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Removed reax/c time-averaging and merged reax and reax/c for fix reax/bonds and replaced integers with chemical symbols in pair_coeff command for reax/c

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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9558 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps
2013-03-04 18:34:42 +00:00
parent 538bd16793
commit dd0d1ab850
8 changed files with 73 additions and 223 deletions
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50
doc/Section_commands.html
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@ -335,7 +335,7 @@ included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "angle_coeff.html">angle_coeff</A></TD><TD ><A HREF = "angle_style.html">angle_style</A></TD><TD ><A HREF = "atom_modify.html">atom_modify</A></TD><TD ><A HREF = "atom_style.html">atom_style</A></TD><TD ><A HREF = "balance.html">balance</A></TD><TD ><A HREF = "bond_coeff.html">bond_coeff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "bond_style.html">bond_style</A></TD><TD ><A HREF = "boundary.html">boundary</A></TD><TD ><A HREF = "box.html">box</A></TD><TD ><A HREF = "change_box.html">change_box</A></TD><TD ><A HREF = "clear.html">clear</A></TD><TD ><A HREF = "communicate.html">communicate</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute.html">compute</A></TD><TD ><A HREF = "compute_modify.html">compute_modify</A></TD><TD ><A HREF = "create_atoms.html">create_atoms</A></TD><TD ><A HREF = "create_box.html">create_box</A></TD><TD ><A HREF = "delete_atoms.html">delete_atoms</A></TD><TD ><A HREF = "delete_bonds.html">delete_bonds</A></TD></TR>
@ -360,7 +360,7 @@ in the command's documentation.
<P>See the <A HREF = "fix.html">fix</A> command for one-line descriptions
of each style or click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_adapt.html">adapt</A></TD><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_append_atoms.html">append/atoms</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_correlate.html">ave/correlate</A></TD><TD ><A HREF = "fix_ave_histo.html">ave/histo</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_balance.html">balance</A></TD><TD ><A HREF = "fix_bond_break.html">bond/break</A></TD><TD ><A HREF = "fix_bond_create.html">bond/create</A></TD><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD><TD ><A HREF = "fix_external.html">external</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gcmc.html">gcmc</A></TD></TR>
@ -379,17 +379,17 @@ of each style or click on the style itself for a full description:
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_colvars.html">colvars</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_meso.html">meso</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_reaxc_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A>
<TR ALIGN="center"><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated fix styles, which can be used if LAMMPS is
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_freeze.html">freeze/cuda</A></TD><TD ><A HREF = "fix_addforce.html">addforce/cuda</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce/cuda</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d/cuda</A></TD><TD ><A HREF = "fix_gravity.html">gravity/cuda</A></TD><TD ><A HREF = "fix_gravity.html">gravity/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nh.html">nph/omp</A></TD><TD ><A HREF = "fix_nphug.html">nphug/omp</A></TD><TD ><A HREF = "fix_nph_asphere.html">nph/asphere/omp</A></TD><TD ><A HREF = "fix_nph_sphere.html">nph/sphere/omp</A></TD><TD ><A HREF = "fix_nh.html">npt/cuda</A></TD><TD ><A HREF = "fix_nh.html">npt/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_npt_asphere.html">npt/asphere/omp</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere/omp</A></TD><TD ><A HREF = "fix_nh.html">nve/cuda</A></TD><TD ><A HREF = "fix_nve.html">nve/omp</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere/omp</A></TD><TD ><A HREF = "fix_nh.html">nvt/cuda</A></TD></TR>
@ -405,7 +405,7 @@ package</A>.
<P>See the <A HREF = "compute.html">compute</A> command for one-line descriptions of
each style or click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_atom_molecule.html">atom/molecule</A></TD><TD ><A HREF = "compute_body_local.html">body/local</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cluster_atom.html">cluster/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_com_molecule.html">com/molecule</A></TD><TD ><A HREF = "compute_contact_atom.html">contact/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_erotate_sphere_atom.html">erotate/sphere/atom</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD></TR>
@ -421,7 +421,7 @@ each style or click on the style itself for a full description:
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD><TD ><A HREF = "compute_ke_atom_eff.html">ke/atom/eff</A></TD><TD ><A HREF = "compute_meso_e_atom.html">meso_e/atom</A></TD><TD ><A HREF = "compute_meso_rho_atom.html">meso_rho/atom</A></TD><TD ><A HREF = "compute_meso_t_atom.html">meso_t/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A>
</TD></TR></TABLE></DIV>
@ -430,7 +430,7 @@ package</A>.
