* 1.0 1.0 2.5 pair_coeff 2 3 2.0 1.0 1.12 diff --git a/doc/src/pair_colloid.rst b/doc/src/pair_colloid.rst index 0e3f42f749..f94c163e1d 100644 --- a/doc/src/pair_colloid.rst +++ b/doc/src/pair_colloid.rst @@ -1,19 +1,19 @@ -.. index:: pair\_style colloid +.. index:: pair_style colloid -pair\_style colloid command -=========================== +pair_style colloid command +========================== -pair\_style colloid/gpu command -=============================== +pair_style colloid/gpu command +============================== -pair\_style colloid/omp command -=============================== +pair_style colloid/omp command +============================== Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style colloid cutoff @@ -23,10 +23,10 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style colloid 10.0 - pair_coeff \* \* 25 1.0 10.0 10.0 + pair_coeff * * 25 1.0 10.0 10.0 pair_coeff 1 1 144 1.0 0.0 0.0 3.0 pair_coeff 1 2 75.398 1.0 0.0 10.0 9.0 pair_coeff 2 2 39.478 1.0 10.0 10.0 25.0 diff --git a/doc/src/pair_comb.rst b/doc/src/pair_comb.rst index 8fdba49f1d..f7fe3dc55a 100644 --- a/doc/src/pair_comb.rst +++ b/doc/src/pair_comb.rst @@ -1,23 +1,26 @@ -.. index:: pair\_style comb +.. index:: pair_style comb -pair\_style comb command +pair_style comb command +======================= + +pair_style comb/omp command +=========================== + +pair_style comb3 command ======================== -pair\_style comb/omp command -============================ - -pair\_style comb3 command -========================= - Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style comb pair_style comb3 keyword + +.. parsed-literal:: + keyword = *polar* *polar* value = *polar_on* or *polar_off* = whether or not to include atomic polarization @@ -27,14 +30,14 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style comb - pair_coeff \* \* ../potentials/ffield.comb Si - pair_coeff \* \* ../potentials/ffield.comb Hf Si O + pair_coeff * * ../potentials/ffield.comb Si + pair_coeff * * ../potentials/ffield.comb Hf Si O pair_style comb3 polar_off - pair_coeff \* \* ../potentials/ffield.comb3 O Cu N C O + pair_coeff * * ../potentials/ffield.comb3 O Cu N C O Description """"""""""" @@ -82,9 +85,9 @@ last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would use the following pair\_coeff command: -.. parsed-literal:: +.. code-block:: LAMMPS - pair_coeff \* \* ../potentials/ffield.comb Si Hf O Si + pair_coeff * * ../potentials/ffield.comb Si Hf O Si The first two arguments must be \* \* so as to span all LAMMPS atom types. The first and last Si arguments map LAMMPS atom types 1 and 4 diff --git a/doc/src/pair_cosine_squared.rst b/doc/src/pair_cosine_squared.rst index f69c053af2..c29dda8224 100644 --- a/doc/src/pair_cosine_squared.rst +++ b/doc/src/pair_cosine_squared.rst @@ -1,20 +1,20 @@ -.. index:: pair\_style cosine/squared +.. index:: pair_style cosine/squared -pair\_style cosine/squared command -================================== +pair_style cosine/squared command +================================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style cosine/squared cutoff * cutoff = global cutoff for cosine-squared interactions (distance units) -.. parsed-literal:: +.. code-block:: LAMMPS pair_coeff i j eps sigma pair_coeff i j eps sigma cutoff @@ -31,7 +31,7 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style cosine/squared 3.0 pair_coeff \* \* 1.0 1.3 diff --git a/doc/src/pair_smd_ulsph.rst