Resolve merge conflict by merging in master and recreating Commands_compute.rst
This commit is contained in:
Axel Kohlmeyer
@ -9,9 +9,7 @@ if(BUILD_DOC)
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set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
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file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt)
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file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)
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list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})
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file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
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add_custom_command(
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OUTPUT docenv
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@ -28,25 +26,10 @@ if(BUILD_DOC)
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COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
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)
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set(RST_FILES "")
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set(RST_DIR ${CMAKE_BINARY_DIR}/rst)
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file(MAKE_DIRECTORY ${RST_DIR})
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foreach(TXT_FILE ${DOC_SOURCES})
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get_filename_component(FILENAME ${TXT_FILE} NAME_WE)
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set(RST_FILE ${RST_DIR}/${FILENAME}.rst)
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list(APPEND RST_FILES ${RST_FILE})
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add_custom_command(
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OUTPUT ${RST_FILE}
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DEPENDS requirements.txt docenv ${TXT_FILE}
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COMMAND ${DOCENV_BINARY_DIR}/txt2rst -o ${RST_DIR} ${TXT_FILE}
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)
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endforeach()
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add_custom_command(
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OUTPUT html
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DEPENDS ${RST_FILES}
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COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src ${RST_DIR}
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COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${RST_DIR} html
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DEPENDS ${DOC_SOURCES} docenv requirements.txt
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COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
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)
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add_custom_target(
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@ -1,4 +1,4 @@
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.TH LAMMPS "30 October 2019" "2019-10-30"
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.TH LAMMPS "20 November 2019" "2019-11-20"
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.SH NAME
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.B LAMMPS
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\- Molecular Dynamics Simulator.
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@ -14,55 +14,55 @@ Some styles have accelerated versions. This is indicated by
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additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
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KOKKOS, o = USER-OMP, t = OPT.
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :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>` |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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| :doc:`voronoi/atom <compute_voronoi_atom>` | :doc:`xrd <compute_xrd>` | | | | |
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+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+------------------------------------------------------------+
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
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| :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>` |
|
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
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| :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>` |
|
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
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| :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>` |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
|
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| :doc:`vcm/chunk <compute_vcm_chunk>` | :doc:`voronoi/atom <compute_voronoi_atom>` | :doc:`xrd <compute_xrd>` | | | |
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+------------------------------------------------------------+--------------------------------------------------------+------------------------------------------------------------------+--------------------------------------------------------------+----------------------------------------------------------+--------------------------------------------------------------+
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.. _lws: http://lammps.sandia.gov
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\documentclass[12pt]{article}
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\begin{document}
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$$
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E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4
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$$
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\end{document}
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\documentclass[12pt]{article}
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\begin{document}
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$$
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E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] +
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4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
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\left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
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$$
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\end{document}
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\documentclass[12pt]{article}
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\begin{document}
|
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$$
|
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E = -0.5 K R_0^2
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\ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] +
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4 \epsilon \left[ \left(\frac{\sigma}{\left(r -
|
||||
\Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r -
|
||||
\Delta\right)}\right)^6 \right] + \epsilon
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 2.1 KiB |
@ -1,10 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
\pagestyle{empty}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K (r^2 - r_0^2)^2
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 1.8 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = K (r - r_0)^2
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 5.0 KiB |
@ -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}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 5.1 KiB |
@ -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}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 5.7 KiB |
@ -1,9 +0,0 @@
|
||||
\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}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 2.5 KiB |
@ -1,10 +0,0 @@
|
||||
\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}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 3.5 KiB |
@ -1,9 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]}
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 3.8 KiB |
@ -1,10 +0,0 @@
|
||||
\documentclass[12pt]{article}
|
||||
\pagestyle{empty}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r0}{\Delta}\right)^2\right]
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 9.3 KiB |
@ -1,11 +0,0 @@
|
||||
\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}
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
|
||||
@ -35,6 +35,7 @@ KOKKOS, o = USER-OMP, t = OPT.
|
||||
"bond"_compute_bond.html,
|
||||
"bond/local"_compute_bond_local.html,
|
||||
"centro/atom"_compute_centro_atom.html,
|
||||
"centroid/stress/atom"_compute_stress_atom.html,
|
||||
"chunk/atom"_compute_chunk_atom.html,
|
||||
"chunk/spread/atom"_compute_chunk_spread_atom.html,
|
||||
"cluster/atom"_compute_cluster_atom.html,
|
||||
|
||||
@ -1,175 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS
|
||||
Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
atom_modify command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
atom_modify keyword values ... :pre
|
||||
|
||||
one or more keyword/value pairs may be appended :ulb,l
|
||||
keyword = {id} or {map} or {first} or {sort} :l
|
||||
{id} value = {yes} or {no}
|
||||
{map} value = {yes} or {array} or {hash}
|
||||
{first} value = group-ID = group whose atoms will appear first in internal atom lists
|
||||
{sort} values = Nfreq binsize
|
||||
Nfreq = sort atoms spatially every this many time steps
|
||||
binsize = bin size for spatial sorting (distance units) :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
atom_modify map yes
|
||||
atom_modify map hash sort 10000 2.0
|
||||
atom_modify first colloid :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Modify certain attributes of atoms defined and stored within LAMMPS,
|
||||
in addition to what is specified by the "atom_style"_atom_style.html
|
||||
command. The {id} and {map} keywords must be specified before a
|
||||
simulation box is defined; other keywords can be specified any time.
|
||||
|
||||
The {id} keyword determines whether non-zero atom IDs can be assigned
|
||||
to each atom. If the value is {yes}, which is the default, IDs are
|
||||
assigned, whether you use the "create atoms"_create_atoms.html or
|
||||
"read_data"_read_data.html or "read_restart"_read_restart.html
|
||||
commands to initialize atoms. If the value is {no} the IDs for all
|
||||
atoms are assumed to be 0.
|
||||
|
||||
If atom IDs are used, they must all be positive integers. They should
|
||||
also be unique, though LAMMPS does not check for this. Typically they
|
||||
should also be consecutively numbered (from 1 to Natoms), though this
|
||||
is not required. Molecular "atom styles"_atom_style.html are those
|
||||
that store bond topology information (styles bond, angle, molecular,
|
||||
full). These styles require atom IDs since the IDs are used to encode
|
||||
the topology. Some other LAMMPS commands also require the use of atom
|
||||
IDs. E.g. some many-body pair styles use them to avoid double
|
||||
computation of the I-J interaction between two atoms.
|
||||
|
||||
The only reason not to use atom IDs is if you are running an atomic
|
||||
simulation so large that IDs cannot be uniquely assigned. For a
|
||||
default LAMMPS build this limit is 2^31 or about 2 billion atoms.
|
||||
However, even in this case, you can use 64-bit atom IDs, allowing 2^63
|
||||
or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG
|
||||
switch. This is described on the "Build_settings"_Build_settings.html
|
||||
doc page. If atom IDs are not used, they must be specified as 0 for
|
||||
all atoms, e.g. in a data or restart file.
|
||||
|
||||
The {map} keyword determines how atoms with specific IDs are found
|
||||
when required. An example are the bond (angle, etc) methods which
|
||||
need to find the local index of an atom with a specific global ID
|
||||
which is a bond (angle, etc) partner. LAMMPS performs this operation
|
||||
efficiently by creating a "map", which is either an {array} or {hash}
|
||||
table, as described below.
|
||||
|
||||
When the {map} keyword is not specified in your input script, LAMMPS
|
||||
only creates a map for "atom_styles"_atom_style.html for molecular
|
||||
systems which have permanent bonds (angles, etc). No map is created
|
||||
for atomic systems, since it is normally not needed. However some
|
||||
LAMMPS commands require a map, even for atomic systems, and will
|
||||
generate an error if one does not exist. The {map} keyword thus
|
||||
allows you to force the creation of a map. The {yes} value will
|
||||
create either an {array} or {hash} style map, as explained in the next
|
||||
paragraph. The {array} and {hash} values create an atom-style or
|
||||
hash-style map respectively.
|
||||
|
||||
For an {array}-style map, each processor stores a lookup table of
|
||||
length N, where N is the largest atom ID in the system. This is a
|
||||
fast, simple method for many simulations, but requires too much memory
|
||||
for large simulations. For a {hash}-style map, a hash table is
|
||||
created on each processor, which finds an atom ID in constant time
|
||||
(independent of the global number of atom IDs). It can be slightly
|
||||
slower than the {array} map, but its memory cost is proportional to
|
||||
the number of atoms owned by a processor, i.e. N/P when N is the total
|
||||
number of atoms in the system and P is the number of processors.
|
||||
|
||||
The {first} keyword allows a "group"_group.html to be specified whose
|
||||
atoms will be maintained as the first atoms in each processor's list
|
||||
of owned atoms. This in only useful when the specified group is a
|
||||
small fraction of all the atoms, and there are other operations LAMMPS
|
||||
is performing that will be sped-up significantly by being able to loop
|
||||
over the smaller set of atoms. Otherwise the reordering required by
|
||||
this option will be a net slow-down. The "neigh_modify
|
||||
include"_neigh_modify.html and "comm_modify group"_comm_modify.html
|
||||
commands are two examples of commands that require this setting to
|
||||
work efficiently. Several "fixes"_fix.html, most notably time
|
||||
integration fixes like "fix nve"_fix_nve.html, also take advantage of
|
||||
this setting if the group they operate on is the group specified by
|
||||
this command. Note that specifying "all" as the group-ID effectively
|
||||
turns off the {first} option.
|
||||
|
||||
It is OK to use the {first} keyword with a group that has not yet been
|
||||
defined, e.g. to use the atom_modify first command at the beginning of
|
||||
your input script. LAMMPS does not use the group until a simulation
|
||||
is run.
|
||||
|
||||
The {sort} keyword turns on a spatial sorting or reordering of atoms
|
||||
within each processor's sub-domain every {Nfreq} timesteps. If
|
||||
{Nfreq} is set to 0, then sorting is turned off. Sorting can improve
|
||||
cache performance and thus speed-up a LAMMPS simulation, as discussed
|
||||
in a paper by "(Meloni)"_#Meloni. Its efficacy depends on the problem
|
||||
size (atoms/processor), how quickly the system becomes disordered, and
|
||||
various other factors. As a general rule, sorting is typically more
|
||||
effective at speeding up simulations of liquids as opposed to solids.
