From 9ed43e55f090ffef11cd71ea45f88cda2b57b371 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 2 Aug 2019 08:41:34 -0400 Subject: [PATCH] add some more descriptions for fixes to list of style in fix command docs --- doc/src/fix.txt | 62 ++++++++++++++++++++++++------------------------- 1 file changed, 31 insertions(+), 31 deletions(-) diff --git a/doc/src/fix.txt b/doc/src/fix.txt index c64d61d949..409fde3503 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -165,9 +165,9 @@ page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. "adapt"_fix_adapt.html - change a simulation parameter over time -"adapt/fep"_fix_adapt_fep.html - +"adapt/fep"_fix_adapt_fep.html - enhanced version of fix adapt "addforce"_fix_addforce.html - add a force to each atom -"addtorque"_fix_addtorque.html - +"addtorque"_fix_addtorque.html - add a torque to a group of atoms "append/atoms"_fix_append_atoms.html - append atoms to a running simulation "atc"_fix_atc.html - initiates a coupled MD/FE simulation "atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping @@ -176,29 +176,29 @@ accelerated styles exist. "ave/correlate"_fix_ave_correlate.html - compute/output time correlations "ave/correlate/long"_fix_ave_correlate_long.html - "ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms -"ave/histo/weight"_fix_ave_histo.html - +"ave/histo/weight"_fix_ave_histo.html - weighted version of fix ave/histo "ave/time"_fix_ave_time.html - compute/output global time-averaged quantities "aveforce"_fix_aveforce.html - add an averaged force to each atom "balance"_fix_balance.html - perform dynamic load-balancing -"bocs"_fix_bocs.html - +"bocs"_fix_bocs.html - NPT style time integration with pressure correction "bond/break"_fix_bond_break.html - break bonds on the fly "bond/create"_fix_bond_create.html - create bonds on the fly -"bond/react"_fix_bond_react.html - +"bond/react"_fix_bond_react.html - apply topology changes to model reactions "bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping "box/relax"_fix_box_relax.html - relax box size during energy minimization -"client/md"_fix_client_md.html - +"client/md"_fix_client_md.html - MD client for client/server simulations "cmap"_fix_cmap.html - enables CMAP cross-terms of the CHARMM force field "colvars"_fix_colvars.html - interface to the collective variables “Colvars” library -"controller"_fix_controller.html - +"controller"_fix_controller.html - apply control loop feedback mechanism "deform"_fix_deform.html - change the simulation box size/shape "deposit"_fix_deposit.html - add new atoms above a surface "dpd/energy"_fix_dpd_energy.html - constant energy dissipative particle dynamics "drag"_fix_drag.html - drag atoms towards a defined coordinate -"drude"_fix_drude.html - -"drude/transform/direct"_fix_drude_transform.html - -"drude/transform/inverse"_fix_drude_transform.html - +"drude"_fix_drude.html - part of Drude oscillator polarization model +"drude/transform/direct"_fix_drude_transform.html - part of Drude oscillator polarization model +"drude/transform/inverse"_fix_drude_transform.html - part of Drude oscillator polarization model "dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces -"edpd/source"_fix_dpd_source.html - +"edpd/source"_fix_dpd_source.html - add heat source to eDPD simulations "efield"_fix_efield.html - impose electric field on system "ehex"_fix_ehex.html - enhanced heat exchange algorithm "electron/stopping"_fix_electron_stopping.html - electronic stopping power as a friction force @@ -209,8 +209,8 @@ accelerated styles exist. "evaporate"_fix_evaporate.html - remove atoms from simulation periodically "external"_fix_external.html - callback to an external driver program "ffl"_fix_ffl.html - apply a Fast-Forward Langevin equation thermostat -"filter/corotate"_fix_filter_corotate.html - -"flow/gauss"_fix_flow_gauss.html - +"filter/corotate"_fix_filter_corotate.html - implement corotation filter to allow larger timesteps