b/doc/src/pair_smd_ulsph.rst index 8586a072db..32a49b14ea 100644 --- a/doc/src/pair_smd_ulsph.rst +++ b/doc/src/pair_smd_ulsph.rst @@ -1,13 +1,13 @@ -.. index:: pair\_style smd/ulsph +.. index:: pair_style smd/ulsph -pair\_style smd/ulsph command +pair_style smd/ulsph command ============================= Syntax """""" -.. parsed-literal:: +.. code-block:: LAMMPS pair_style smd/ulsph args @@ -22,9 +22,9 @@ Examples """""""" -.. parsed-literal:: +.. code-block:: LAMMPS - pair_style smd/ulsph \*DENSITY_CONTINUITY \*VELOCITY_GRADIENT \*NO_GRADIENT_CORRECTION + pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION Description """"""""""" @@ -36,11 +36,11 @@ Smooth-Particle Hydrodynamics algorithm. This pair style is invoked similar to the following command: -.. parsed-literal:: +.. code-block:: LAMMPS - pair_style smd/ulsph \*DENSITY_CONTINUITY \*VELOCITY_GRADIENT \*NO_GRADIENT_CORRECTION - pair_coeff i j \*COMMON rho0 c0 Q1 Cp hg & - \*END + pair_style smd/ulsph *DENSITY_CONTINUITY *VELOCITY_GRADIENT *NO_GRADIENT_CORRECTION + pair_coeff i j *COMMON rho0 c0 Q1 Cp hg & + *END Here, *i* and *j* denote the *LAMMPS* particle types for which this pair style is defined. Note that *i* and *j* can be different, i.e., From 9ef5949798203ca98fb49d781bc40d53c20034f6 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Wed, 26 Feb 2020 16:31:05 -0500 Subject: [PATCH 3/3] Second batch of index cleanup and code-blocks --- doc/src/pair_coul.rst | 167 +++++++++-------- doc/src/pair_coul_diel.rst | 14 +- doc/src/pair_coul_shield.rst | 16 +- doc/src/pair_cs.rst | 38 ++-- doc/src/pair_dipole.rst | 52 +++--- doc/src/pair_dpd.rst | 38 ++-- doc/src/pair_dpd_fdt.rst | 34 ++-- doc/src/pair_drip.rst | 34 ++-- doc/src/pair_dsmc.rst | 18 +- doc/src/pair_e3b.rst | 18 +- doc/src/pair_eam.rst | 126 ++++++------- doc/src/pair_edip.rst | 36 ++-- doc/src/pair_eff.rst | 15 +- doc/src/pair_eim.rst | 24 +-- doc/src/pair_exp6_rx.rst | 24 +-- doc/src/pair_extep.rst | 14 +- doc/src/pair_fep_soft.rst | 130 +++++++------- doc/src/pair_gauss.rst | 30 ++-- doc/src/pair_gayberne.rst | 24 +-- doc/src/pair_gran.rst | 38 ++-- doc/src/pair_granular.rst | 20 +-- doc/src/pair_gromacs.rst | 38 ++-- doc/src/pair_gw.rst | 25 ++- doc/src/pair_hbond_dreiding.rst | 24 +-- doc/src/pair_hybrid.rst | 71 ++++---- doc/src/pair_ilp_graphene_hbn.rst | 44 ++--- doc/src/pair_kim.rst | 16 +- doc/src/pair_kolmogorov_crespi_full.rst | 20 +-- doc/src/pair_kolmogorov_crespi_z.rst | 22 +-- doc/src/pair_lcbop.rst | 16 +- doc/src/pair_lebedeva_z.rst | 14 +- doc/src/pair_line_lj.rst | 12 +- doc/src/pair_lj.rst | 190 ++++++++++---------- doc/src/pair_lj96.rst | 22 +-- doc/src/pair_lj_cubic.rst | 20 +-- doc/src/pair_lj_expand.rst | 42 ++--- doc/src/pair_lj_long.rst | 38 ++-- doc/src/pair_lj_smooth.rst | 26 +-- doc/src/pair_lj_smooth_linear.rst | 16 +- doc/src/pair_lj_switch3_coulgauss_long.rst | 10 +- doc/src/pair_local_density.rst | 12 +- doc/src/pair_lubricate.rst | 28 +-- doc/src/pair_lubricateU.rst | 16 +- doc/src/pair_mdf.rst | 26 +-- doc/src/pair_meam_spline.rst | 26 +-- doc/src/pair_meam_sw_spline.rst | 14 +- doc/src/pair_meamc.rst | 31 ++-- doc/src/pair_meso.rst | 34 ++-- doc/src/pair_mesocnt.rst | 12 +- doc/src/pair_mgpt.rst | 16 +- doc/src/pair_mie.rst | 22 +-- doc/src/pair_mm3_switch3_coulgauss_long.rst | 26 +-- doc/src/pair_modify.rst | 22 +-- doc/src/pair_momb.rst | 10 +- 54 files changed, 935 insertions(+), 936 deletions(-) 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