|
||||
In tests we have done, the speed-up can range from zero to 3-4x.
|
||||
|
||||
Reordering is performed every {Nfreq} timesteps during a dynamics run
|
||||
or iterations during a minimization. More precisely, reordering
|
||||
occurs at the first reneighboring that occurs after the target
|
||||
timestep. The reordering is performed locally by each processor,
|
||||
using bins of the specified {binsize}. If {binsize} is set to 0.0,
|
||||
then a binsize equal to half the "neighbor"_neighbor.html cutoff
|
||||
distance (force cutoff plus skin distance) is used, which is a
|
||||
reasonable value. After the atoms have been binned, they are
|
||||
reordered so that atoms in the same bin are adjacent to each other in
|
||||
the processor's 1d list of atoms.
|
||||
|
||||
The goal of this procedure is for atoms to put atoms close to each
|
||||
other in the processor's one-dimensional list of atoms that are also
|
||||
near to each other spatially. This can improve cache performance when
|
||||
pairwise interactions and neighbor lists are computed. Note that if
|
||||
bins are too small, there will be few atoms/bin. Likewise if bins are
|
||||
too large, there will be many atoms/bin. In both cases, the goal of
|
||||
cache locality will be undermined.
|
||||
|
||||
NOTE: Running a simulation with sorting on versus off should not
|
||||
change the simulation results in a statistical sense. However, a
|
||||
different ordering will induce round-off differences, which will lead
|
||||
to diverging trajectories over time when comparing two simulations.
|
||||
Various commands, particularly those which use random numbers
|
||||
(e.g. "velocity create"_velocity.html, and "fix
|
||||
langevin"_fix_langevin.html), may generate (statistically identical)
|
||||
results which depend on the order in which atoms are processed. The
|
||||
order of atoms in a "dump"_dump.html file will also typically change
|
||||
if sorting is enabled.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The {first} and {sort} options cannot be used together. Since sorting
|
||||
is on by default, it will be turned off if the {first} keyword is
|
||||
used with a group-ID that is not "all".
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
[Default:]
|
||||
|
||||
By default, {id} is yes. By default, atomic systems (no bond topology
|
||||
info) do not use a map. For molecular systems (with bond topology
|
||||
info), a map is used. The default map style is array if no atom ID is
|
||||
larger than 1 million, otherwise the default is hash. By default, a
|
||||
"first" group is not defined. By default, sorting is enabled with a
|
||||
frequency of 1000 and a binsize of 0.0, which means the neighbor
|
||||
cutoff will be used to set the bin size. If no neighbor cutoff is
|
||||
defined, sorting will be turned off.
|
||||
|
||||
:line
|
||||
|
||||
:link(Meloni)
|
||||
[(Meloni)] Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).
|
||||
@ -1,338 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
atom_style command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
atom_style style args :pre
|
||||
|
||||
style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
|
||||
{dpd} or {edpd} or {mdpd} or {tdpd} or {electron} or {ellipsoid} or \
|
||||
{full} or {line} or {meso} or {molecular} or {peri} or {smd} or \
|
||||
{sphere} or {spin} or {tri} or {template} or {hybrid} :ulb,l
|
||||
args = none for any style except the following
|
||||
{body} args = bstyle bstyle-args
|
||||
bstyle = style of body particles
|
||||
bstyle-args = additional arguments specific to the bstyle
|
||||
see the "Howto body"_Howto_body.html doc page for details
|
||||
{tdpd} arg = Nspecies
|
||||
Nspecies = # of chemical species
|
||||
{template} arg = template-ID
|
||||
template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
|
||||
{hybrid} args = list of one or more sub-styles, each with their args :pre
|
||||
|
||||
accelerated styles (with same args) = {angle/kk} or {atomic/kk} or {bond/kk} or {charge/kk} or {full/kk} or {molecular/kk} :l
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
atom_style atomic
|
||||
atom_style bond
|
||||
atom_style full
|
||||
atom_style body nparticle 2 10
|
||||
atom_style hybrid charge bond
|
||||
atom_style hybrid charge body nparticle 2 5
|
||||
atom_style spin
|
||||
atom_style template myMols
|
||||
atom_style tdpd 2 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define what style of atoms to use in a simulation. This determines
|
||||
what attributes are associated with the atoms. This command must be
|
||||
used before a simulation is setup via a "read_data"_read_data.html,
|
||||
"read_restart"_read_restart.html, or "create_box"_create_box.html
|
||||
command.
|
||||
|
||||
NOTE: Many of the atom styles discussed here are only enabled if
|
||||
LAMMPS was built with a specific package, as listed below in the
|
||||
Restrictions section.
|
||||
|
||||
Once a style is assigned, it cannot be changed, so use a style general
|
||||
enough to encompass all attributes. E.g. with style {bond}, angular
|
||||
terms cannot be used or added later to the model. It is OK to use a
|
||||
style more general than needed, though it may be slightly inefficient.
|
||||
|
||||
The choice of style affects what quantities are stored by each atom,
|
||||
what quantities are communicated between processors to enable forces
|
||||
to be computed, and what quantities are listed in the data file read
|
||||
by the "read_data"_read_data.html command.
|
||||
|
||||
These are the additional attributes of each style and the typical
|
||||
kinds of physical systems they are used to model. All styles store
|
||||
coordinates, velocities, atom IDs and types. See the
|
||||
"read_data"_read_data.html, "create_atoms"_create_atoms.html, and
|
||||
"set"_set.html commands for info on how to set these various
|
||||
quantities.
|
||||
|
||||
{angle} | bonds and angles | bead-spring polymers with stiffness |
|
||||
{atomic} | only the default values | coarse-grain liquids, solids, metals |
|
||||
{body} | mass, inertia moments, quaternion, angular momentum | arbitrary bodies |
|
||||
{bond} | bonds | bead-spring polymers |
|
||||
{charge} | charge | atomic system with charges |
|
||||
{dipole} | charge and dipole moment | system with dipolar particles |
|
||||
{dpd} | internal temperature and internal energies | DPD particles |
|
||||
{edpd} | temperature and heat capacity | eDPD particles |
|
||||
{mdpd} | density | mDPD particles |
|
||||
{tdpd} | chemical concentration | tDPD particles |
|
||||
{electron} | charge and spin and eradius | electronic force field |
|
||||
{ellipsoid} | shape, quaternion, angular momentum | aspherical particles |
|
||||
{full} | molecular + charge | bio-molecules |
|
||||
{line} | end points, angular velocity | rigid bodies |
|
||||
{meso} | rho, e, cv | SPH particles |
|
||||
{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
|
||||
{peri} | mass, volume | mesoscopic Peridynamic models |
|
||||
{smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
|
||||
{sphere} | diameter, mass, angular velocity | granular models |
|
||||
{spin} | magnetic moment | system with magnetic particles |
|
||||
{template} | template index, template atom | small molecules with fixed topology |
|
||||
{tri} | corner points, angular momentum | rigid bodies |
|
||||
{wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|)
|
||||
|
||||
NOTE: It is possible to add some attributes, such as a molecule ID, to
|
||||
atom styles that do not have them via the "fix
|
||||
property/atom"_fix_property_atom.html command. This command also
|
||||
allows new custom attributes consisting of extra integer or
|
||||
floating-point values to be added to atoms. See the "fix
|
||||
property/atom"_fix_property_atom.html doc page for examples of cases
|
||||
where this is useful and details on how to initialize, access, and
|
||||
output the custom values.
|
||||
|
||||
All of the above styles define point particles, except the {sphere},
|
||||
{ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, {tri}, and
|
||||
{body} styles, which define finite-size particles. See the "Howto
|
||||
spherical"_Howto_spherical.html doc page for an overview of using
|
||||
finite-size particle models with LAMMPS.
|
||||
|
||||
All of the point-particle styles assign mass to particles on a
|
||||
per-type basis, using the "mass"_mass.html command, The finite-size
|
||||
particle styles assign mass to individual particles on a per-particle
|
||||
basis.
|
||||
|
||||
For the {sphere} style, the particles are spheres and each stores a
|
||||
per-particle diameter and mass. If the diameter > 0.0, the particle
|
||||
is a finite-size sphere. If the diameter = 0.0, it is a point
|
||||
particle. Note that by use of the {disc} keyword with the "fix
|
||||
nve/sphere"_fix_nve_sphere.html, "fix nvt/sphere"_fix_nvt_sphere.html,
|
||||
"fix nph/sphere"_fix_nph_sphere.html, "fix
|
||||
npt/sphere"_fix_npt_sphere.html commands, spheres can be effectively
|
||||
treated as 2d discs for a 2d simulation if desired. See also the "set
|
||||
density/disc"_set.html command.
|
||||
|
||||
For the {ellipsoid} style, the particles are ellipsoids and each
|
||||
stores a flag which indicates whether it is a finite-size ellipsoid or
|
||||
a point particle. If it is an ellipsoid, it also stores a shape
|
||||
vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
|
||||
with its orientation.
|
||||
|
||||
For the {dipole} style, a point dipole is defined for each point
|
||||
particle. Note that if you wish the particles to be finite-size
|
||||
spheres as in a Stockmayer potential for a dipolar fluid, so that the
|
||||
particles can rotate due to dipole-dipole interactions, then you need
|
||||
to use atom_style hybrid sphere dipole, which will assign both a
|
||||
diameter and dipole moment to each particle.
|
||||
|
||||
For the {electron} style, the particles representing electrons are 3d
|
||||
Gaussians with a specified position and bandwidth or uncertainty in
|
||||
position, which is represented by the eradius = electron size.
|
||||
|
||||
For the {peri} style, the particles are spherical and each stores a
|
||||
per-particle mass and volume.
|
||||
|
||||
The {dpd} style is for dissipative particle dynamics (DPD) particles.
|
||||
Note that it is part of the USER-DPD package, and is not for use with
|
||||
the "pair_style dpd or dpd/stat"_pair_dpd.html commands, which can
|
||||
simply use atom_style atomic. Atom_style dpd extends DPD particle
|
||||
properties with internal temperature (dpdTheta), internal conductive
|
||||
energy (uCond), internal mechanical energy (uMech), and internal
|
||||
chemical energy (uChem).