with r-RESPA +"flow/gauss"_fix_flow_gauss.html - Gaussian dynamics for constant mass flux "freeze"_fix_freeze.html - freeze atoms in a granular simulation "gcmc"_fix_gcmc.html - grand canonical insertions/deletions "gld"_fix_gld.html - generalized Langevin dynamics integrator @@ -223,7 +223,7 @@ accelerated styles exist. "hyper/local"_fix_hyper_local.html - local hyperdynamics "imd"_fix_imd.html - implements the “Interactive MD” (IMD) protocol "indent"_fix_indent.html - impose force due to an indenter -"ipi"_fix_ipi.html - +"ipi"_fix_ipi.html - enable LAMMPS to run as a client for i-PI path-integral simulations "langevin"_fix_langevin.html - Langevin temperature control "langevin/drude"_fix_langevin_drude.html - Langevin temperature control of Drude oscillators "langevin/eff"_fix_langevin_eff.html - Langevin temperature control for the electron force field model @@ -235,13 +235,13 @@ accelerated styles exist. "lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html - "lb/viscous"_fix_lb_viscous.html - "lineforce"_fix_lineforce.html - constrain atoms to move in a line -"manifoldforce"_fix_manifoldforce.html - -"meso"_fix_meso.html - +"manifoldforce"_fix_manifoldforce.html - restrain atoms to a manifold during minimization +"meso"_fix_meso.html - time integration for SPH/DPDE particles "meso/move"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion "meso/stationary"_fix_meso_stationary.html - "momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms "move"_fix_move.html - move atoms in a prescribed fashion -"mscg"_fix_mscg.html - +"mscg"_fix_mscg.html - apply MSCG method for force-matching to generate coarse grain models "msst"_fix_msst.html - multi-scale shock technique (MSST) integration "mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm "mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algrithm @@ -258,14 +258,14 @@ accelerated styles exist. "npt/body"_fix_npt_body.html - NPT for body particles "npt/eff"_fix_nh_eff.html - NPT for nuclei and electrons in the electron force field model "npt/sphere"_fix_npt_sphere.html - NPT for spherical particles -"npt/uef"_fix_nh_uef.html - +"npt/uef"_fix_nh_uef.html - NPT style time integration with diagonal flow "nve"_fix_nve.html - constant NVE time integration "nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles "nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces "nve/awpmd"_fix_nve_awpmd.html - NVE for the Antisymmetrized Wave Packet Molecular Dynamics model "nve/body"_fix_nve_body.html - NVE for body particles -"nve/dot"_fix_nve_dot.html - -"nve/dotc/langevin"_fix_nve_dotc_langevin.html - +"nve/dot"_fix_nve_dot.html - rigid body constant energy time integrator for coarse grain models +"nve/dotc/langevin"_fix_nve_dotc_langevin.html - Langevin style rigid body time integrator for coarse grain models "nve/eff"_fix_nve_eff.html - NVE for nuclei and electrons in the electron force field model "nve/limit"_fix_nve_limit.html - NVE with limited step length "nve/line"_fix_nve_line.html - NVE for line segments @@ -283,11 +283,11 @@ accelerated styles exist. "nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations "nvt/sllod/eff"_fix_nvt_sllod_eff.html - NVT for NEMD with SLLOD equations for the electron force field model "nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles -"nvt/uef"_fix_nh_uef.html - +"nvt/uef"_fix_nh_uef.html - NVT style time integration with diagonal flow "oneway"_fix_oneway.html - constrain particles on move in one direction "orient/bcc"_fix_orient.html - add grain boundary migration force for BCC "orient/fcc"_fix_orient.html - add grain boundary migration force for FCC -"phonon"_fix_phonon.html - +"phonon"_fix_phonon.html - calculate dynamical matrix from MD simulations "pimd"_fix_pimd.html - Feynman path integral molecular dynamics "planeforce"_fix_planeforce.html - constrain atoms to move in a plane "plumed"_fix_plumed.html - wrapper on PLUMED free energy library @@ -297,9 +297,9 @@ accelerated styles exist. "press/berendsen"_fix_press_berendsen.html - pressure control by Berendsen barostat "print"_fix_print.html - print text and variables during a simulation "property/atom"_fix_property_atom.html - add customized per-atom values -"python/invoke"_fix_python_invoke.html - +"python/invoke"_fix_python_invoke.html - call a Python function during a simulation "python/move"_fix_python_move.html - call a Python function during a simulation run -"qbmsst"_fix_qbmsst.html - +"qbmsst"_fix_qbmsst.html - quantum bath multi-scale shock technique time integrator "qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential "qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method "qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer @@ -308,13 +308,13 @@ accelerated styles exist. "qeq/shielded"_fix_qeq.html - charge equilibration via shielded method "qeq/slater"_fix_qeq.html - charge equilibration via Slater method "qmmm"_fix_qmmm.html - functionality to enable a quantum mechanics/molecular mechanics coupling -"qtb"_fix_qtb.html - +"qtb"_fix_qtb.html - implement quantum thermal bath scheme "rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles "reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information "reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information "recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms "restrain"_fix_restrain.html - constrain a bond, angle, dihedral -"rhok"_fix_rhok.html - +"rhok"_fix_rhok.html - add bias potential for long-range ordered systems "rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration "rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body "rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration @@ -327,11 +327,11 @@ accelerated styles exist. "rigid/nvt/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration "rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration "rx"_fix_rx.html - -"saed/vtk"_fix_saed_vtk.html - +"saed/vtk"_fix_saed_vtk.html - "setforce"_fix_setforce.html - set the force on each atom "shake"_fix_shake.html - SHAKE constraints on bonds and/or angles "shardlow"_fix_shardlow.html - integration of DPD equations of motion using the Shardlow splitting -"smd"_fix_smd.html - +"smd"_fix_smd.html - applied a steered MD force to a group "smd/adjust_dt"_fix_smd_adjust_dt.html - "smd/integrate_tlsph"_fix_smd_integrate_tlsph.html - "smd/integrate_ulsph"_fix_smd_integrate_ulsph.html - @@ -356,7 +356,7 @@ accelerated styles exist. "ti/spring"_fix_ti_spring.html - "tmd"_fix_tmd.html - guide a group of atoms to a new configuration "ttm"_fix_ttm.html - two-temperature model for electronic/atomic coupling -"ttm/mod"_fix_ttm.html - +"ttm/mod"_fix_ttm.html - enhanced two-temperature model with additional options "tune/kspace"_fix_tune_kspace.html - auto-tune KSpace parameters "vector"_fix_vector.html - accumulate a global vector every N timesteps "viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for viscosity calculation @@ -364,7 +364,7 @@ accelerated styles exist. "wall/body/polygon"_fix_wall_body_polygon.html - "wall/body/polyhedron"_fix_wall_body_polyhedron.html - "wall/colloid"_fix_wall.html - Lennard-Jones wall interacting with finite-size particles -"wall/ees"_fix_wall_ees.html - +"wall/ees"_fix_wall_ees.html - wall for ellipsoidal particles "wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations "wall/gran/region"_fix_wall_gran_region.html - "wall/harmonic"_fix_wall.html - harmonic spring wall @@ -374,7 +374,7 @@ accelerated styles exist. "wall/piston"_fix_wall_piston.html - moving reflective piston wall "wall/reflect"_fix_wall_reflect.html - reflecting wall(s) "wall/region"_fix_wall_region.html - use region surface as wall -"wall/region/ees"_fix_wall_ees.html - +"wall/region/ees"_fix_wall_ees.html - use region surface as wall for ellipsoidal particles "wall/srd"_fix_wall_srd.html - slip/no-slip wall for SRD particles :ul [Restrictions:]