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Resolve merge conflict by merging in master and recreating Commands_compute.rst

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Axel Kohlmeyer
2019-11-26 08:20:42 -05:00
parent 2e4f514d40 738f155cc4
commit a171efa149
287 changed files with 2206 additions and 3278 deletions
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98
doc/src/Commands_compute.rst
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@ -14,55 +14,55 @@ Some styles have accelerated versions. This is indicated by
additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
KOKKOS, o = USER-OMP, t = OPT.
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`ackland/atom <compute_ackland_atom>` | :doc:`adf <compute_adf>` | :doc:`aggregate/atom <compute_cluster_atom>` | :doc:`angle <compute_angle>` | :doc:`angle/local <compute_angle_local>` | :doc:`angmom/chunk <compute_angmom_chunk>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`basal/atom <compute_basal_atom>` | :doc:`body/local <compute_body_local>` | :doc:`bond <compute_bond>` | :doc:`bond/local <compute_bond_local>` | :doc:`centro/atom <compute_centro_atom>` | :doc:`chunk/atom <compute_chunk_atom>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`chunk/spread/atom <compute_chunk_spread_atom>` | :doc:`cluster/atom <compute_cluster_atom>` | :doc:`cna/atom <compute_cna_atom>` | :doc:`cnp/atom <compute_cnp_atom>` | :doc:`com <compute_com>` | :doc:`com/chunk <compute_com_chunk>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`contact/atom <compute_contact_atom>` | :doc:`coord/atom <compute_coord_atom>` | :doc:`damage/atom <compute_damage_atom>` | :doc:`dihedral <compute_dihedral>` | :doc:`dihedral/local <compute_dihedral_local>` | :doc:`dilatation/atom <compute_dilatation_atom>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`dipole/chunk <compute_dipole_chunk>` | :doc:`displace/atom <compute_displace_atom>` | :doc:`dpd <compute_dpd>` | :doc:`dpd/atom <compute_dpd_atom>` | :doc:`edpd/temp/atom <compute_edpd_temp_atom>` | :doc:`entropy/atom <compute_entropy_atom>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`erotate/asphere <compute_erotate_asphere>` | :doc:`erotate/rigid <compute_erotate_rigid>` | :doc:`erotate/sphere <compute_erotate_sphere>` | :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>` | :doc:`event/displace <compute_event_displace>` | :doc:`fep <compute_fep>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`force/tally <compute_tally>` | :doc:`fragment/atom <compute_cluster_atom>` | :doc:`global/atom <compute_global_atom>` | :doc:`group/group <compute_group_group>` | :doc:`gyration <compute_gyration>` | :doc:`gyration/chunk <compute_gyration_chunk>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`gyration/shape <compute_gyration_shape>` | :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>` | :doc:`heat/flux <compute_heat_flux>` | :doc:`heat/flux/tally <compute_tally>` | :doc:`hexorder/atom <compute_hexorder_atom>` | :doc:`hma <compute_hma>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`improper <compute_improper>` | :doc:`improper/local <compute_improper_local>` | :doc:`inertia/chunk <compute_inertia_chunk>` | :doc:`ke <compute_ke>` | :doc:`ke/atom <compute_ke_atom>` | :doc:`ke/atom/eff <compute_ke_atom_eff>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`ke/eff <compute_ke_eff>` | :doc:`ke/rigid <compute_ke_rigid>` | :doc:`meso/e/atom <compute_meso_e_atom>` | :doc:`meso/rho/atom <compute_meso_rho_atom>` | :doc:`meso/t/atom <compute_meso_t_atom>` | :doc:`momentum <compute_momentum>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`msd <compute_msd>` | :doc:`msd/chunk <compute_msd_chunk>` | :doc:`msd/nongauss <compute_msd_nongauss>` | :doc:`omega/chunk <compute_omega_chunk>` | :doc:`orientorder/atom <compute_orientorder_atom>` | :doc:`pair <compute_pair>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`pair/local <compute_pair_local>` | :doc:`pe <compute_pe>` | :doc:`pe/atom <compute_pe_atom>` | :doc:`pe/mol/tally <compute_tally>` | :doc:`pe/tally <compute_tally>` | :doc:`plasticity/atom <compute_plasticity_atom>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`pressure <compute_pressure>` | :doc:`pressure/cylinder <compute_pressure_cylinder>` | :doc:`pressure/uef <compute_pressure_uef>` | :doc:`property/atom <compute_property_atom>` | :doc:`property/chunk <compute_property_chunk>` | :doc:`property/local <compute_property_local>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`ptm/atom <compute_ptm_atom>` | :doc:`rdf <compute_rdf>` | :doc:`reduce <compute_reduce>` | :doc:`reduce/chunk <compute_reduce_chunk>` | :doc:`reduce/region <compute_reduce>` | :doc:`rigid/local <compute_rigid_local>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`saed <compute_saed>` | :doc:`slice <compute_slice>` | :doc:`smd/contact/radius <compute_smd_contact_radius>` | :doc:`smd/damage <compute_smd_damage>` | :doc:`smd/hourglass/error <compute_smd_hourglass_error>` | :doc:`smd/internal/energy <compute_smd_internal_energy>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`smd/plastic/strain <compute_smd_plastic_strain>` | :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>` | :doc:`smd/rho <compute_smd_rho>` | :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>` | :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>` | :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>` | :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>` | :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` | :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>` | :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>` | :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>` | :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>` | :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>` | :doc:`smd/vol <compute_smd_vol>` | :doc:`snap <compute_sna_atom>` | :doc:`sna/atom <compute_sna_atom>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`snad/atom <compute_sna_atom>` | :doc:`snav/atom <compute_sna_atom>` | :doc:`spin <compute_spin>` | :doc:`stress/atom <compute_stress_atom>` | :doc:`stress/mop <compute_stress_mop>` | :doc:`stress/mop/profile <compute_stress_mop>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`stress/tally <compute_tally>` | :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>` | :doc:`temp (k) <compute_temp>` | :doc:`temp/asphere <compute_temp_asphere>` | :doc:`temp/body <compute_temp_body>` | :doc:`temp/chunk <compute_temp_chunk>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`temp/com <compute_temp_com>` | :doc:`temp/cs <compute_temp_cs>` | :doc:`temp/deform <compute_temp_deform>` | :doc:`temp/deform/eff <compute_temp_deform_eff>` | :doc:`temp/drude <compute_temp_drude>` | :doc:`temp/eff <compute_temp_eff>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`temp/partial <compute_temp_partial>` | :doc:`temp/profile <compute_temp_profile>` | :doc:`temp/ramp <compute_temp_ramp>` | :doc:`temp/region <compute_temp_region>` | :doc:`temp/region/eff <compute_temp_region_eff>` | :doc:`temp/rotate <compute_temp_rotate>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`temp/sphere <compute_temp_sphere>` | :doc:`temp/uef <compute_temp_uef>` | :doc:`ti <compute_ti>` | :doc:`torque/chunk <compute_torque_chunk>` | :doc:`vacf <compute_vacf>` | :doc:`vcm/chunk <compute_vcm_chunk>` |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