|
||||
|
||||
The {edpd} style is for energy-conserving dissipative particle
|
||||
dynamics (eDPD) particles which store a temperature (edpd_temp), and
|
||||
heat capacity(edpd_cv).
|
||||
|
||||
The {mdpd} style is for many-body dissipative particle dynamics (mDPD)
|
||||
particles which store a density (rho) for considering
|
||||
density-dependent many-body interactions.
|
||||
|
||||
The {tdpd} style is for transport dissipative particle dynamics (tDPD)
|
||||
particles which store a set of chemical concentration. An integer
|
||||
"cc_species" is required to specify the number of chemical species
|
||||
involved in a tDPD system.
|
||||
|
||||
The {meso} style is for smoothed particle hydrodynamics (SPH)
|
||||
particles which store a density (rho), energy (e), and heat capacity
|
||||
(cv).
|
||||
|
||||
The {smd} style is for a general formulation of Smooth Particle
|
||||
Hydrodynamics. Both fluids and solids can be modeled. Particles
|
||||
store the mass and volume of an integration point, a kernel diameter
|
||||
used for calculating the field variables (e.g. stress and deformation)
|
||||
and a contact radius for calculating repulsive forces which prevent
|
||||
individual physical bodies from penetrating each other.
|
||||
|
||||
For the {spin} style, a magnetic spin is associated to each atom.
|
||||
Those spins have a norm (their magnetic moment) and a direction.
|
||||
|
||||
The {wavepacket} style is similar to {electron}, but the electrons may
|
||||
consist of several Gaussian wave packets, summed up with coefficients
|
||||
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
|
||||
particle in LAMMPS, wave packets belonging to the same electron must
|
||||
have identical {etag} values.
|
||||
|
||||
For the {line} style, the particles are idealized line segments and
|
||||
each stores a per-particle mass and length and orientation (i.e. the
|
||||
end points of the line segment).
|
||||
|
||||
For the {tri} style, the particles are planar triangles and each
|
||||
stores a per-particle mass and size and orientation (i.e. the corner
|
||||
points of the triangle).
|
||||
|
||||
The {template} style allows molecular topology (bonds,angles,etc) to be
|
||||
defined via a molecule template using the "molecule"_molecule.html
|
||||
command. The template stores one or more molecules with a single copy
|
||||
of the topology info (bonds,angles,etc) of each. Individual atoms
|
||||
only store a template index and template atom to identify which
|
||||
molecule and which atom-within-the-molecule they represent. Using the
|
||||
{template} style instead of the {bond}, {angle}, {molecular} styles
|
||||
can save memory for systems comprised of a large number of small
|
||||
molecules, all of a single type (or small number of types). See the
|
||||
paper by Grime and Voth, in "(Grime)"_#Grime, for examples of how this
|
||||
can be advantageous for large-scale coarse-grained systems.
|
||||
|
||||
NOTE: When using the {template} style with a "molecule
|
||||
template"_molecule.html that contains multiple molecules, you should
|
||||
insure the atom types, bond types, angle_types, etc in all the
|
||||
molecules are consistent. E.g. if one molecule represents H2O and
|
||||
another CO2, then you probably do not want each molecule file to
|
||||
define 2 atom types and a single bond type, because they will conflict
|
||||
with each other when a mixture system of H2O and CO2 molecules is
|
||||
defined, e.g. by the "read_data"_read_data.html command. Rather the
|
||||
H2O molecule should define atom types 1 and 2, and bond type 1. And
|
||||
the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
|
||||
2 if a single oxygen type is desired), and bond type 2.
|
||||
|
||||
For the {body} style, the particles are arbitrary bodies with internal
|
||||
attributes defined by the "style" of the bodies, which is specified by
|
||||
the {bstyle} argument. Body particles can represent complex entities,
|
||||
such as surface meshes of discrete points, collections of
|
||||
sub-particles, deformable objects, etc.
|
||||
|
||||
The "Howto body"_Howto_body.html doc page describes the body styles
|
||||
LAMMPS currently supports, and provides more details as to the kind of
|
||||
body particles they represent. For all styles, each body particle
|
||||
stores moments of inertia and a quaternion 4-vector, so that its
|
||||
orientation and position can be time integrated due to forces and
|
||||
torques.
|
||||
|
||||
Note that there may be additional arguments required along with the
|
||||
{bstyle} specification, in the atom_style body command. These
|
||||
arguments are described on the "Howto body"_Howto_body.html doc page.
|
||||
|
||||
:line
|
||||
|
||||
Typically, simulations require only a single (non-hybrid) atom style.
|
||||
If some atoms in the simulation do not have all the properties defined
|
||||
by a particular style, use the simplest style that defines all the
|
||||
needed properties by any atom. For example, if some atoms in a
|
||||
simulation are charged, but others are not, use the {charge} style.
|
||||
If some atoms have bonds, but others do not, use the {bond} style.
|
||||
|
||||
The only scenario where the {hybrid} style is needed is if there is no
|
||||
single style which defines all needed properties of all atoms. For
|
||||
example, as mentioned above, if you want dipolar particles which will
|
||||
rotate due to torque, you need to use "atom_style hybrid sphere
|
||||
dipole". When a hybrid style is used, atoms store and communicate the
|
||||
union of all quantities implied by the individual styles.
|
||||
|
||||
When using the {hybrid} style, you cannot combine the {template} style
|
||||
with another molecular style that stores bond,angle,etc info on a
|
||||
per-atom basis.
|
||||
|
||||
LAMMPS can be extended with new atom styles as well as new body
|
||||
styles; see the "Modify"_Modify.html doc page.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {kk} suffix are functionally the same as the
|
||||
corresponding style without the suffix. They have been optimized to
|
||||
run faster, depending on your available hardware, as discussed in on
|
||||
the "Speed packages"_Speed_packages.html doc page. The accelerated
|
||||
styles take the same arguments and should produce the same results,
|
||||
except for round-off and precision issues.
|
||||
|
||||
Note that other acceleration packages in LAMMPS, specifically the GPU,
|
||||
USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom
|
||||
styles.
|
||||
|
||||
The accelerated styles are part of the KOKKOS package. They are only
|
||||
enabled if LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command cannot be used after the simulation box is defined by a
|
||||
"read_data"_read_data.html or "create_box"_create_box.html command.
|
||||
|
||||
Many of the styles listed above are only enabled if LAMMPS was built
|
||||
with a specific package, as listed below. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
The {angle}, {bond}, {full}, {molecular}, and {template} styles are
|
||||
part of the MOLECULE package.
|
||||
|
||||
The {line} and {tri} styles are part of the ASPHERE package.
|
||||
|
||||
The {body} style is part of the BODY package.
|
||||
|
||||
The {dipole} style is part of the DIPOLE package.
|
||||
|
||||
The {peri} style is part of the PERI package for Peridynamics.
|
||||
|
||||
The {electron} style is part of the USER-EFF package for "electronic
|
||||
force fields"_pair_eff.html.
|
||||
|
||||
The {dpd} style is part of the USER-DPD package for dissipative
|
||||
particle dynamics (DPD).
|
||||
|
||||
The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package
|
||||
for energy-conserving dissipative particle dynamics (eDPD), many-body
|
||||
dissipative particle dynamics (mDPD), and transport dissipative particle
|
||||
dynamics (tDPD), respectively.
|
||||
|
||||
The {meso} style is part of the USER-SPH package for smoothed particle
|
||||
hydrodynamics (SPH). See "this PDF
|
||||
guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS.
|
||||
|
||||
The {spin} style is part of the SPIN package.
|
||||
|
||||
The {wavepacket} style is part of the USER-AWPMD package for the
|
||||
"antisymmetrized wave packet MD method"_pair_awpmd.html.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"read_data"_read_data.html, "pair_style"_pair_style.html
|
||||
|
||||
[Default:]
|
||||
|
||||
atom_style atomic
|
||||
|
||||
:line
|
||||
|
||||
:link(Grime)
|
||||
[(Grime)] Grime and Voth, to appear in J Chem Theory & Computation
|
||||
(2014).
|
||||
@ -1,81 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_style class2 command :h3
|
||||
bond_style class2/omp command :h3
|
||||
bond_style class2/kk command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style class2 :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_style class2
|
||||
bond_coeff 1 1.0 100.0 80.0 80.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {class2} bond style uses the potential
|
||||
|
||||
:c,image(Eqs/bond_class2.jpg)
|
||||
|
||||
where r0 is the equilibrium bond distance.
|
||||
|
||||
See "(Sun)"_#bond-Sun for a description of the COMPASS class2 force field.