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_pe.html">pe/cuda</A></TD><TD ><A HREF = "compute_pressure.html">pressure/cuda</A></TD><TD ><A HREF = "compute_temp.html">temp/cuda</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial/cuda</A>
</TD></TR></TABLE></DIV>
@ -441,7 +441,7 @@ package</A>.
<P>See the <A HREF = "pair_style.html">pair_style</A> command for an overview of pair
potentials. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid/overlay</A></TD><TD ><A HREF = "pair_adp.html">adp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">airebo</A></TD><TD ><A HREF = "pair_beck.html">beck</A></TD><TD ><A HREF = "pair_body.html">body</A></TD><TD ><A HREF = "pair_bop.html">bop</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born</A></TD><TD ><A HREF = "pair_born.html">born/coul/long</A></TD><TD ><A HREF = "pair_born.html">born/coul/msm</A></TD><TD ><A HREF = "pair_born.html">born/coul/wolf</A></TD></TR>
@ -470,7 +470,7 @@ potentials. Click on the style itself for a full description:
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_awpmd.html">awpmd/cut</A></TD><TD ><A HREF = "pair_coul_diel.html">coul/diel</A></TD><TD ><A HREF = "pair_dipole.html">dipole/sf</A></TD><TD ><A HREF = "pair_eam.html">eam/cd</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_edip.html">edip</A></TD><TD ><A HREF = "pair_eff.html">eff/cut</A></TD><TD ><A HREF = "pair_gauss.html">gauss/cut</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/msm</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf</A></TD><TD ><A HREF = "pair_meam_spline.html">meam/spline</A></TD></TR>
@ -483,7 +483,7 @@ package</A>.
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_adp.html">adp/omp</A></TD><TD ><A HREF = "pair_airebo.html">airebo/omp</A></TD><TD ><A HREF = "pair_beck.html">beck/omp</A></TD><TD ><A HREF = "pair_born.html">born/coul/long/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born/coul/long/gpu</A></TD><TD ><A HREF = "pair_born.html">born/coul/long/omp</A></TD><TD ><A HREF = "pair_born.html">born/coul/msm/omp</A></TD><TD ><A HREF = "pair_born.html">born/coul/wolf/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born/coul/wolf/omp</A></TD><TD ><A HREF = "pair_born.html">born/gpu</A></TD><TD ><A HREF = "pair_born.html">born/omp</A></TD><TD ><A HREF = "pair_brownian.html">brownian/omp</A></TD></TR>
@ -530,7 +530,7 @@ package</A>.
<P>See the <A HREF = "bond_style.html">bond_style</A> command for an overview of bond
potentials. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_none.html">none</A></TD><TD WIDTH="100"><A HREF = "bond_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "bond_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "bond_fene.html">fene</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_fene_expand.html">fene/expand</A></TD><TD WIDTH="100"><A HREF = "bond_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "bond_morse.html">morse</A></TD><TD WIDTH="100"><A HREF = "bond_nonlinear.html">nonlinear</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_quartic.html">quartic</A></TD><TD WIDTH="100"><A HREF = "bond_table.html">table</A>
@ -540,7 +540,7 @@ potentials. Click on the style itself for a full description:
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "bond_harmonic_shift.html">harmonic/shift</A></TD><TD ><A HREF = "bond_harmonic_shift_cut.html">harmonic/shift/cut</A>
</TD></TR></TABLE></DIV>
@ -548,7 +548,7 @@ package</A>.
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_class2.html">class2/omp</A></TD><TD WIDTH="100"><A HREF = "bond_fene.html">fene/omp</A></TD><TD WIDTH="100"><A HREF = "bond_fene_expand.html">fene/expand/omp</A></TD><TD WIDTH="100"><A HREF = "bond_harmonic.html">harmonic/omp</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_harmonic_shift.html">harmonic/shift/omp</A></TD><TD WIDTH="100"><A HREF = "bond_harmonic_shift_cut.html">harmonic/shift/cut/omp</A></TD><TD WIDTH="100"><A HREF = "bond_morse.html">morse/omp</A></TD><TD WIDTH="100"><A HREF = "bond_nonlinear.html">nonlinear/omp</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_quartic.html">quartic/omp</A></TD><TD WIDTH="100"><A HREF = "bond_table.html">table/omp</A>
@ -561,7 +561,7 @@ package</A>.