| :doc:`voronoi/atom <compute_voronoi_atom>` | :doc:`xrd <compute_xrd>` | | | | |
+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`ackland/atom <compute_ackland_atom>` | :doc:`adf <compute_adf>` | :doc:`aggregate/atom <compute_cluster_atom>` | :doc:`angle <compute_angle>` | :doc:`angle/local <compute_angle_local>` | :doc:`angmom/chunk <compute_angmom_chunk>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`basal/atom <compute_basal_atom>` | :doc:`body/local <compute_body_local>` | :doc:`bond <compute_bond>` | :doc:`bond/local <compute_bond_local>` | :doc:`centro/atom <compute_centro_atom>` | :doc:`centroid/stress/atom <compute_stress_atom>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`chunk/atom <compute_chunk_atom>` | :doc:`chunk/spread/atom <compute_chunk_spread_atom>` | :doc:`cluster/atom <compute_cluster_atom>` | :doc:`cna/atom <compute_cna_atom>` | :doc:`cnp/atom <compute_cnp_atom>` | :doc:`com <compute_com>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`com/chunk <compute_com_chunk>` | :doc:`contact/atom <compute_contact_atom>` | :doc:`coord/atom <compute_coord_atom>` | :doc:`damage/atom <compute_damage_atom>` | :doc:`dihedral <compute_dihedral>` | :doc:`dihedral/local <compute_dihedral_local>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`dilatation/atom <compute_dilatation_atom>` | :doc:`dipole/chunk <compute_dipole_chunk>` | :doc:`displace/atom <compute_displace_atom>` | :doc:`dpd <compute_dpd>` | :doc:`dpd/atom <compute_dpd_atom>` | :doc:`edpd/temp/atom <compute_edpd_temp_atom>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`entropy/atom <compute_entropy_atom>` | :doc:`erotate/asphere <compute_erotate_asphere>` | :doc:`erotate/rigid <compute_erotate_rigid>` | :doc:`erotate/sphere <compute_erotate_sphere>` | :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>` | :doc:`event/displace <compute_event_displace>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`fep <compute_fep>` | :doc:`force/tally <compute_tally>` | :doc:`fragment/atom <compute_cluster_atom>` | :doc:`global/atom <compute_global_atom>` | :doc:`group/group <compute_group_group>` | :doc:`gyration <compute_gyration>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`gyration/chunk <compute_gyration_chunk>` | :doc:`gyration/shape <compute_gyration_shape>` | :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>` | :doc:`heat/flux <compute_heat_flux>` | :doc:`heat/flux/tally <compute_tally>` | :doc:`hexorder/atom <compute_hexorder_atom>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`hma <compute_hma>` | :doc:`improper <compute_improper>` | :doc:`improper/local <compute_improper_local>` | :doc:`inertia/chunk <compute_inertia_chunk>` | :doc:`ke <compute_ke>` | :doc:`ke/atom <compute_ke_atom>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`ke/atom/eff <compute_ke_atom_eff>` | :doc:`ke/eff <compute_ke_eff>` | :doc:`ke/rigid <compute_ke_rigid>` | :doc:`meso/e/atom <compute_meso_e_atom>` | :doc:`meso/rho/atom <compute_meso_rho_atom>` | :doc:`meso/t/atom <compute_meso_t_atom>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`momentum <compute_momentum>` | :doc:`msd <compute_msd>` | :doc:`msd/chunk <compute_msd_chunk>` | :doc:`msd/nongauss <compute_msd_nongauss>` | :doc:`omega/chunk <compute_omega_chunk>` | :doc:`orientorder/atom <compute_orientorder_atom>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`pair <compute_pair>` | :doc:`pair/local <compute_pair_local>` | :doc:`pe <compute_pe>` | :doc:`pe/atom <compute_pe_atom>` | :doc:`pe/mol/tally <compute_tally>` | :doc:`pe/tally <compute_tally>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`plasticity/atom <compute_plasticity_atom>` | :doc:`pressure <compute_pressure>` | :doc:`pressure/cylinder <compute_pressure_cylinder>` | :doc:`pressure/uef <compute_pressure_uef>` | :doc:`property/atom <compute_property_atom>` | :doc:`property/chunk <compute_property_chunk>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`property/local <compute_property_local>` | :doc:`ptm/atom <compute_ptm_atom>` | :doc:`rdf <compute_rdf>` | :doc:`reduce <compute_reduce>` | :doc:`reduce/chunk <compute_reduce_chunk>` | :doc:`reduce/region <compute_reduce>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`rigid/local <compute_rigid_local>` | :doc:`saed <compute_saed>` | :doc:`slice <compute_slice>` | :doc:`smd/contact/radius <compute_smd_contact_radius>` | :doc:`smd/damage <compute_smd_damage>` | :doc:`smd/hourglass/error <compute_smd_hourglass_error>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`smd/internal/energy <compute_smd_internal_energy>` | :doc:`smd/plastic/strain <compute_smd_plastic_strain>` | :doc:`smd/plastic/strain/rate <compute_smd_plastic_strain_rate>` | :doc:`smd/rho <compute_smd_rho>` | :doc:`smd/tlsph/defgrad <compute_smd_tlsph_defgrad>` | :doc:`smd/tlsph/dt <compute_smd_tlsph_dt>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`smd/tlsph/num/neighs <compute_smd_tlsph_num_neighs>` | :doc:`smd/tlsph/shape <compute_smd_tlsph_shape>` | :doc:`smd/tlsph/strain <compute_smd_tlsph_strain>` | :doc:`smd/tlsph/strain/rate <compute_smd_tlsph_strain_rate>` | :doc:`smd/tlsph/stress <compute_smd_tlsph_stress>` | :doc:`smd/triangle/vertices <compute_smd_triangle_vertices>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`smd/ulsph/num/neighs <compute_smd_ulsph_num_neighs>` | :doc:`smd/ulsph/strain <compute_smd_ulsph_strain>` | :doc:`smd/ulsph/strain/rate <compute_smd_ulsph_strain_rate>` | :doc:`smd/ulsph/stress <compute_smd_ulsph_stress>` | :doc:`smd/vol <compute_smd_vol>` | :doc:`snap <compute_sna_atom>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`sna/atom <compute_sna_atom>` | :doc:`snad/atom <compute_sna_atom>` | :doc:`snav/atom <compute_sna_atom>` | :doc:`spin <compute_spin>` | :doc:`stress/atom <compute_stress_atom>` | :doc:`stress/mop <compute_stress_mop>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`stress/mop/profile <compute_stress_mop>` | :doc:`stress/tally <compute_tally>` | :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>` | :doc:`temp (k) <compute_temp>` | :doc:`temp/asphere <compute_temp_asphere>` | :doc:`temp/body <compute_temp_body>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`temp/chunk <compute_temp_chunk>` | :doc:`temp/com <compute_temp_com>` | :doc:`temp/cs <compute_temp_cs>` | :doc:`temp/deform <compute_temp_deform>` | :doc:`temp/deform/eff <compute_temp_deform_eff>` | :doc:`temp/drude <compute_temp_drude>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`temp/eff <compute_temp_eff>` | :doc:`temp/partial <compute_temp_partial>` | :doc:`temp/profile <compute_temp_profile>` | :doc:`temp/ramp <compute_temp_ramp>` | :doc:`temp/region <compute_temp_region>` | :doc:`temp/region/eff <compute_temp_region_eff>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`temp/rotate <compute_temp_rotate>` | :doc:`temp/sphere <compute_temp_sphere>` | :doc:`temp/uef <compute_temp_uef>` | :doc:`ti <compute_ti>` | :doc:`torque/chunk <compute_torque_chunk>` | :doc:`vacf <compute_vacf>` |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
| :doc:`vcm/chunk <compute_vcm_chunk>` | :doc:`voronoi/atom <compute_voronoi_atom>` | :doc:`xrd <compute_xrd>` | | | |
+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
.. _lws: http://lammps.sandia.gov