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
"bond_coeff"_bond_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
R0 (distance)
|
||||
K2 (energy/distance^2)
|
||||
K3 (energy/distance^3)
|
||||
K4 (energy/distance^4) :ul
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This bond style can only be used if LAMMPS was built with the CLASS2
|
||||
package. See the "Build package"_Build_package.html doc page for more
|
||||
info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(bond-Sun)
|
||||
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).
|
||||
@ -1,82 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_coeff command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_coeff N args :pre
|
||||
|
||||
N = bond type (see asterisk form below)
|
||||
args = coefficients for one or more bond types :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
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 1 harmonic 200.0 1.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Specify the bond force field coefficients for one or more bond types.
|
||||
The number and meaning of the coefficients depends on the bond style.
|
||||
Bond coefficients can also be set in the data file read by the
|
||||
"read_data"_read_data.html command or in a restart file.
|
||||
|
||||
N can be specified in one of two ways. An explicit numeric value can
|
||||
be used, as in the 1st example above. Or a wild-card asterisk can be
|
||||
used to set the coefficients for multiple bond types. This takes the
|
||||
form "*" or "*n" or "n*" or "m*n". If N = the number of bond types,
|
||||
then an asterisk with no numeric values means all types from 1 to N. A
|
||||
leading asterisk means all types from 1 to n (inclusive). A trailing
|
||||
asterisk means all types from n to N (inclusive). A middle asterisk
|
||||
means all types from m to n (inclusive).
|
||||
|
||||
Note that using a bond_coeff command can override a previous setting
|
||||
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:
|
||||
|
||||
bond_coeff * 100.0 1.2
|
||||
bond_coeff 2 200.0 1.2 :pre
|
||||
|
||||
A line in a data file that specifies bond coefficients uses the exact
|
||||
same format as the arguments of the bond_coeff command in an input
|
||||
script, except that wild-card asterisks should not be used since
|
||||
coefficients for all N types must be listed in the file. For example,
|
||||
under the "Bond Coeffs" section of a data file, the line that
|
||||
corresponds to the 1st example above would be listed as
|
||||
|
||||
5 80.0 1.2 :pre
|
||||
|
||||
:line
|
||||
|
||||
The list of all bond styles defined in LAMMPS is given on the
|
||||
"bond_style"_bond_style.html doc page. They are also listed in more
|
||||
compact form on the "Commands bond"_Commands_bond.html doc page.
|
||||
|
||||
On either of those pages, click on the style to display the formula it
|
||||
computes and its coefficients as specified by the associated
|
||||
bond_coeff command.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This command must come after the simulation box is defined by a
|
||||
"read_data"_read_data.html, "read_restart"_read_restart.html, or
|
||||
"create_box"_create_box.html command.
|
||||
|
||||
A bond style must be defined before any bond coefficients are set,
|
||||
either in the input script or in a data file.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_style"_bond_style.html
|
||||
|
||||
[Default:] none
|
||||
@ -1,88 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_style fene command :h3
|
||||
bond_style fene/intel command :h3
|
||||
bond_style fene/kk command :h3
|
||||
bond_style fene/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style fene :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_style fene
|
||||
bond_coeff 1 30.0 1.5 1.0 1.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {fene} bond style uses the potential
|
||||
|
||||
:c,image(Eqs/bond_fene.jpg)
|
||||
|
||||
to define a finite extensible nonlinear elastic (FENE) potential
|
||||
"(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.
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
"bond_coeff"_bond_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
K (energy/distance^2)
|
||||
R0 (distance)
|
||||
epsilon (energy)
|
||||
sigma (distance) :ul
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This bond style can only be used if LAMMPS was built with the MOLECULE
|
||||
package. See the "Build package"_Build_package.html doc page for more
|
||||
info.
|
||||
|
||||
You typically should specify "special_bonds fene"_special_bonds.html
|
||||
or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
|
||||
style. LAMMPS will issue a warning it that's not the case.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(fene-Kremer)
|
||||
[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).
|
||||
@ -1,91 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_style fene/expand command :h3
|
||||
bond_style fene/expand/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style fene/expand :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_style fene/expand
|
||||
bond_coeff 1 30.0 1.5 1.0 1.0 0.5 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {fene/expand} bond style uses the potential
|
||||
|
||||
:c,image(Eqs/bond_fene_expand.jpg)
|
||||
|
||||
to define a finite extensible nonlinear elastic (FENE) potential
|
||||
"(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
|
||||
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.
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
"bond_coeff"_bond_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
K (energy/distance^2)
|
||||
R0 (distance)
|
||||
epsilon (energy)
|
||||
sigma (distance)
|
||||
delta (distance) :ul
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This bond style can only be used if LAMMPS was built with the MOLECULE
|
||||
package. See the "Build package"_Build_package.html doc page for more
|
||||
info.
|
||||
|
||||
You typically should specify "special_bonds fene"_special_bonds.html
|
||||
or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
|
||||
style. LAMMPS will issue a warning it that's not the case.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(feneexpand-Kremer)
|
||||
[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).
|
||||
@ -1,72 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_style gromos command :h3
|
||||
bond_style gromos/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style gromos :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_style gromos
|
||||
bond_coeff 5 80.0 1.2 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {gromos} bond style uses the potential
|
||||
|
||||
:c,image(Eqs/bond_gromos.jpg)
|
||||
|
||||
where r0 is the equilibrium bond distance. Note that the usual 1/4
|
||||
factor is included in K.
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
"bond_coeff"_bond_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
K (energy/distance^4)
|
||||
r0 (distance) :ul
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This bond style can only be used if LAMMPS was built with the MOLECULE
|
||||
package. See the "Build package"_Build_package.html doc page for more
|
||||
info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
|
||||
|
||||
[Default:] none
|
||||
@ -1,74 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_style harmonic command :h3
|
||||
bond_style harmonic/intel command :h3
|
||||
bond_style harmonic/kk command :h3
|
||||
bond_style harmonic/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style harmonic :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 5 80.0 1.2 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {harmonic} bond style uses the potential
|
||||
|
||||
:c,image(Eqs/bond_harmonic.jpg)
|
||||
|
||||
where r0 is the equilibrium bond distance. Note that the usual 1/2
|
||||
factor is included in K.
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
"bond_coeff"_bond_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
K (energy/distance^2)
|
||||
r0 (distance) :ul
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This bond style can only be used if LAMMPS was built with the MOLECULE
|
||||
package. See the "Build package"_Build_package.html doc page for more
|
||||
info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
|
||||
|
||||
[Default:] none
|
||||
@ -1,76 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_style harmonic/shift command :h3
|
||||
bond_style harmonic/shift/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style harmonic/shift :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_style harmonic/shift
|
||||
bond_coeff 5 10.0 0.5 1.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {harmonic/shift} bond style is a shifted harmonic bond that uses
|
||||
the potential
|
||||
|
||||
:c,image(Eqs/bond_harmonic_shift.jpg)
|
||||
|
||||
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 / \[ 2 (r0-rc)^2\].
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
"bond_coeff"_bond_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
Umin (energy) :ul
|
||||
r0 (distance) :ul
|
||||
rc (distance) :ul
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This bond style can only be used if LAMMPS was built with the
|
||||
USER-MISC package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html,
|
||||
"bond_harmonic"_bond_harmonic.html
|
||||
|
||||
[Default:] none
|
||||
@ -1,77 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_style harmonic/shift/cut command :h3
|
||||
bond_style harmonic/shift/cut/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style harmonic/shift/cut :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_style harmonic/shift/cut
|
||||
bond_coeff 5 10.0 0.5 1.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {harmonic/shift/cut} bond style is a shifted harmonic bond that
|
||||
uses the potential
|
||||
|
||||
:c,image(Eqs/bond_harmonic_shift_cut.jpg)
|
||||
|
||||
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 / \[ 2 (r0-rc)^2\].
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
"bond_coeff"_bond_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
Umin (energy)
|
||||
r0 (distance)
|
||||
rc (distance) :ul
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This bond style can only be used if LAMMPS was built with the
|
||||
USER-MISC package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html,
|
||||
"bond_harmonic"_bond_harmonic.html,
|
||||
"bond_harmonic_shift"_bond_harmonic_shift.html
|
||||
|
||||
[Default:] none
|
||||
@ -1,74 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_style hybrid command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style hybrid style1 style2 ... :pre
|
||||
|
||||
style1,style2 = list of one or more bond styles :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
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 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {hybrid} style enables the use of multiple bond styles in one
|
||||
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 "bond_coeff"_bond_coeff.html 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
|
||||
(2-N) are computed with a {fene} potential with coefficients 30.0,
|
||||
1.5, 1.0, 1.0 for K, R0, epsilon, sigma.
|
||||
|
||||
If bond coefficients are specified in the data file read via the
|
||||
"read_data"_read_data.html 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.
|
||||
|
||||
Bond Coeffs :pre
|
||||
|
||||
1 harmonic 80.0 1.2
|
||||
2 fene 30.0 1.5 1.0 1.0
|
||||
... :pre
|
||||
|
||||
A bond style of {none} with no additional coefficients can be used in
|
||||
place of a bond style, either in a input script bond_coeff command or
|
||||
in the data file, if you desire to turn off interactions for specific
|
||||
bond types.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This bond style can only be used if LAMMPS was built with the MOLECULE
|
||||
package. See the "Build package"_Build_package.html doc page for more
|
||||
info.
|
||||
|
||||
Unlike other bond styles, the hybrid bond style does not store bond
|
||||
coefficient info for individual sub-styles in a "binary restart
|
||||
files"_restart.html. Thus when restarting a simulation from a restart
|
||||
file, you need to re-specify bond_coeff commands.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
|
||||
|
||||
[Default:] none
|
||||
@ -1,58 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_style mm3 command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style mm3 :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_style mm3
|
||||
bond_coeff 1 100.0 107.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {mm3} bond style uses the potential that is anharmonic in the bond
|
||||
as defined in "(Allinger)"_#mm3-allinger1989
|
||||
|
||||
:c,image(Eqs/bond_mm3.jpg)
|
||||
|
||||
where r0 is the equilibrium value of the bond, and 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.
|
||||
Note that the MM3 papers contains an error in Eq (1):
|
||||
(7/12)2.55 should be replaced with (7/12)2.55^2
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
"bond_coeff"_bond_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
K (energy/distance^2)
|
||||
r0 (distance) :ul
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This bond style can only be used if LAMMPS was built with the
|
||||
USER_YAFF package. See the "Build package"_Build_package.html doc
|
||||
page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_coeff"_bond_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(mm3-allinger1989)
|
||||
[(Allinger)] Allinger, Yuh, Lii, JACS, 111(23), 8551-8566
|
||||
(1989),
|
||||
@ -1,73 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_style morse command :h3
|
||||
bond_style morse/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style morse :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_style morse
|
||||
bond_coeff 5 1.0 2.0 1.2 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {morse} bond style uses the potential
|
||||
|
||||
:c,image(Eqs/bond_morse.jpg)
|
||||
|
||||
where r0 is the equilibrium bond distance, alpha is a stiffness
|
||||
parameter, and D determines the depth of the potential well.