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\documentclass[12pt]{article}
\begin{document}
$$
E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] +
4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = -0.5 K R_0^2
\ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] +
4 \epsilon \left[ \left(\frac{\sigma}{\left(r -
\Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r -
\Delta\right)}\right)^6 \right] + \epsilon
$$
\end{document}

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@ -1,10 +0,0 @@
\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
$$
E = K (r^2 - r_0^2)^2
$$
\end{document}

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@ -1,9 +0,0 @@
\documentclass[12pt]{article}
\begin{document}
$$
E = K (r - r_0)^2
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
$$
\end{document}

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@ -1,9 +0,0 @@
\documentclass[12pt]{article}
\begin{document}
$$
E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
$$
\end{document}

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doc/src/Eqs/bond_mm3.tex
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\documentclass[12pt]{article}
\begin{document}
\thispagestyle{empty}
$$
E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
% E = D \left[ 1 - \exp \left( -\alpha (r - r_0) \right) \right]^2
E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]}
$$
\end{document}

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\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
$$
E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r0}{\Delta}\right)^2\right]
$$
\end{document}

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\documentclass[12pt]{article}
\begin{document}
$$
E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 +
4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
$$
\end{document}

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@ -1,13 +1,13 @@
.. index:: atom\_modify
.. index:: atom_modify
atom\_modify command
====================
atom_modify command
===================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
atom_modify keyword values ...
@ -29,7 +29,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
atom_modify map yes
atom_modify map hash sort 10000 2.0
@ -188,8 +188,3 @@ defined, sorting will be turned off.
**(Meloni)** Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

15
doc/src/atom_style.rst
View File

@ -1,13 +1,13 @@
.. index:: atom\_style
.. index:: atom_style
atom\_style command
===================
atom_style command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
atom_style style args
@ -33,7 +33,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
atom_style atomic
atom_style bond
@ -371,8 +371,3 @@ atom\_style atomic
**(Grime)** Grime and Voth, to appear in J Chem Theory & Computation
(2014).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

39
doc/src/bond_class2.rst
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@ -1,19 +1,19 @@
.. index:: bond\_style class2
.. index:: bond_style class2
bond\_style class2 command
==========================
bond_style class2 command
=========================
bond\_style class2/omp command
==============================
bond\_style class2/kk command
bond_style class2/omp command
=============================
bond_style class2/kk command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style class2
@ -21,7 +21,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style class2
bond_coeff 1 1.0 100.0 80.0 80.0
@ -31,10 +31,12 @@ Description
The *class2* bond style uses the potential
.. image:: Eqs/bond_class2.jpg
:align: center
.. math::
where r0 is the equilibrium bond distance.
E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4
where :math:`r_0` is the equilibrium bond distance.
See :ref:`(Sun) <bond-Sun>` for a description of the COMPASS class2 force field.
@ -43,10 +45,10 @@ The following coefficients must be defined for each bond type via the
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
* R0 (distance)
* K2 (energy/distance\^2)
* K3 (energy/distance\^3)
* K4 (energy/distance\^4)
* :math:`r_0` (distance)
* :math:`K_2` (energy/distance\^2)
* :math:`K_3` (energy/distance\^3)
* :math:`K_4` (energy/distance\^4)
----------
@ -98,8 +100,3 @@ Related commands
**(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

23
doc/src/bond_coeff.rst
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@ -1,13 +1,13 @@
.. index:: bond\_coeff
.. index:: bond_coeff
bond\_coeff command
===================
bond_coeff command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_coeff N args
@ -18,11 +18,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_coeff 5 80.0 1.2
bond_coeff \* 30.0 1.5 1.0 1.0
bond_coeff 1\*4 30.0 1.5 1.0 1.0
bond_coeff * 30.0 1.5 1.0 1.0
bond_coeff 1*4 30.0 1.5 1.0 1.0
bond_coeff 1 harmonic 200.0 1.0
Description
@ -47,9 +47,9 @@ for the same bond type. For example, these commands set the coeffs
for all bond types, then overwrite the coeffs for just bond type 2:
.. parsed-literal::
.. code-block:: LAMMPS
bond_coeff \* 100.0 1.2
bond_coeff * 100.0 1.2
bond_coeff 2 200.0 1.2
A line in a data file that specifies bond coefficients uses the exact
@ -97,8 +97,3 @@ Related commands
:doc:`bond\_style <bond_style>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

45
doc/src/bond_fene.rst
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@ -1,22 +1,22 @@
.. index:: bond\_style fene
.. index:: bond_style fene
bond\_style fene command
========================
bond_style fene command
=======================
bond\_style fene/intel command
==============================
bond_style fene/intel command
=============================
bond\_style fene/kk command
bond_style fene/kk command
==========================
bond_style fene/omp command
===========================
bond\_style fene/omp command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style fene
@ -24,7 +24,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
@ -34,24 +34,26 @@ Description
The *fene* bond style uses the potential
.. image:: Eqs/bond_fene.jpg
:align: center
.. math::
E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
to define a finite extensible nonlinear elastic (FENE) potential
:ref:`(Kremer) <fene-Kremer>`, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to R0, the maximum extent of the bond. The 2nd
term is cutoff at 2\^(1/6) sigma, the minimum of the LJ potential.
first term extends to :math:`R_0`, the maximum extent of the bond. The 2nd
term is cutoff at :math:`2^\frac{1}{6} \sigma`, the minimum of the LJ potential.
The following coefficients must be defined for each bond type via the
:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
* K (energy/distance\^2)
* R0 (distance)
* epsilon (energy)
* sigma (distance)
* :math:`K` (energy/distance\^2)
* :math:`R_0` (distance)
* :math:`\epsilon` (energy)
* :math:`\sigma` (distance)
----------
@ -107,8 +109,3 @@ Related commands
**(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

40
doc/src/bond_fene_expand.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style fene/expand
.. index:: bond_style fene/expand
bond\_style fene/expand command
===============================
bond_style fene/expand command
==============================
bond\_style fene/expand/omp command
===================================
bond_style fene/expand/omp command
==================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style fene/expand
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style fene/expand
bond_coeff 1 30.0 1.5 1.0 1.0 0.5
@ -28,29 +28,30 @@ Description
The *fene/expand* bond style uses the potential
.. image:: Eqs/bond_fene_expand.jpg
:align: center
.. math::
E = -0.5 K R_0^2 \ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] + 4 \epsilon \left[ \left(\frac{\sigma}{\left(r - \Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r - \Delta\right)}\right)^6 \right] + \epsilon
to define a finite extensible nonlinear elastic (FENE) potential
:ref:`(Kremer) <feneexpand-Kremer>`, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive.
The *fene/expand* bond style is similar to *fene* except that an extra
shift factor of delta (positive or negative) is added to *r* to
shift factor of :math:`\Delta` (positive or negative) is added to :math:`r` to
effectively change the bead size of the bonded atoms. The first term
now extends to R0 + delta and the 2nd term is cutoff at 2\^(1/6) sigma
+ delta.
now extends to :math:`R_0 + \Delta` and the 2nd term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`.
The following coefficients must be defined for each bond type via the
:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
* K (energy/distance\^2)
* R0 (distance)
* epsilon (energy)
* sigma (distance)
* delta (distance)
* :math:`K` (energy/distance\^2)
* :math:`R_0` (distance)
* :math:`\epsilon` (energy)
* :math:`\sigma` (distance)
* :math:`\Delta` (distance)
----------
@ -106,8 +107,3 @@ Related commands
**(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

33
doc/src/bond_gromos.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style gromos
.. index:: bond_style gromos
bond\_style gromos command
==========================
bond_style gromos command
=========================
bond\_style gromos/omp command
==============================
bond_style gromos/omp command
=============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style gromos
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style gromos
bond_coeff 5 80.0 1.2
@ -28,19 +28,21 @@ Description
The *gromos* bond style uses the potential
.. image:: Eqs/bond_gromos.jpg
:align: center
.. math::
where r0 is the equilibrium bond distance. Note that the usual 1/4
factor is included in K.
E = K (r^2 - r_0^2)^2
where :math:`r_0` is the equilibrium bond distance. Note that the usual 1/4
factor is included in :math:`K`.
The following coefficients must be defined for each bond type via the
:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
* K (energy/distance\^4)
* r0 (distance)
* :math:`K` (energy/distance\^4)
* :math:`r_0` (distance)
----------
@ -82,8 +84,3 @@ Related commands
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

41
doc/src/bond_harmonic.rst
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@ -1,22 +1,22 @@
.. index:: bond\_style harmonic
.. index:: bond_style harmonic
bond\_style harmonic command
============================
bond_style harmonic command
===========================
bond\_style harmonic/intel command
==================================
bond_style harmonic/intel command
=================================
bond\_style harmonic/kk command
bond_style harmonic/kk command
==============================
bond_style harmonic/omp command
===============================
bond\_style harmonic/omp command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style harmonic
@ -24,7 +24,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style harmonic
bond_coeff 5 80.0 1.2
@ -34,19 +34,21 @@ Description
The *harmonic* bond style uses the potential
.. image:: Eqs/bond_harmonic.jpg
:align: center
.. math::
where r0 is the equilibrium bond distance. Note that the usual 1/2
factor is included in K.
E = K (r - r_0)^2
where :math:`r_0` is the equilibrium bond distance. Note that the usual 1/2
factor is included in :math:`K`.
The following coefficients must be defined for each bond type via the
:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
* K (energy/distance\^2)
* r0 (distance)
* :math:`K` (energy/distance\^2)
* :math:`r_0` (distance)
----------
@ -88,8 +90,3 @@ Related commands
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

37
doc/src/bond_harmonic_shift.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style harmonic/shift
.. index:: bond_style harmonic/shift
bond\_style harmonic/shift command
==================================
bond_style harmonic/shift command
=================================
bond\_style harmonic/shift/omp command
======================================
bond_style harmonic/shift/omp command
=====================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style harmonic/shift
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style harmonic/shift
bond_coeff 5 10.0 0.5 1.0
@ -29,23 +29,25 @@ Description
The *harmonic/shift* bond style is a shifted harmonic bond that uses
the potential
.. image:: Eqs/bond_harmonic_shift.jpg
:align: center
.. math::
where r0 is the equilibrium bond distance, and rc the critical distance.
The potential is -Umin at r0 and zero at rc. The spring constant is
k = Umin / [ 2 (r0-rc)\^2].
E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the critical distance.
The potential is :math:`-U_{\text{min}}` at :math:`r0` and zero at :math:`r_c`. The spring constant is
:math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`.
The following coefficients must be defined for each bond type via the
:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
* Umin (energy)
* :math:`U_{\text{min}}` (energy)
* r0 (distance)
* :math:`r_0` (distance)
* rc (distance)
* :math:`r_c` (distance)
----------
@ -88,8 +90,3 @@ Related commands
:doc:`bond\_harmonic <bond_harmonic>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

37
doc/src/bond_harmonic_shift_cut.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style harmonic/shift/cut
.. index:: bond_style harmonic/shift/cut
bond\_style harmonic/shift/cut command
======================================
bond_style harmonic/shift/cut command
=====================================
bond\_style harmonic/shift/cut/omp command
==========================================
bond_style harmonic/shift/cut/omp command
=========================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style harmonic/shift/cut
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style harmonic/shift/cut
bond_coeff 5 10.0 0.5 1.0
@ -29,21 +29,23 @@ Description
The *harmonic/shift/cut* bond style is a shifted harmonic bond that
uses the potential
.. image:: Eqs/bond_harmonic_shift_cut.jpg
:align: center
.. math::
where r0 is the equilibrium bond distance, and rc the critical distance.
The bond potential is zero for distances r > rc. The potential is -Umin
at r0 and zero at rc. The spring constant is k = Umin / [ 2 (r0-rc)\^2].
E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
where :math:`r_0` is the equilibrium bond distance, and rc the critical distance.
The bond potential is zero for distances :math:`r > r_c`. The potential is :math:`-U_{\text{min}}`
at :math:`r_0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`.
The following coefficients must be defined for each bond type via the
:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
* Umin (energy)
* r0 (distance)
* rc (distance)
* :math:`U_{\text{min}}` (energy)
* :math:`r_0` (distance)
* :math:`r_c` (distance)
----------
@ -87,8 +89,3 @@ Related commands
:doc:`bond\_harmonic\_shift <bond_harmonic_shift>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

27
doc/src/bond_hybrid.rst
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@ -1,13 +1,13 @@
.. index:: bond\_style hybrid
.. index:: bond_style hybrid
bond\_style hybrid command
==========================
bond_style hybrid command
=========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style hybrid style1 style2 ...
@ -17,11 +17,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block: LAMMPS
bond_style hybrid harmonic fene
bond_coeff 1 harmonic 80.0 1.2
bond_coeff 2\* fene 30.0 1.5 1.0 1.0
bond_coeff 2* fene 30.0 1.5 1.0 1.0
Description
"""""""""""
@ -31,19 +31,19 @@ simulation. A bond style is assigned to each bond type. For example,
bonds in a polymer flow (of bond type 1) could be computed with a
*fene* potential and bonds in the wall boundary (of bond type 2) could
be computed with a *harmonic* potential. The assignment of bond type
to style is made via the :doc:`bond\_coeff <bond_coeff>` command or in
to style is made via the :doc:`bond_coeff <bond_coeff>` command or in
the data file.
In the bond\_coeff commands, the name of a bond style must be added
after the bond type, with the remaining coefficients being those
appropriate to that style. In the example above, the 2 bond\_coeff
commands set bonds of bond type 1 to be computed with a *harmonic*
potential with coefficients 80.0, 1.2 for K, r0. All other bond types
potential with coefficients 80.0, 1.2 for :math:`K`, :math:`r_0`. All other bond types
(2-N) are computed with a *fene* potential with coefficients 30.0,
1.5, 1.0, 1.0 for K, R0, epsilon, sigma.
1.5, 1.0, 1.0 for :math:`K`, :math:`R_0`, :math:`\epsilon`, :math:`\sigma`.
If bond coefficients are specified in the data file read via the
:doc:`read\_data <read_data>` command, then the same rule applies.
:doc:`read_data <read_data>` command, then the same rule applies.
E.g. "harmonic" or "fene" must be added after the bond type, for each
line in the "Bond Coeffs" section, e.g.
@ -80,11 +80,6 @@ file, you need to re-specify bond\_coeff commands.
Related commands
""""""""""""""""
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

27
doc/src/bond_mm3.rst
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@ -1,13 +1,13 @@
.. index:: bond\_style mm3
.. index:: bond_style mm3
bond\_style mm3 command
=======================
bond_style mm3 command
======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style mm3
@ -15,7 +15,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style mm3
bond_coeff 1 100.0 107.0
@ -26,10 +26,12 @@ Description
The *mm3* bond style uses the potential that is anharmonic in the bond
as defined in :ref:`(Allinger) <mm3-allinger1989>`
.. image:: Eqs/bond_mm3.jpg
:align: center
.. math::
where r0 is the equilibrium value of the bond, and K is a
E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
where :math:`r_0` is the equilibrium value of the bond, and :math:`K` is a
prefactor. The anharmonic prefactors have units angstrom\^(-n):
-2.55 angstrom\^(-1) and (7/12)2.55\^2 angstrom\^(-2). The code takes
care of the necessary unit conversion for these factors internally.
@ -41,8 +43,8 @@ The following coefficients must be defined for each bond type via the
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
* K (energy/distance\^2)
* r0 (distance)
* :math:`K` (energy/distance\^2)
* :math:`r_0` (distance)
Restrictions
""""""""""""
@ -69,8 +71,3 @@ Related commands
**(Allinger)** Allinger, Yuh, Lii, JACS, 111(23), 8551-8566
(1989),
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

35
doc/src/bond_morse.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style morse
.. index:: bond_style morse
bond\_style morse command
=========================
bond_style morse command
========================
bond\_style morse/omp command
=============================
bond_style morse/omp command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style morse
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style morse
bond_coeff 5 1.0 2.0 1.2
@ -28,20 +28,22 @@ Description
The *morse* bond style uses the potential
.. image:: Eqs/bond_morse.jpg
:align: center
.. math::
where r0 is the equilibrium bond distance, alpha is a stiffness
parameter, and D determines the depth of the potential well.
E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2
where :math:`r_0` is the equilibrium bond distance, :math:`\alpha` is a stiffness
parameter, and :math:`D` determines the depth of the potential well.
The following coefficients must be defined for each bond type via the
:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
* D (energy)
* alpha (inverse distance)
* r0 (distance)
* :math:`D` (energy)
* :math:`\alpha` (inverse distance)
* :math:`r_0` (distance)
----------
@ -83,8 +85,3 @@ Related commands
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