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
"bond_coeff"_bond_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
D (energy)
|
||||
alpha (inverse distance)
|
||||
r0 (distance) :ul
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This bond style can only be used if LAMMPS was built with the MOLECULE
|
||||
package. See the "Build package"_Build_package.html doc page for more
|
||||
info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
|
||||
|
||||
[Default:] none
|
||||
@ -1,34 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_style none command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style none :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_style none :pre
|
||||
|
||||
[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 "read_data"_read_data.html command.
|
||||
|
||||
See the "bond_style zero"_bond_zero.html command for a way to
|
||||
calculate bond statistics, but compute no bond interactions.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:] none
|
||||
|
||||
"bond_style zero"_bond_zero.html
|
||||
|
||||
[Default:] none
|
||||
@ -1,78 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_style nonlinear command :h3
|
||||
bond_style nonlinear/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style nonlinear :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_style nonlinear
|
||||
bond_coeff 2 100.0 1.1 1.4 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {nonlinear} bond style uses the potential
|
||||
|
||||
:c,image(Eqs/bond_nonlinear.jpg)
|
||||
|
||||
to define an anharmonic spring "(Rector)"_#Rector of equilibrium
|
||||
length r0 and maximum extension lamda.
|
||||
|
||||
The following coefficients must be defined for each bond type via the
|
||||
"bond_coeff"_bond_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
epsilon (energy)
|
||||
r0 (distance)
|
||||
lamda (distance) :ul
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This bond style can only be used if LAMMPS was built with the MOLECULE
|
||||
package. See the "Build package"_Build_package.html doc page for more
|
||||
info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Rector)
|
||||
[(Rector)] Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994).
|
||||
@ -1,99 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_style oxdna/fene command :h3
|
||||
bond_style oxdna2/fene command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style oxdna/fene :pre
|
||||
bond_style oxdna2/fene :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_style oxdna/fene
|
||||
bond_coeff * 2.0 0.25 0.7525 :pre
|
||||
|
||||
bond_style oxdna2/fene
|
||||
bond_coeff * 2.0 0.25 0.7564 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {oxdna/fene} and {oxdna2/fene} bond styles use the potential
|
||||
|
||||
:c,image(Eqs/bond_oxdna_fene.jpg)
|
||||
|
||||
to define a modified finite extensible nonlinear elastic (FENE)
|
||||
potential "(Ouldridge)"_#oxdna_fene to model the connectivity of the
|
||||
phosphate backbone in the oxDNA force field for coarse-grained
|
||||
modelling of DNA.
|
||||
|
||||
The following coefficients must be defined for the bond type via the
|
||||
"bond_coeff"_bond_coeff.html command as given in the above example, or
|
||||
in the data file or restart files read by the
|
||||
"read_data"_read_data.html or "read_restart"_read_restart.html
|
||||
commands:
|
||||
|
||||
epsilon (energy)
|
||||
Delta (distance)
|
||||
r0 (distance) :ul
|
||||
|
||||
NOTE: The oxDNA bond style has to be used together with the
|
||||
corresponding oxDNA pair styles for excluded volume interaction
|
||||
{oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} and
|
||||
coaxial stacking interaction {oxdna/coaxstk} as well as
|
||||
hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
|
||||
"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2
|
||||
"(Snodin)"_#oxdna2 bond style the analogous pair styles and an
|
||||
additional Debye-Hueckel pair style {oxdna2/dh} have to be defined.
|
||||
The coefficients in the above example have to be kept fixed and cannot
|
||||
be changed without reparameterizing the entire model.
|
||||
|
||||
Example input and data files for DNA duplexes can be found in
|
||||
examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python
|
||||
setup tool which creates single straight or helical DNA strands, DNA
|
||||
duplexes or arrays of DNA duplexes can be found in
|
||||
examples/USER/cgdna/util/.
|
||||
|
||||
Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in
|
||||
any publication that uses this implementation. The article contains
|
||||
more information on the model, the structure of the input file, the
|
||||
setup tool and the performance of the LAMMPS-implementation of oxDNA.
|
||||
The preprint version of the article can be found
|
||||
"here"_PDF/USER-CGDNA.pdf.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This bond style can only be used if LAMMPS was built with the
|
||||
USER-CGDNA package and the MOLECULE and ASPHERE package. See the
|
||||
"Build package"_Build_package.html doc page for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style oxdna/excv"_pair_oxdna.html, "pair_style
|
||||
oxdna2/excv"_pair_oxdna2.html, "fix
|
||||
nve/dotc/langevin"_fix_nve_dotc_langevin.html,
|
||||
"bond_coeff"_bond_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Henrich2)
|
||||
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk,
|
||||
T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
|
||||
|
||||
:link(oxdna_fene)
|
||||
[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye,
|
||||
J. Chem. Phys. 134, 085101 (2011).
|
||||
|
||||
:link(oxdna2)
|
||||
[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al.,
|
||||
J. Chem. Phys. 142, 234901 (2015).
|
||||
@ -1,112 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_style quartic command :h3
|
||||
bond_style quartic/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style quartic :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_style quartic
|
||||
bond_coeff 2 1200 -0.55 0.25 1.3 34.6878 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
The {quartic} bond style uses the potential
|
||||
|
||||
:c,image(Eqs/bond_quartic.jpg)
|
||||
|
||||
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
|
||||
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
|
||||
"bond_coeff"_bond_coeff.html command as in the example above, or in
|
||||
the data file or restart files read by the "read_data"_read_data.html
|
||||
or "read_restart"_read_restart.html commands:
|
||||
|
||||
K (energy/distance^4)
|
||||
B1 (distance)
|
||||
B2 (distance)
|
||||
Rc (distance)
|
||||
U0 (energy) :ul
|
||||
|
||||
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 "bond_coeff"_bond_coeff.html command, but
|
||||
you will need to choose them carefully so they form a suitable bond
|
||||
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"
|
||||
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
|
||||
are no longer bonded.
|
||||
|
||||
LAMMPS does the second task via a computational sleight-of-hand. It
|
||||
subtracts the pairwise interaction as part of the bond computation.
|
||||
When the bond breaks, the subtraction stops. For this to work, the
|
||||
pairwise interaction must always be computed by the
|
||||
"pair_style"_pair_style.html command, whether the bond is broken or
|
||||
not. This means that "special_bonds"_special_bonds.html must be set
|
||||
to 1,1,1, as indicated as a restriction below.
|
||||
|
||||
Note that when bonds are dumped to a file via the "dump
|
||||
local"_dump.html command, bonds with type 0 are not included. The
|
||||
"delete_bonds"_delete_bonds.html command can also be used to query the
|
||||
status of broken bonds or permanently delete them, e.g.:
|
||||
|
||||
delete_bonds all stats
|
||||
delete_bonds all bond 0 remove :pre
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This bond style can only be used if LAMMPS was built with the MOLECULE
|
||||
package. See the "Build package"_Build_package.html doc page for more
|
||||
info.
|
||||
|
||||
The {quartic} style requires that "special_bonds"_special_bonds.html
|
||||
parameters be set to 1,1,1. Three- and four-body interactions (angle,
|
||||
dihedral, etc) cannot be used with {quartic} bonds.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
|
||||
|
||||
[Default:] none
|
||||
@ -1,115 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_style command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style style args :pre
|
||||
|
||||
style = {none} or {hybrid} or {class2} or {fene} or {fene/expand} or \
|
||||
{harmonic} or {morse} or {nonlinear} or {quartic} :ul
|
||||
args = none for any style except {hybrid}
|
||||
{hybrid} args = list of one or more styles :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_style harmonic
|
||||
bond_style fene
|
||||
bond_style hybrid harmonic fene :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Set the formula(s) LAMMPS uses to compute bond interactions between
|
||||
pairs of atoms. In LAMMPS, a bond differs from a pairwise
|
||||
interaction, which are set via the "pair_style"_pair_style.html
|
||||
command. Bonds are defined between specified pairs of atoms and
|
||||
remain in force for the duration of the simulation (unless the bond
|
||||
breaks which is possible in some bond potentials). The list of bonded
|
||||
atoms is read in by a "read_data"_read_data.html or
|
||||
"read_restart"_read_restart.html command from a data or restart file.
|
||||
By contrast, pair potentials are typically defined between all pairs
|
||||
of atoms within a cutoff distance and the set of active interactions
|
||||
changes over time.
|
||||
|
||||
Hybrid models where bonds are computed using different bond potentials
|
||||
can be setup using the {hybrid} bond style.
|
||||
|
||||
The coefficients associated with a bond style can be specified in a
|
||||
data or restart file or via the "bond_coeff"_bond_coeff.html command.
|
||||
|
||||
All bond potentials store their coefficient data in binary restart
|
||||
files which means bond_style and "bond_coeff"_bond_coeff.html commands
|
||||
do not need to be re-specified in an input script that restarts a
|
||||
simulation. See the "read_restart"_read_restart.html command for
|
||||
details on how to do this. The one exception is that bond_style
|
||||
{hybrid} only stores the list of sub-styles in the restart file; bond
|
||||
coefficients need to be re-specified.
|
||||
|
||||
NOTE: When both a bond and pair style is defined, the
|
||||
"special_bonds"_special_bonds.html command often needs to be used to
|
||||
turn off (or weight) the pairwise interaction that would otherwise
|
||||
exist between 2 bonded atoms.
|
||||
|
||||
In the formulas listed for each bond style, {r} is the distance
|
||||
between the 2 atoms in the bond.
|
||||
|
||||
:line
|
||||
|
||||
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 "bond_coeff"_bond_coeff.html 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 "bond_coeff"_bond_coeff.html command.
|
||||
|
||||
There are also additional accelerated pair styles included in the
|
||||
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
|
||||
The individual style names on the "Commands bond"_Commands_bond.html
|
||||
doc page are followed by one or more of (g,i,k,o,t) to indicate which
|
||||
accelerated styles exist.
|
||||
|
||||
"none"_bond_none.html - turn off bonded interactions
|
||||
"zero"_bond_zero.html - topology but no interactions
|
||||
"hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
|
||||
|
||||
"class2"_bond_class2.html - COMPASS (class 2) bond
|
||||
"fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond
|
||||
"fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles
|
||||
"gromos"_bond_gromos.html - GROMOS force field bond
|
||||
"harmonic"_bond_harmonic.html - harmonic bond
|
||||
"harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond
|
||||
"harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff
|
||||
"mm3"_bond_mm3.html - MM3 anharmonic bond
|
||||
"morse"_bond_morse.html - Morse bond
|
||||
"nonlinear"_bond_nonlinear.html - nonlinear bond
|
||||
"oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling
|
||||
"oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles
|
||||
"quartic"_bond_quartic.html - breakable quartic bond
|
||||
"table"_bond_table.html - tabulated by bond length :ul
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
Bond styles can only be set for atom styles that allow bonds to be
|
||||
defined.