21
doc/src/bond_none.rst
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@ -1,13 +1,13 @@
.. index:: bond\_style none
.. index:: bond_style none
bond\_style none command
========================
bond_style none command
=======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style none
@ -15,7 +15,7 @@ Examples
""""""""
.. parsed-literal::
.. code-blocK:: LAMMPS
bond_style none
@ -24,9 +24,9 @@ Description
Using a bond style of none means bond forces and energies are not
computed, even if pairs of bonded atoms were listed in the data file
read by the :doc:`read\_data <read_data>` command.
read by the :doc:`read_data <read_data>` command.
See the :doc:`bond\_style zero <bond_zero>` command for a way to
See the :doc:`bond_style zero <bond_zero>` command for a way to
calculate bond statistics, but compute no bond interactions.
Restrictions
@ -35,11 +35,6 @@ Restrictions
**Related commands:** none
:doc:`bond\_style zero <bond_zero>`
:doc:`bond_style zero <bond_zero>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

33
doc/src/bond_nonlinear.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style nonlinear
.. index:: bond_style nonlinear
bond\_style nonlinear command
=============================
bond_style nonlinear command
============================
bond\_style nonlinear/omp command
=================================
bond_style nonlinear/omp command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style nonlinear
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style nonlinear
bond_coeff 2 100.0 1.1 1.4
@ -28,20 +28,22 @@ Description
The *nonlinear* bond style uses the potential
.. image:: Eqs/bond_nonlinear.jpg
:align: center
.. math::
E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]}
to define an anharmonic spring :ref:`(Rector) <Rector>` of equilibrium
length r0 and maximum extension lamda.
length :math:`r_0` and maximum extension lamda.
The following coefficients must be defined for each bond type via the
:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
* epsilon (energy)
* r0 (distance)
* lamda (distance)
* :math:`\epsilon` (energy)
* :math:`r_0` (distance)
* :math:`\lambda` (distance)
----------
@ -93,8 +95,3 @@ Related commands
**(Rector)** Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

35
doc/src/bond_oxdna.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style oxdna/fene
.. index:: bond_style oxdna/fene
bond\_style oxdna/fene command
bond_style oxdna/fene command
=============================
bond_style oxdna2/fene command
==============================
bond\_style oxdna2/fene command
===============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style oxdna/fene
@ -20,21 +20,23 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style oxdna/fene
bond_coeff \* 2.0 0.25 0.7525
bond_coeff * 2.0 0.25 0.7525
bond_style oxdna2/fene
bond_coeff \* 2.0 0.25 0.7564
bond_coeff * 2.0 0.25 0.7564
Description
"""""""""""
The *oxdna/fene* and *oxdna2/fene* bond styles use the potential
.. image:: Eqs/bond_oxdna_fene.jpg
:align: center
.. math::
E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r_0}{\Delta}\right)^2\right]
to define a modified finite extensible nonlinear elastic (FENE)
potential :ref:`(Ouldridge) <oxdna_fene>` to model the connectivity of the
@ -47,9 +49,9 @@ in the data file or restart files read by the
:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
commands:
* epsilon (energy)
* Delta (distance)
* r0 (distance)
* :math:`\epsilon` (energy)
* :math:`\Delta` (distance)
* :math:`r_0` (distance)
.. note::
@ -121,8 +123,3 @@ J. Chem. Phys. 134, 085101 (2011).
**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al.,
J. Chem. Phys. 142, 234901 (2015).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

64
doc/src/bond_quartic.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style quartic
.. index:: bond_style quartic
bond\_style quartic command
===========================
bond_style quartic command
==========================
bond\_style quartic/omp command
===============================
bond_style quartic/omp command
==============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style quartic
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style quartic
bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
@ -28,11 +28,12 @@ Description
The *quartic* bond style uses the potential
.. image:: Eqs/bond_quartic.jpg
:align: center
.. math::
E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 + 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
to define a bond that can be broken as the simulation proceeds (e.g.
due to a polymer being stretched). The sigma and epsilon used in the
due to a polymer being stretched). The :math:`\sigma` and :math:`\epsilon` used in the
LJ portion of the formula are both set equal to 1.0 by LAMMPS.
The following coefficients must be defined for each bond type via the
@ -40,23 +41,31 @@ The following coefficients must be defined for each bond type via the
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
* K (energy/distance\^4)
* B1 (distance)
* B2 (distance)
* Rc (distance)
* U0 (energy)
* :math:`K` (energy/distance\^4)
* :math:`B_1` (distance)
* :math:`B_2` (distance)
* :math:`R_c` (distance)
* :math:`U_0` (energy)
This potential was constructed to mimic the FENE bond potential for
coarse-grained polymer chains. When monomers with sigma = epsilon =
1.0 are used, the following choice of parameters gives a quartic
potential that looks nearly like the FENE potential: K = 1200, B1 =
-0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters
can be specified using the :doc:`bond\_coeff <bond_coeff>` command, but
you will need to choose them carefully so they form a suitable bond
potential.
coarse-grained polymer chains. When monomers with :math:`\sigma = \epsilon = 1.0`
are used, the following choice of parameters gives a quartic potential that
looks nearly like the FENE potential:
Rc is the cutoff length at which the bond potential goes smoothly to a
local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks"
.. math::
K &= 1200 \\
B_1 &= -0.55 \\
B_2 &= 0.25 \\
R_c &= 1.3 \\
U_0 &= 34.6878
Different parameters can be specified using the :doc:`bond_coeff <bond_coeff>`
command, but you will need to choose them carefully so they form a suitable
bond potential.
:math:`R_c` is the cutoff length at which the bond potential goes smoothly to a
local maximum. If a bond length ever becomes :math:`> R_c`, LAMMPS "breaks"
the bond, which means two things. First, the bond potential is turned
off by setting its type to 0, and is no longer computed. Second, a
pairwise interaction between the two atoms is turned on, since they
@ -75,7 +84,7 @@ Note that when bonds are dumped to a file via the :doc:`dump local <dump>` comma
status of broken bonds or permanently delete them, e.g.:
.. parsed-literal::
.. code-block:: LAMMPS
delete_bonds all stats
delete_bonds all bond 0 remove
@ -124,8 +133,3 @@ Related commands
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

27
doc/src/bond_style.rst
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@ -1,29 +1,27 @@
.. index:: bond\_style
.. index:: bond_style
bond\_style command
===================
bond_style command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style style args
* style = *none* or *hybrid* or *class2* or *fene* or *fene/expand* or *harmonic* or *morse* or *nonlinear* or *quartic*
* args = none for any style except *hybrid*
.. parsed-literal::
args = none for any style except *hybrid*
*hybrid* args = list of one or more styles
* *hybrid* args = list of one or more styles
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style harmonic
bond_style fene
@ -74,11 +72,11 @@ between the 2 atoms in the bond.
Here is an alphabetic list of bond styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated :doc:`bond\_coeff <bond_coeff>` command.
specified by the associated :doc:`bond_coeff <bond_coeff>` command.
Click on the style to display the formula it computes, any additional
arguments specified in the bond\_style command, and coefficients
specified by the associated :doc:`bond\_coeff <bond_coeff>` command.
specified by the associated :doc:`bond_coeff <bond_coeff>` command.
There are also additional accelerated pair styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
@ -128,9 +126,6 @@ Related commands
Default
"""""""
bond\_style none
.. code-block:: LAMMPS
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html
bond_style none

36
doc/src/bond_table.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style table
.. index:: bond_style table
bond\_style table command
=========================
bond_style table command
========================
bond\_style table/omp command
=============================
bond_style table/omp command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style table style N
@ -21,7 +21,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style table linear 1000
bond_coeff 1 file.table ENTRY1
@ -31,14 +31,14 @@ Description
Style *table* creates interpolation tables of length *N* from bond
potential and force values listed in a file(s) as a function of bond
length. The files are read by the :doc:`bond\_coeff <bond_coeff>`
length. The files are read by the :doc:`bond_coeff <bond_coeff>`
command.
The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and force values at each of *N*
distances. During a simulation, these tables are used to interpolate
energy and force values as needed. The interpolation is done in one
of 2 styles: *linear* or *spline*\ .
of 2 styles: *linear* or *spline*.
For the *linear* style, the bond length is used to find 2 surrounding
table values from which an energy or force is computed by linear
@ -50,7 +50,7 @@ used to find the appropriate set of coefficients which are used to
evaluate a cubic polynomial which computes the energy or force.
The following coefficients must be defined for each bond type via the
:doc:`bond\_coeff <bond_coeff>` command as in the example above.
:doc:`bond_coeff <bond_coeff>` command as in the example above.
* filename
* keyword
@ -84,14 +84,14 @@ A section begins with a non-blank line whose 1st character is not a
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the
:doc:`bond\_coeff <bond_coeff>` command. The next line lists (in any
:doc:`bond_coeff <bond_coeff>` command. The next line lists (in any
order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values.
The parameter "N" is required and its value is the number of table
entries that follow. Note that this may be different than the *N*
specified in the :doc:`bond\_style table <bond_style>` command. Let
Ntable = *N* in the bond\_style command, and Nfile = "N" in the
Ntable = *N* in the bond_style command, and Nfile = "N" in the
tabulated file. What LAMMPS does is a preliminary interpolation by
creating splines using the Nfile tabulated values as nodal points. It
uses these to interpolate as needed to generate energy and force
@ -119,8 +119,9 @@ the bond length r (in distance units), the 3rd value is the energy (in
energy units), and the 4th is the force (in force units). The bond
lengths must range from a LO value to a HI value, and increase from
one line to the next. If the actual bond length is ever smaller than
the LO value or larger than the HI value, then the bond energy and
force is evaluated as if the bond were the LO or HI length.
the LO value or larger than the HI value, then the calculation is
aborted with an error, so it is advisable to cover the whole range
of possible bond lengths.
Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds
@ -173,11 +174,6 @@ info.
Related commands
""""""""""""""""
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

24
doc/src/bond_write.rst
View File

@ -1,13 +1,13 @@
.. index:: bond\_write
.. index:: bond_write
bond\_write command
===================
bond_write command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_write btype N inner outer file keyword itype jtype
@ -17,13 +17,12 @@ Syntax
* file = name of file to write values to
* keyword = section name in file for this set of tabulated values
* itype,jtype = 2 atom types (optional)
*
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_write 1 500 0.5 3.5 table.txt Harmonic_1
bond_write 3 1000 0.1 6.0 table.txt Morse
@ -40,14 +39,14 @@ file.
The energy and force values are computed at distances from inner to
outer for 2 interacting atoms forming a bond of type btype, using the
appropriate :doc:`bond\_coeff <bond_coeff>` coefficients. N evenly spaced
appropriate :doc:`bond_coeff <bond_coeff>` coefficients. N evenly spaced
distances are used.
For example, for N = 7, inner = 1.0, and outer = 4.0,
values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0.
The file is written in the format used as input for the
:doc:`bond\_style <bond_style>` *table* option with *keyword* as the
:doc:`bond_style <bond_style>` *table* option with *keyword* as the
section name. Each line written to the file lists an index number
(1-N), a distance (in distance units), an energy (in energy units),
and a force (in force units).
@ -65,12 +64,7 @@ be specified even if the potential has a finite value at r = 0.0.
Related commands
""""""""""""""""
:doc:`bond\_style table <bond_table>`,
:doc:`bond\_style <bond_style>`, :doc:`bond\_coeff <bond_coeff>`
:doc:`bond_style table <bond_table>`,
:doc:`bond_style <bond_style>`, :doc:`bond_coeff <bond_coeff>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

21
doc/src/bond_zero.rst
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@ -1,26 +1,26 @@
.. index:: bond\_style zero
.. index:: bond_style zero
bond\_style zero command
========================
bond_style zero command
=======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style zero *nocoeff*
bond_style zero [nocoeff]
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style zero
bond_style zero nocoeff
bond_coeff \*
bond_coeff \* 2.14
bond_coeff *
bond_coeff * 2.14
Description
"""""""""""
@ -53,8 +53,3 @@ Related commands
:doc:`bond\_style none <bond_none>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

1
doc/src/compute.rst
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@ -191,6 +191,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` doc
* :doc:`bond <compute_bond>` - energy of each bond sub-style
* :doc:`bond/local <compute_bond_local>` - distance and energy of each bond
* :doc:`centro/atom <compute_centro_atom>` - centro-symmetry parameter for each atom
* :doc:`centroid/stress/atom <compute_stress_atom>` - centroid based stress tensor for each atom
* :doc:`chunk/atom <compute_chunk_atom>` - assign chunk IDs to each atom
* :doc:`chunk/spread/atom <compute_chunk_spread_atom>` - spreads chunk values to each atom in chunk
* :doc:`cluster/atom <compute_cluster_atom>` - cluster ID for each atom