|
||||
|
||||
Most bond styles are part of the MOLECULE package. They are only
|
||||
enabled if LAMMPS was built with that package. See the "Build
|
||||
package"_Build_package.html doc page for more info. The doc pages for
|
||||
individual bond potentials tell if it is part of a package.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
|
||||
|
||||
[Default:]
|
||||
|
||||
bond_style none
|
||||
@ -1,163 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_style table command :h3
|
||||
bond_style table/omp command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style table style N :pre
|
||||
|
||||
style = {linear} or {spline} = method of interpolation
|
||||
N = use N values in table :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_style table linear 1000
|
||||
bond_coeff 1 file.table ENTRY1 :pre
|
||||
|
||||
[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 "bond_coeff"_bond_coeff.html
|
||||
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}.
|
||||
|
||||
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
|
||||
interpolation.
|
||||
|
||||
For the {spline} style, a cubic spline coefficients are computed and
|
||||
stored at each of the {N} values in the table. The bond length is
|
||||
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
|
||||
"bond_coeff"_bond_coeff.html command as in the example above.
|
||||
|
||||
filename
|
||||
keyword :ul
|
||||
|
||||
The filename specifies a file containing tabulated energy and force
|
||||
values. The keyword specifies a section of the file. The format of
|
||||
this file is described below.
|
||||
|
||||
:line
|
||||
|
||||
The format of a tabulated file is as follows (without the
|
||||
parenthesized comments):
|
||||
|
||||
# Bond potential for harmonic (one or more comment or blank lines) :pre
|
||||
|
||||
HAM (keyword is the first text on line)
|
||||
N 101 FP 0 0 EQ 0.5 (N, FP, EQ parameters)
|
||||
(blank line)
|
||||
1 0.00 338.0000 1352.0000 (index, bond-length, energy, force)
|
||||
2 0.01 324.6152 1324.9600
|
||||
...
|
||||
101 1.00 338.0000 -1352.0000 :pre
|
||||
|
||||
A section begins with a non-blank line whose 1st character is not a
|
||||
"#"; blank lines or lines starting with "#" can be used as comments
|
||||
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
|
||||
"bond_coeff"_bond_coeff.html 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 "bond_style table"_bond_style.html command. Let
|
||||
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
|
||||
values at Ntable different points. The resulting tables of length
|
||||
Ntable are then used as described above, when computing energy and
|
||||
force for individual bond lengths. This means that if you want the
|
||||
interpolation tables of length Ntable to match exactly what is in the
|
||||
tabulated file (with effectively no preliminary interpolation), you
|
||||
should set Ntable = Nfile.
|
||||
|
||||
The "FP" parameter is optional. If used, it is followed by two values
|
||||
fplo and fphi, which are the derivatives of the force at the innermost
|
||||
and outermost bond lengths. These values are needed by the spline
|
||||
construction routines. If not specified by the "FP" parameter, they
|
||||
are estimated (less accurately) by the first two and last two force
|
||||
values in the table.
|
||||
|
||||
The "EQ" parameter is also optional. If used, it is followed by a the
|
||||
equilibrium bond length, which is used, for example, by the "fix
|
||||
shake"_fix_shake.html command. If not used, the equilibrium bond
|
||||
length is to the distance in the table with the lowest potential energy.
|
||||
|
||||
Following a blank line, the next N lines list the tabulated values.
|
||||
On each line, the 1st value is the index from 1 to N, the 2nd value is
|
||||
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.
|
||||
|
||||
Note that one file can contain many sections, each with a tabulated
|
||||
potential. LAMMPS reads the file section by section until it finds
|
||||
one that matches the specified keyword.
|
||||
|
||||
:line
|
||||
|
||||
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
|
||||
functionally the same as the corresponding style without the suffix.
|
||||
They have been optimized to run faster, depending on your available
|
||||
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
|
||||
page. The accelerated styles take the same arguments and should
|
||||
produce the same results, except for round-off and precision issues.
|
||||
|
||||
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
|
||||
USER-OMP and OPT packages, respectively. They are only enabled if
|
||||
LAMMPS was built with those packages. See the "Build
|
||||
package"_Build_package.html doc page for more info.
|
||||
|
||||
You can specify the accelerated styles explicitly in your input script
|
||||
by including their suffix, or you can use the "-suffix command-line
|
||||
switch"_Run_options.html when you invoke LAMMPS, or you can use the
|
||||
"suffix"_suffix.html command in your input script.
|
||||
|
||||
See the "Speed packages"_Speed_packages.html doc page for more
|
||||
instructions on how to use the accelerated styles effectively.
|
||||
|
||||
:line
|
||||
|
||||
[Restart info:]
|
||||
|
||||
This bond style writes the settings for the "bond_style table"
|
||||
command to "binary restart files"_restart.html, so a bond_style
|
||||
command does not need to specified in an input script that reads a
|
||||
restart file. However, the coefficient information is not stored in
|
||||
the restart file, since it is tabulated in the potential files. Thus,
|
||||
bond_coeff commands do need to be specified in the restart input
|
||||
script.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This bond style can only be used if LAMMPS was built with the MOLECULE
|
||||
package. See the "Build package"_Build_package.html doc page for more
|
||||
info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
|
||||
|
||||
[Default:] none
|
||||
@ -1,64 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_write command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_write btype N inner outer file keyword itype jtype :pre
|
||||
|
||||
btype = bond types
|
||||
N = # of values
|
||||
inner,outer = inner and outer bond length (distance units)
|
||||
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)
|
||||
:ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_write 1 500 0.5 3.5 table.txt Harmonic_1
|
||||
bond_write 3 1000 0.1 6.0 table.txt Morse :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Write energy and force values to a file as a function of distance for
|
||||
the currently defined bond potential. This is useful for plotting the
|
||||
potential function or otherwise debugging its values. If the file
|
||||
already exists, the table of values is appended to the end of the file
|
||||
to allow multiple tables of energy and force to be included in one
|
||||
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 "bond_coeff"_bond_coeff.html 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
|
||||
"bond_style"_bond_style.html {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).
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
All force field coefficients for bond and other kinds of interactions
|
||||
must be set before this command can be invoked.
|
||||
|
||||
Due to how the bond force is computed, an inner value > 0.0 must
|
||||
be specified even if the potential has a finite value at r = 0.0.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_style table"_bond_table.html,
|
||||
"bond_style"_bond_style.html, "bond_coeff"_bond_coeff.html
|
||||
|
||||
[Default:] none
|
||||
@ -1,48 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
bond_style zero command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
bond_style zero {nocoeff} :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
bond_style zero
|
||||
bond_style zero nocoeff
|
||||
bond_coeff *
|
||||
bond_coeff * 2.14 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Using an bond style of zero means bond forces and energies are not
|
||||
computed, but the geometry of bond pairs is still accessible to other
|
||||
commands.
|
||||
|
||||
As an example, the "compute bond/local"_compute_bond_local.html
|
||||
command can be used to compute distances for the list of pairs of bond
|
||||
atoms listed in the data file read by the "read_data"_read_data.html
|
||||
command. If no bond style is defined, this command cannot be used.
|
||||
|
||||
The optional {nocoeff} flag allows to read data files with a BondCoeff
|
||||
section for any bond style. Similarly, any bond_coeff commands
|
||||
will only be checked for the bond type number and the rest ignored.
|
||||
|
||||
Note that the "bond_coeff"_bond_coeff.html command must be used for
|
||||
all bond types. If specified, there can be only one value, which is
|
||||
going to be used to assign an equilibrium distance, e.g. for use with
|
||||
"fix shake"_fix_shake.html.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"bond_style none"_bond_none.html
|
||||
|
||||
[Default:] none
|
||||
@ -182,6 +182,7 @@ compute"_Commands_compute.html doc page are followed by one or more of
|
||||
"bond"_compute_bond.html - energy of each bond sub-style
|
||||
"bond/local"_compute_bond_local.html - distance and energy of each bond
|
||||
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
|
||||
"centroid/stress/atom"_compute_stress_atom.html - centroid based stress tensor for each atom
|
||||
"chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom
|
||||
"chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk
|
||||
"cluster/atom"_compute_cluster_atom.html - cluster ID for each atom
|
||||
|
||||
@ -1,168 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
compute stress/atom command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID stress/atom temp-ID keyword ... :pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
stress/atom = style name of this compute command
|
||||
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} :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute 1 mobile stress/atom NULL
|
||||
compute 1 mobile stress/atom myRamp
|
||||
compute 1 all stress/atom NULL pair bond :pre
|
||||
|
||||
[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
|
||||
components and is stored as a 6-element vector in the following order:
|
||||
xx, yy, zz, xy, xz, yz. See the "compute
|
||||
pressure"_compute_pressure.html 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:
|
||||
|
||||
:c,image(Eqs/stress_tensor.jpg)
|
||||
|
||||
The first term is a kinetic energy contribution for atom {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} "fixes"_fix.html that apply
|
||||
internal constraint forces to atom {I}. Currently, only the "fix
|
||||
shake"_fix_shake.html and "fix rigid"_fix_rigid.html 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
|
||||
to each atom in the set. E.g. 1/4 of the dihedral virial to each of
|
||||
the 4 atoms, or 1/3 of the fix virial due to SHAKE constraints applied
|
||||
to atoms in a water molecule via the "fix shake"_fix_shake.html
|
||||
command.
|
||||
|
||||
If no extra keywords are listed, all of the terms in this formula 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
|
||||
{ke}.
|
||||
|
||||
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
|
||||
either pairwise or many-body potentials, and including the effects of
|
||||
periodic boundary conditions is discussed in "(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
|
||||
so that the cluster of atoms is close together. The total
|
||||
contribution for the cluster interaction is divided evenly among those
|
||||
atoms.
|
||||
|
||||
The "dihedral_style charmm"_dihedral_charmm.html style calculates
|
||||
pairwise interactions between 1-4 atoms. The virial contribution of
|
||||
these terms is included in the pair virial, not the dihedral virial.