91
doc/src/compute_heat_flux.rst
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@ -54,38 +54,57 @@ third calculates per-atom stress (\ *stress-ID*\ ).
(or any group whose atoms are superset of the atoms in this compute's
group). LAMMPS does not check for this.
The Green-Kubo formulas relate the ensemble average of the
auto-correlation of the heat flux J to the thermal conductivity kappa:
In case of two-body interactions, the heat flux is defined as:
.. image:: Eqs/heat_flux_J.jpg
:align: center
.. math::
\mathbf{J} &= \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i - \sum_{i} \mathbf{S}_{i} \mathbf{v}_i \right] \\
&= \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i + \sum_{i<j} \left( \mathbf{F}_{ij} \cdot \mathbf{v}_j \right) \mathbf{r}_{ij} \right] \\
&= \frac{1}{V} \left[ \sum_i e_i \mathbf{v}_i + \frac{1}{2} \sum_{i<j} \left( \mathbf{F}_{ij} \cdot \left(\mathbf{v}_i + \mathbf{v}_j \right) \right) \mathbf{r}_{ij} \right]
.. image:: Eqs/heat_flux_k.jpg
:align: center
Ei in the first term of the equation for J is the per-atom energy
(potential and kinetic). This is calculated by the computes *ke-ID*
and *pe-ID*\ . Si in the second term of the equation for J is the
per-atom stress tensor calculated by the compute *stress-ID*\ . The
tensor multiplies Vi as a 3x3 matrix-vector multiply to yield a
vector. Note that as discussed below, the 1/V scaling factor in the
equation for J is NOT included in the calculation performed by this
compute; you need to add it for a volume appropriate to the atoms
:math:`e_i` in the first term of the equation
is the per-atom energy (potential and kinetic).
This is calculated by the computes *ke-ID*
and *pe-ID*. :math:`\mathbf{S}_i` in the second term is the
per-atom stress tensor calculated by the compute *stress-ID*.
See :doc:`compute stress/atom <compute_stress_atom>`
and :doc:`compute centroid/stress/atom <compute_stress_atom>`
for possible definitions of atomic stress :math:`\mathbf{S}_i`
in the case of bonded and many-body interactions.
The tensor multiplies :math:`\mathbf{v}_i` as a 3x3 matrix-vector multiply
to yield a vector.
Note that as discussed below, the 1/:math:`{V}` scaling factor in the
equation for :math:`\mathbf{J}` is NOT included in the calculation performed by
these computes; you need to add it for a volume appropriate to the atoms
included in the calculation.
.. note::
The :doc:`compute pe/atom <compute_pe_atom>` and :doc:`compute stress/atom <compute_stress_atom>` commands have options for which
The :doc:`compute pe/atom <compute_pe_atom>` and
:doc:`compute stress/atom <compute_stress_atom>`
commands have options for which
terms to include in their calculation (pair, bond, etc). The heat
flux calculation will thus include exactly the same terms. Normally
flux calculation will thus include exactly the same terms. Normally
you should use :doc:`compute stress/atom virial <compute_stress_atom>`
or :doc:`compute centroid/stress/atom virial <compute_stress_atom>`
so as not to include a kinetic energy term in the heat flux.
This compute calculates 6 quantities and stores them in a 6-component
vector. The first 3 components are the x, y, z components of the full
heat flux vector, i.e. (Jx, Jy, Jz). The next 3 components are the x,
y, z components of just the convective portion of the flux, i.e. the
first term in the equation for J above.
.. warning::
The compute *heat/flux* has been reported to produce unphysical
values for angle, dihedral and improper contributions
when used with :doc:`compute stress/atom <compute_stress_atom>`,
as discussed in :ref:`(Surblys) <Surblys2>` and :ref:`(Boone) <Boone>`.
You are strongly advised to
use :doc:`compute centroid/stress/atom <compute_stress_atom>`,
which has been implemented specifically for such cases.
The Green-Kubo formulas relate the ensemble average of the
auto-correlation of the heat flux :math:`\mathbf{J}`
to the thermal conductivity :math:`\kappa`:
.. math::
\kappa = \frac{V}{k_B T^2} \int_0^\infty \langle J_x(0) J_x(t) \rangle \, \mathrm{d} t = \frac{V}{3 k_B T^2} \int_0^\infty \langle \mathbf{J}(0) \cdot \mathbf{J}(t) \rangle \, \mathrm{d}t
----------
@ -109,9 +128,15 @@ result should be: average conductivity ~0.29 in W/mK.
**Output info:**
This compute calculates a global vector of length 6 (total heat flux
vector, followed by convective heat flux vector), which can be
accessed by indices 1-6. These values can be used by any command that
This compute calculates a global vector of length 6.
The first 3 components are the :math:`x`, :math:`y`, :math:`z`
components of the full heat flux vector,
i.e. (:math:`J_x`, :math:`J_y`, :math:`J_z`).
The next 3 components are the :math:`x`, :math:`y`, :math:`z` components
of just the convective portion of the flux, i.e. the
first term in the equation for :math:`\mathbf{J}`.
Each component can be
accessed by indices 1-6. These values can be used by any command that
uses global vector values from a compute as input. See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
options.
@ -212,6 +237,22 @@ Related commands
print "average conductivity: $k[W/mK] @ $T K, ${ndens} /A\^3"
----------
.. _Surblys2:
**(Surblys)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
.. _Boone:
**(Boone)** Boone, Babaei, Wilmer, J Chem Theory Comput, 15, 5579--5587 (2019).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