|
||||
|
||||
The KSpace contribution is calculated using the method in
|
||||
"(Heyes)"_#Heyes2 for the Ewald method and by the methodology described
|
||||
in "(Sirk)"_#Sirk1 for PPPM. The choice of KSpace solver is specified
|
||||
by the "kspace_style pppm"_kspace_style.html command. Note that for
|
||||
PPPM, the calculation requires 6 extra FFTs each timestep that
|
||||
per-atom stress is calculated. Thus it can significantly increase the
|
||||
cost of the PPPM calculation if it is needed on a large fraction of
|
||||
the simulation timesteps.
|
||||
|
||||
The {temp-ID} argument can be used to affect the per-atom velocities
|
||||
used in the kinetic energy contribution to the total stress. If the
|
||||
kinetic energy is not included in the stress, than the temperature
|
||||
compute is not used and can be specified as NULL. If the kinetic
|
||||
energy is included and you wish to use atom velocities as-is, then
|
||||
{temp-ID} can also be specified as NULL. If desired, the specified
|
||||
temperature compute can be one that subtracts off a bias to leave each
|
||||
atom with only a thermal velocity to use in the formula above, e.g. by
|
||||
subtracting a background streaming velocity. See the doc pages for
|
||||
individual "compute commands"_compute.html to determine which ones
|
||||
include a bias.
|
||||
|
||||
:line
|
||||
|
||||
Note that as defined in the formula, per-atom stress is the negative
|
||||
of the per-atom pressure tensor. It is also really a stress*volume
|
||||
formulation, meaning the computed quantity is in units of
|
||||
pressure*volume. It would need to be divided by a per-atom volume to
|
||||
have units of stress (pressure), but an individual atom's volume is
|
||||
not well defined or easy to compute in a deformed solid or a liquid.
|
||||
See the "compute voronoi/atom"_compute_voronoi_atom.html 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.
|
||||
|
||||
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:
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\]
|
||||
variable press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol)
|
||||
thermo_style custom step temp etotal press v_press :pre
|
||||
|
||||
NOTE: The per-atom stress does not include any Lennard-Jones tail
|
||||
corrections to the pressure added by the "pair_modify tail
|
||||
yes"_pair_modify.html command, since those are contributions to the
|
||||
global system pressure.
|
||||
|
||||
[Output info:]
|
||||
|
||||
This compute 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 "Howto output"_Howto_output.html doc page
|
||||
for an overview of LAMMPS output options.
|
||||
|
||||
The per-atom array values will be in pressure*volume
|
||||
"units"_units.html as discussed above.
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(Heyes2)
|
||||
[(Heyes)] Heyes, Phys Rev B 49, 755 (1994),
|
||||
|
||||
:link(Sirk1)
|
||||
[(Sirk)] Sirk, Moore, Brown, J Chem Phys, 138, 064505 (2013).
|
||||
|
||||
:link(Thompson2)
|
||||
[(Thompson)] Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).
|
||||
@ -1,144 +0,0 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Commands_all.html)
|
||||
|
||||
:line
|
||||
|
||||
pair_style list command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style list listfile cutoff keyword :pre
|
||||
|
||||
listfile = name of file with list of pairwise interactions
|
||||
cutoff = global cutoff (distance units)
|
||||
keyword = optional flag {nocheck} or {check} (default is {check}) :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style list restraints.txt 200.0
|
||||
pair_coeff * * :pre
|
||||
|
||||
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 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {list} computes interactions between explicitly listed pairs of
|
||||
atoms with the option to select functional form and parameters for
|
||||
each individual pair. Because the parameters are set in the list
|
||||
file, the pair_coeff command has no parameters (but still needs to be
|
||||
provided). The {check} and {nocheck} keywords enable/disable a test
|
||||
that checks whether all listed bonds were present and computed.
|
||||
|
||||
This pair style can be thought of as a hybrid between bonded,
|
||||
non-bonded, and restraint interactions. It will typically be used as
|
||||
an additional interaction within the {hybrid/overlay} pair style. It
|
||||
currently supports three interaction styles: a 12-6 Lennard-Jones, a
|
||||
Morse and a harmonic potential.
|
||||
|
||||
The format of the list file is as follows:
|
||||
|
||||
one line per pair of atoms :ulb,l
|
||||
empty lines will be ignored :l
|
||||
comment text starts with a '#' character :l
|
||||
line syntax: {ID1 ID2 style coeffs cutoff} :l
|
||||
ID1 = atom ID of first atom
|
||||
ID2 = atom ID of second atom
|
||||
style = style of interaction
|
||||
coeffs = list of coeffs
|
||||
cutoff = cutoff for interaction (optional) :pre
|
||||
:ule
|
||||
|
||||
The cutoff parameter is optional. If not specified, the global cutoff
|
||||
is used.
|
||||
|
||||
Here is an example file:
|
||||
|
||||
# this is a comment :pre
|
||||
|
||||
15 259 lj126 1.0 1.0 50.0
|
||||
15 603 morse 10.0 1.2 2.0 10.0 # and another comment
|
||||
18 470 harmonic 50.0 1.2 5.0 :pre
|
||||
|
||||
The style {lj126} computes pairwise interactions with the formula
|
||||
|
||||
:c,image(Eqs/pair_lj.jpg)
|
||||
|
||||
and the coefficients:
|
||||
|
||||
epsilon (energy units)
|
||||
sigma (distance units) :ul
|
||||
|
||||
The style {morse} computes pairwise interactions with the formula
|
||||
|
||||
:c,image(Eqs/pair_morse.jpg)
|
||||
|
||||
and the coefficients:
|
||||
|
||||
D0 (energy units)
|
||||
alpha (1/distance units)
|
||||
r0 (distance units) :ul
|
||||
|
||||
The style {harmonic} computes pairwise interactions with the formula
|
||||
|
||||
:c,image(Eqs/bond_harmonic.jpg)
|
||||
|
||||
and the coefficients:
|
||||
|
||||
K (energy units)
|
||||
r0 (distance units) :ul
|
||||
|
||||
Note that the usual 1/2 factor is included in K.
|
||||
|
||||
:line
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
This pair style does not support mixing since all parameters are
|
||||
explicit for each pair.
|
||||
|
||||
The "pair_modify"_pair_modify.html shift option is supported by this
|
||||
pair style.
|
||||
|
||||
The "pair_modify"_pair_modify.html table and tail options are not
|
||||
relevant for this pair style.
|
||||
|
||||
This pair style does not write its information to "binary restart
|
||||
files"_restart.html, so pair_style and pair_coeff commands need
|
||||
to be specified in an input script that reads a restart file.
|
||||
|
||||
This pair style can only be used via the {pair} keyword of the
|
||||
"run_style respa"_run_style.html command. It does not support the
|
||||
{inner}, {middle}, {outer} keywords.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This pair style does not use a neighbor list and instead identifies
|
||||
atoms by their IDs. This has two consequences: 1) The cutoff has to be
|
||||
chosen sufficiently large, so that the second atom of a pair has to be
|
||||
a ghost atom on the same node on which the first atom is local;
|
||||
otherwise the interaction will be skipped. You can use the {check}
|
||||
option to detect, if interactions are missing. 2) Unlike other pair
|
||||
styles in LAMMPS, an atom I will not interact with multiple images of
|
||||
atom J (assuming the images are within the cutoff distance), but only
|
||||
with the nearest image.
|
||||
|
||||
This style is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS is build with that package. See the "Build
|
||||
package"_Build_package.html doc page on for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html,
|
||||
"pair_style hybrid/overlay"_pair_hybrid.html,
|
||||
"pair_style lj/cut"_pair_lj.html,
|
||||
"pair_style morse"_pair_morse.html,
|
||||
"bond_style harmonic"_bond_harmonic.html
|
||||
|
||||
[Default:] none
|
||||
@ -164,6 +164,7 @@ azimuthal
|
||||
Azuri
|
||||
ba
|
||||
Babadi
|
||||
Babaei
|
||||
backcolor
|
||||
Baczewski
|
||||
Bagi
|
||||
@ -1340,6 +1341,7 @@ Khersonskii
|
||||
Khrapak
|
||||
Khvostov
|
||||
Ki
|
||||
Kikugawa
|
||||
kim
|
||||
kJ
|
||||
kk
|
||||
@ -1594,6 +1596,7 @@ Materias
|
||||
mathbf
|
||||
matlab
|
||||
matplotlib
|
||||
Matsubara
|
||||
Mattice
|
||||
Mattox
|
||||
Mattson
|
||||
@ -2017,6 +2020,7 @@ Nz
|
||||
ocl
|
||||
octahedral
|
||||
octants
|
||||
Ohara
|
||||
ohenrich
|
||||
ok
|
||||
Okabe
|
||||
@ -2688,6 +2692,7 @@ Sunderland
|
||||
superset
|
||||
supersphere
|
||||
Supinski
|
||||
Surblys
|
||||
surfactants
|
||||
Suter
|
||||
Sutmann
|
||||
|
||||
@ -35,6 +35,7 @@ PairLJClass2::PairLJClass2(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
respa_enable = 1;
|
||||
writedata = 1;
|
||||
centroidstressflag = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -33,6 +33,7 @@ using namespace MathConst;
|
||||
PairLJClass2CoulCut::PairLJClass2CoulCut(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
writedata = 1;
|
||||
centroidstressflag = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -54,7 +54,7 @@ FixPour::FixPour(LAMMPS *lmp, int narg, char **arg) :
|
||||
{
|
||||
if (narg < 6) error->all(FLERR,"Illegal fix pour command");
|
||||
|
||||
if (lmp->kokkos)
|
||||
if (lmp->kokkos)
|
||||
error->all(FLERR,"Cannot yet use fix pour with the KOKKOS package");
|
||||
|
||||
time_depend = 1;
|
||||
@ -797,7 +797,7 @@ bool FixPour::outside(int dim, double value, double lo, double hi)
|
||||
bool outside_range = (value < lo || value > hi);
|
||||
if (!outside_range || !domain->periodicity[dim]) return outside_range;
|
||||
|
||||
// for periodic dimension:
|
||||
// for periodic dimension:
|
||||
// must perform additional tests if range wraps around the periodic box
|
||||
|
||||
bool outside_pbc_range = true;
|
||||
|
||||
@ -37,6 +37,7 @@ template<class DeviceType>
|
||||
PairEAMKokkos<DeviceType>::PairEAMKokkos(LAMMPS *lmp) : PairEAM(lmp)
|
||||
{
|
||||
respa_enable = 0;
|
||||
single_enable = 0;
|
||||
|
||||
atomKK = (AtomKokkos *) atom;
|
||||
execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
|
||||
|
||||
@ -43,6 +43,7 @@ PairEAM::PairEAM(LAMMPS *lmp) : Pair(lmp)
|
||||
nmax = 0;
|
||||
rho = NULL;
|
||||
fp = NULL;
|
||||
numforce = NULL;
|
||||
map = NULL;
|
||||
type2frho = NULL;
|
||||
|
||||
@ -77,6 +78,7 @@ PairEAM::~PairEAM()
|
||||
|
||||
memory->destroy(rho);
|
||||
memory->destroy(fp);
|
||||
memory->destroy(numforce);
|
||||
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
@ -151,9 +153,11 @@ void PairEAM::compute(int eflag, int vflag)
|
||||
if (atom->nmax > nmax) {
|
||||
memory->destroy(rho);
|
||||
memory->destroy(fp);
|
||||
memory->destroy(numforce);
|
||||
nmax = atom->nmax;
|
||||
memory->create(rho,nmax,"pair:rho");
|
||||
memory->create(fp,nmax,"pair:fp");
|
||||
memory->create(numforce,nmax,"pair:numforce");
|
||||
}
|
||||
|
||||
double **x = atom->x;
|
||||
@ -255,6 +259,7 @@ void PairEAM::compute(int eflag, int vflag)
|
||||
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
numforce[i] = 0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
@ -266,6 +271,7 @@ void PairEAM::compute(int eflag, int vflag)
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
|
||||
if (rsq < cutforcesq) {
|
||||
++numforce[i];
|
||||
jtype = type[j];
|
||||
r = sqrt(rsq);
|
||||
p = r*rdr + 1.0;
|
||||
@ -802,6 +808,18 @@ double PairEAM::single(int i, int j, int itype, int jtype,
|
||||
double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip;
|
||||
double *coeff;
|
||||
|
||||
if (numforce[i] > 0) {
|
||||
p = rho[i]*rdrho + 1.0;
|
||||
m = static_cast<int> (p);
|
||||
m = MAX(1,MIN(m,nrho-1));
|
||||
p -= m;
|
||||
p = MIN(p,1.0);
|
||||
coeff = frho_spline[type2frho[itype]][m];
|
||||
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
|
||||
if (rho[i] > rhomax) phi += fp[i] * (rho[i]-rhomax);
|
||||
phi *= 1.0/static_cast<double>(numforce[i]);
|
||||
} else phi = 0.0;
|
||||
|
||||
r = sqrt(rsq);
|
||||
p = r*rdr + 1.0;
|
||||
m = static_cast<int> (p);
|
||||
@ -818,7 +836,7 @@ double PairEAM::single(int i, int j, int itype, int jtype,
|
||||
z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
|
||||
|
||||
recip = 1.0/r;
|
||||
phi = z2*recip;
|
||||
phi += z2*recip;
|
||||
phip = z2p*recip - phi*recip;
|
||||
psip = fp[i]*rhojp + fp[j]*rhoip + phip;
|
||||
fforce = -psip*recip;
|
||||
|
||||
@ -70,6 +70,7 @@ class PairEAM : public Pair {
|
||||
// per-atom arrays
|
||||
|
||||
double *rho,*fp;
|
||||
int *numforce;
|
||||
|
||||
// potentials as file data
|
||||
|
||||
|
||||
@ -945,7 +945,7 @@ void FixGCMC::attempt_atomic_insertion()
|
||||
ninsertion_attempts += 1.0;
|
||||
|
||||
if (ngas >= max_ngas) return;
|
||||
|
||||
|
||||
// pick coordinates for insertion point
|
||||
|
||||
double coord[3];
|
||||
@ -1300,7 +1300,7 @@ void FixGCMC::attempt_molecule_insertion()
|
||||
ninsertion_attempts += 1.0;
|
||||
|
||||
if (ngas >= max_ngas) return;
|
||||
|
||||
|
||||
double com_coord[3];
|
||||
if (regionflag) {
|
||||
int region_attempt = 0;
|
||||
@ -1634,7 +1634,7 @@ void FixGCMC::attempt_atomic_insertion_full()
|
||||
ninsertion_attempts += 1.0;
|
||||
|
||||
if (ngas >= max_ngas) return;
|
||||
|
||||
|
||||
double energy_before = energy_stored;
|
||||
|
||||
double coord[3];
|
||||
|
||||
@ -80,11 +80,13 @@ void PairEAMOpt::eval()
|
||||
// grow energy array if necessary
|
||||
|
||||
if (atom->nmax > nmax) {
|
||||
memory->sfree(rho);
|
||||
memory->sfree(fp);
|
||||
memory->destroy(rho);
|
||||
memory->destroy(fp);
|
||||
memory->destroy(numforce);
|
||||
nmax = atom->nmax;
|
||||
rho = (double *) memory->smalloc(nmax*sizeof(double),"pair:rho");
|
||||
fp = (double *) memory->smalloc(nmax*sizeof(double),"pair:fp");
|
||||
memory->create(rho,nmax,"pair:rho");
|
||||
memory->create(fp,nmax,"pair:fp");
|
||||
memory->create(numforce,nmax,"pair:numforce");
|
||||
}
|
||||
|
||||
double** _noalias x = atom->x;
|
||||
@ -269,6 +271,7 @@ void PairEAMOpt::eval()
|
||||
|
||||
fast_gamma_t* _noalias tabssi = &tabss[itype1*ntypes*nr];
|
||||
double* _noalias scale_i = scale[itype1+1]+1;
|
||||
numforce[i] = 0;
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
@ -280,6 +283,7 @@ void PairEAMOpt::eval()
|
||||
double rsq = delx*delx + dely*dely + delz*delz;
|
||||
|
||||
if (rsq < tmp_cutforcesq) {
|
||||
++numforce[i];
|
||||
jtype = type[j] - 1;
|
||||
double r = sqrt(rsq);
|
||||
double rhoip,rhojp,z2,z2p;
|
||||
|
||||
@ -40,6 +40,7 @@ PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) {
|
||||
one_coeff = 1;
|
||||
reinitflag = 0;
|
||||
cut_global = 0.0;
|
||||
centroidstressflag = 1;
|
||||
|
||||
py_potential = NULL;
|
||||
skip_types = NULL;
|
||||
|
||||
@ -32,7 +32,9 @@ using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairCoulCutSoft::PairCoulCutSoft(LAMMPS *lmp) : Pair(lmp) {}
|
||||
PairCoulCutSoft::PairCoulCutSoft(LAMMPS *lmp) : Pair(lmp) {
|
||||
centroidstressflag = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
|
||||
@ -33,6 +33,7 @@ using namespace MathConst;
|
||||
PairLJClass2CoulCutSoft::PairLJClass2CoulCutSoft(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
writedata = 1;
|
||||
centroidstressflag = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -32,6 +32,7 @@ using namespace MathConst;
|
||||
PairLJClass2Soft::PairLJClass2Soft(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
writedata = 1;
|
||||
centroidstressflag = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -37,6 +37,7 @@ using namespace MathConst;
|
||||
PairLJCutCoulCutSoft::PairLJCutCoulCutSoft(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
writedata = 1;
|
||||
centroidstressflag = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -43,6 +43,7 @@ PairLJCutSoft::PairLJCutSoft(LAMMPS *lmp) : Pair(lmp)
|
||||
respa_enable = 1;
|
||||
writedata = 1;
|
||||
allocated = 0;
|
||||
centroidstressflag = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -39,7 +39,7 @@ ComputeGyrationShapeChunk::ComputeGyrationShapeChunk(LAMMPS *lmp, int narg, char
|
||||
int n = strlen(arg[3]) + 1;
|
||||
id_gyration_chunk = new char[n];
|
||||
strcpy(id_gyration_chunk,arg[3]);
|
||||
|
||||
|
||||
init();
|
||||
|
||||
array_flag = 1;
|
||||
|
||||
@ -55,7 +55,7 @@ void AngleCharmmOMP::compute(int eflag, int vflag)
|
||||
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
thr->timer(Timer::START);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
|
||||
|
||||
if (inum > 0) {
|
||||
if (evflag) {
|
||||
|
||||
@ -55,7 +55,7 @@ void AngleClass2OMP::compute(int eflag, int vflag)
|
||||
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
thr->timer(Timer::START);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
|
||||
|
||||
if (inum > 0) {
|
||||
if (evflag) {
|
||||
|
||||
@ -55,7 +55,7 @@ void AngleCosineDeltaOMP::compute(int eflag, int vflag)
|
||||
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
thr->timer(Timer::START);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
|
||||
|
||||
if (inum > 0) {
|
||||
if (evflag) {
|
||||
|
||||
@ -55,7 +55,7 @@ void AngleCosineOMP::compute(int eflag, int vflag)
|
||||
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
thr->timer(Timer::START);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
|
||||
|
||||
if (inum > 0) {
|
||||
if (evflag) {
|
||||
|
||||
@ -57,7 +57,7 @@ void AngleCosinePeriodicOMP::compute(int eflag, int vflag)
|
||||
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
thr->timer(Timer::START);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
|
||||
|
||||
if (inum > 0) {
|
||||
if (evflag) {
|
||||
|
||||
@ -55,7 +55,7 @@ void AngleCosineShiftExpOMP::compute(int eflag, int vflag)
|
||||
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
thr->timer(Timer::START);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
|
||||
|
||||
if (inum > 0) {
|
||||
if (evflag) {
|
||||
|
||||
@ -55,7 +55,7 @@ void AngleCosineShiftOMP::compute(int eflag, int vflag)
|
||||
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
|
||||
ThrData *thr = fix->get_thr(tid);
|
||||
thr->timer(Timer::START);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
|
||||
ev_setup_thr(eflag, vflag, nall, eatom, vatom, cvatom, thr);
|
||||
|
||||
if (inum > 0) {
|
||||
if (evflag) {
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user