155
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@ -2,6 +2,8 @@
compute stress/atom command
===========================
compute centroid/stress/atom command
====================================
Syntax
""""""
@ -9,10 +11,10 @@ Syntax
.. parsed-literal::
compute ID group-ID stress/atom temp-ID keyword ...
compute ID group-ID style temp-ID keyword ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* stress/atom = style name of this compute command
* style = *stress/atom* or *centroid/stress/atom*
* temp-ID = ID of compute that calculates temperature, can be NULL if not needed
* zero or more keywords may be appended
* keyword = *ke* or *pair* or *bond* or *angle* or *dihedral* or *improper* or *kspace* or *fix* or *virial*
@ -26,38 +28,62 @@ Examples
compute 1 mobile stress/atom NULL
compute 1 mobile stress/atom myRamp
compute 1 all stress/atom NULL pair bond
compute 1 all centroid/stress/atom NULL bond dihedral improper
Description
"""""""""""
Define a computation that computes the symmetric per-atom stress
tensor for each atom in a group. The tensor for each atom has 6
Define a computation that computes per-atom stress
tensor for each atom in a group. In case of compute *stress/atom*,
the tensor for each atom is symmetric with 6
components and is stored as a 6-element vector in the following order:
xx, yy, zz, xy, xz, yz. See the :doc:`compute pressure <compute_pressure>` command if you want the stress tensor
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`.
In case of compute *centroid/stress/atom*,
the tensor for each atom is asymmetric with 9 components
and is stored as a 9-element vector in the following order:
:math:`xx`, :math:`yy`, :math:`zz`, :math:`xy`, :math:`xz`, :math:`yz`,
:math:`yx`, :math:`zx`, :math:`zy`.
See the :doc:`compute pressure <compute_pressure>` command if you want the stress tensor
(pressure) of the entire system.
The stress tensor for atom *I* is given by the following formula,
where *a* and *b* take on values x,y,z to generate the 6 components of
the symmetric tensor:
The stress tensor for atom :math:`I` is given by the following formula,
where :math:`a` and :math:`b` take on values :math:`x`, :math:`y`, :math:`z`
to generate the components of the tensor:
.. image:: Eqs/stress_tensor.jpg
:align: center
.. math::
The first term is a kinetic energy contribution for atom *I*\ . See
S_{ab} = - m v_a v_b - W_{ab}
The first term is a kinetic energy contribution for atom :math:`I`. See
details below on how the specified *temp-ID* can affect the velocities
used in this calculation. The second term is a pairwise energy
contribution where *n* loops over the *Np* neighbors of atom *I*\ , *r1*
and *r2* are the positions of the 2 atoms in the pairwise interaction,
and *F1* and *F2* are the forces on the 2 atoms resulting from the
pairwise interaction. The third term is a bond contribution of
similar form for the *Nb* bonds which atom *I* is part of. There are
similar terms for the *Na* angle, *Nd* dihedral, and *Ni* improper
interactions atom *I* is part of. There is also a term for the KSpace
contribution from long-range Coulombic interactions, if defined.
Finally, there is a term for the *Nf* :doc:`fixes <fix>` that apply
internal constraint forces to atom *I*\ . Currently, only the :doc:`fix shake <fix_shake>` and :doc:`fix rigid <fix_rigid>` commands
contribute to this term.
used in this calculation. The second term is the virial
contribution due to intra and intermolecular interactions,
where the exact computation details are determined by the compute style.
In case of compute *stress/atom*, the virial contribution is:
.. math::
W_{ab} & = \frac{1}{2} \sum_{n = 1}^{N_p} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b}) + \frac{1}{2} \sum_{n = 1}^{N_b} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b}) \\
& + \frac{1}{3} \sum_{n = 1}^{N_a} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b}) + \frac{1}{4} \sum_{n = 1}^{N_d} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) \\
& + \frac{1}{4} \sum_{n = 1}^{N_i} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
The first term is a pairwise energy
contribution where :math:`n` loops over the :math:`N_p`
neighbors of atom :math:`I`, :math:`\mathbf{r}_1` and :math:`\mathbf{r}_2`
are the positions of the 2 atoms in the pairwise interaction,
and :math:`\mathbf{F}_1` and :math:`\mathbf{F}_2` are the forces
on the 2 atoms resulting from the pairwise interaction.
The second term is a bond contribution of
similar form for the :math:`N_b` bonds which atom :math:`I` is part of.
There are similar terms for the :math:`N_a` angle, :math:`N_d` dihedral,
and :math:`N_i` improper interactions atom :math:`I` is part of.
There is also a term for the KSpace
contribution from long-range Coulombic interactions, if defined.
Finally, there is a term for the :math:`N_f` :doc:`fixes <fix>` that apply
internal constraint forces to atom :math:`I`. Currently, only the
:doc:`fix shake <fix_shake>` and :doc:`fix rigid <fix_rigid>` commands
contribute to this term.
As the coefficients in the formula imply, a virial contribution
produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
atoms in a Tersoff 3-body interaction) is assigned in equal portions
@ -66,7 +92,31 @@ the 4 atoms, or 1/3 of the fix virial due to SHAKE constraints applied
to atoms in a water molecule via the :doc:`fix shake <fix_shake>`
command.
If no extra keywords are listed, all of the terms in this formula are
In case of compute *centroid/stress/atom*, the virial contribution is:
.. math::
W_{ab} & = \sum_{n = 1}^{N_p} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_b} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_a} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_d} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_i} r_{I0_a} F_{I_b} \\
& + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
As with compute *stress/atom*, the first, second, third, fourth and fifth terms
are pairwise, bond, angle, dihedral and improper contributions,
but instead of assigning the virial contribution equally to each atom,
only the force :math:`\mathbf{F}_I` acting on atom :math:`I`
due to the interaction and the relative
position :math:`\mathbf{r}_{I0}` of the atom :math:`I` to the geometric center
of the interacting atoms, i.e. centroid, is used.
As the geometric center is different
for each interaction, the :math:`\mathbf{r}_{I0}` also differs.
The sixth and seventh terms, Kspace and :doc:`fix <fix>` contribution
respectively, are computed identical to compute *stress/atom*.
Although the total system virial is the same as compute *stress/atom*,
compute *centroid/stress/atom* is know to result in more consistent
heat flux values for angle, dihedrals and improper contributions
when computed via :doc:`compute heat/flux <compute_heat_flux>`.
If no extra keywords are listed, the kinetic contribution
all of the virial contribution terms are
included in the per-atom stress tensor. If any extra keywords are
listed, only those terms are summed to compute the tensor. The
*virial* keyword means include all terms except the kinetic energy
@ -75,17 +125,32 @@ listed, only those terms are summed to compute the tensor. The
Note that the stress for each atom is due to its interaction with all
other atoms in the simulation, not just with other atoms in the group.
Details of how LAMMPS computes the virial for individual atoms for
Details of how compute *stress/atom* obtains the virial for individual atoms for
either pairwise or many-body potentials, and including the effects of
periodic boundary conditions is discussed in :ref:`(Thompson) <Thompson2>`.
The basic idea for many-body potentials is to treat each component of
the force computation between a small cluster of atoms in the same
manner as in the formula above for bond, angle, dihedral, etc
interactions. Namely the quantity R dot F is summed over the atoms in
the interaction, with the R vectors unwrapped by periodic boundaries
interactions. Namely the quantity :math:`\mathbf{r} \cdot \mathbf{F}`
is summed over the atoms in
the interaction, with the :math:`r` vectors unwrapped by periodic boundaries
so that the cluster of atoms is close together. The total
contribution for the cluster interaction is divided evenly among those
atoms.
atoms. Details of how compute *centroid/stress/atom* obtains
the virial for individual atoms
is given in :ref:`(Surblys) <Surblys1>`,
where the idea is that the virial of the atom :math:`I`
is the result of only the force :math:`\mathbf{F}_I` on the atom due
to the interaction
and its positional vector :math:`\mathbf{r}_{I0}`,
relative to the geometric center of the
interacting atoms, regardless of the number of participating atoms.
The periodic boundary treatment is identical to
that of compute *stress/atom*, and both of them reduce to identical
expressions for two-body interactions,
i.e. computed values for contributions from bonds and two-body pair styles,
such as :doc:`Lennard-Jones <pair_lj>`, will be the same,
while contributions from angles, dihedrals and impropers will be different.
The :doc:`dihedral\_style charmm <dihedral_charmm>` style calculates
pairwise interactions between 1-4 atoms. The virial contribution of
@ -126,12 +191,13 @@ See the :doc:`compute voronoi/atom <compute_voronoi_atom>` command for
one possible way to estimate a per-atom volume.
Thus, if the diagonal components of the per-atom stress tensor are
summed for all atoms in the system and the sum is divided by dV, where
d = dimension and V is the volume of the system, the result should be
-P, where P is the total pressure of the system.
summed for all atoms in the system and the sum is divided by :math:`dV`, where
:math:`d` = dimension and :math:`V` is the volume of the system,
the result should be :math:`-P`, where :math:`P`
is the total pressure of the system.
These lines in an input script for a 3d system should yield that
result. I.e. the last 2 columns of thermo output will be the same:
result. I.e. the last 2 columns of thermo output will be the same:
.. parsed-literal::
@ -149,9 +215,12 @@ result. I.e. the last 2 columns of thermo output will be the same:
**Output info:**
This compute calculates a per-atom array with 6 columns, which can be
This compute *stress/atom* calculates a per-atom array with 6 columns, which can be
accessed by indices 1-6 by any command that uses per-atom values from
a compute as input. See the :doc:`Howto output <Howto_output>` doc page
a compute as input.
The compute *centroid/stress/atom* produces a per-atom array with 9 columns,
but otherwise can be used in an identical manner to compute *stress/atom*.
See the :doc:`Howto output <Howto_output>` doc page
for an overview of LAMMPS output options.
The per-atom array values will be in pressure\*volume
@ -159,7 +228,15 @@ The per-atom array values will be in pressure\*volume
Restrictions
""""""""""""
none
Currently, compute *centroid/stress/atom* does not support
pair styles with many-body interactions,
such as :doc:`Tersoff <pair_tersoff>`,
and LAMMPS will generate an error in such cases.
In principal, equivalent formulation
to that of angle, dihedral and improper contributions
in the virial :math:`W_{ab}` formula
can also be applied to the many-body pair styles,
and is planned in the future.
Related commands
""""""""""""""""
@ -176,7 +253,7 @@ Related commands
**(Heyes)** Heyes, Phys Rev B 49, 755 (1994),
**(Heyes)** Heyes, Phys Rev B, 49, 755 (1994).
.. _Sirk1:
@ -190,6 +267,12 @@ Related commands
**(Thompson)** Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).
.. _Surblys1:
**(Surblys)** Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html

54
doc/src/pair_list.rst
View File

@ -1,13 +1,13 @@
.. index:: pair\_style list
.. index:: pair_style list
pair\_style list command
========================
pair_style list command
=======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style list listfile cutoff keyword
@ -19,14 +19,14 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style list restraints.txt 200.0
pair_coeff \* \*
pair_coeff * *
pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
pair_coeff \* \* lj/cut 1.0 1.0
pair_coeff 3\* 3\* list
pair_coeff * * lj/cut 1.0 1.0
pair_coeff 3* 3* list
Description
"""""""""""
@ -77,36 +77,41 @@ Here is an example file:
The style *lj126* computes pairwise interactions with the formula
.. image:: Eqs/pair_lj.jpg
:align: center
.. math::
E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c
and the coefficients:
* epsilon (energy units)
* sigma (distance units)
* :math:`\epsilon` (energy units)
* :math:`\sigma` (distance units)
The style *morse* computes pairwise interactions with the formula
.. image:: Eqs/pair_morse.jpg
:align: center
.. math::
E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c
and the coefficients:
* D0 (energy units)
* alpha (1/distance units)
* r0 (distance units)
* :math:`D_0` (energy units)
* :math:`\alpha` (1/distance units)
* :math:`r_0` (distance units)
The style *harmonic* computes pairwise interactions with the formula
.. image:: Eqs/bond_harmonic.jpg
:align: center
.. math::
E = K (r - r_0)^2
and the coefficients:
* K (energy units)
* r0 (distance units)
* :math:`K` (energy units)
* :math:`r_0` (distance units)
Note that the usual 1/2 factor is included in K.
Note that the usual 1/2 factor is included in :math:`K`.
----------
@ -161,8 +166,3 @@ Related commands
:doc:`bond\_style harmonic <bond_harmonic>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html