<P>See the <A HREF = "angle_style.html">angle_style</A> command for an overview of
angle potentials. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_none.html">none</A></TD><TD WIDTH="100"><A HREF = "angle_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "angle_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "angle_class2.html">class2</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_cosine.html">cosine</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_delta.html">cosine/delta</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_periodic.html">cosine/periodic</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_squared.html">cosine/squared</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "angle_table.html">table</A>
@ -571,7 +571,7 @@ angle potentials. Click on the style itself for a full description:
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "angle_sdk.html">sdk</A></TD><TD ><A HREF = "angle_cosine_shift.html">cosine/shift</A></TD><TD ><A HREF = "angle_cosine_shift_exp.html">cosine/shift/exp</A></TD><TD ><A HREF = "angle_dipole.html">dipole</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "angle_fourier.html">fourier</A></TD><TD ><A HREF = "angle_fourier_simple.html">fourier/simple</A></TD><TD ><A HREF = "angle_quartic.html">quartic</A>
</TD></TR></TABLE></DIV>
@ -580,7 +580,7 @@ package</A>.
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_charmm.html">charmm/omp</A></TD><TD WIDTH="100"><A HREF = "angle_class2.html">class2/omp</A></TD><TD WIDTH="100"><A HREF = "angle_cosine.html">cosine/omp</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_delta.html">cosine/delta/omp</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_cosine_periodic.html">cosine/periodic/omp</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_shift.html">cosine/shift/omp</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_shift_exp.html">cosine/shift/exp/omp</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_squared.html">cosine/squared/omp</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_dipole.html">dipole/omp</A><A HREF = "angle_fourier.html">fourier/omp</A></TD><TD WIDTH="100"><A HREF = "angle_fourier_simple.html">fourier/simple/omp</A></TD><TD WIDTH="100"><A HREF = "angle_harmonic.html">harmonic/omp</A></TD><TD WIDTH="100"><A HREF = "angle_quartic.html">quartic/omp</A><A HREF = "angle_table.html">table/omp</A>
@ -594,7 +594,7 @@ package</A>.
of dihedral potentials. Click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_none.html">none</A></TD><TD WIDTH="100"><A HREF = "dihedral_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "dihedral_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "dihedral_class2.html">class2</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "dihedral_helix.html">helix</A></TD><TD WIDTH="100"><A HREF = "dihedral_multi_harmonic.html">multi/harmonic</A></TD><TD WIDTH="100"><A HREF = "dihedral_opls.html">opls</A>
</TD></TR></TABLE></DIV>
@ -603,7 +603,7 @@ description:
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "dihedral_cosine_shift_exp.html">cosine/shift/exp</A></TD><TD ><A HREF = "dihedral_fourier.html">fourier</A></TD><TD ><A HREF = "dihedral_nharmonic.html">nharmonic</A></TD><TD ><A HREF = "dihedral_quadratic.html">quadratic</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "dihedral_table.html">table</A>
</TD></TR></TABLE></DIV>
@ -612,7 +612,7 @@ package</A>.
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_charmm.html">charmm/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_class2.html">class2/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_cosine_shift_exp.html">cosine/shift/exp/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_fourier.html">fourier/omp</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_harmonic.html">harmonic/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_helix.html">helix/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_multi_harmonic.html">multi/harmonic/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_nharmonic.html">nharmonic/omp</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_opls.html">opls/omp</A><A HREF = "dihedral_quadratic.html">quadratic/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_table.html">table/omp</A>
@ -626,7 +626,7 @@ package</A>.
of improper potentials. Click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_none.html">none</A></TD><TD WIDTH="100"><A HREF = "improper_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "improper_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "improper_cvff.html">cvff</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "improper_umbrella.html">umbrella</A>
</TD></TR></TABLE></DIV>
@ -635,7 +635,7 @@ description:
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "improper_cossq.html">cossq</A></TD><TD ><A HREF = "improper_fourier.html">fourier</A></TD><TD ><A HREF = "improper_ring.html">ring</A>
</TD></TR></TABLE></DIV>
@ -643,7 +643,7 @@ package</A>.
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_class2.html">class2/omp</A></TD><TD WIDTH="100"><A HREF = "improper_cossq.html">cossq/omp</A></TD><TD WIDTH="100"><A HREF = "improper_cvff.html">cvff/omp</A></TD><TD WIDTH="100"><A HREF = "improper_fourier.html">fourier/omp</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_harmonic.html">harmonic/omp</A></TD><TD WIDTH="100"><A HREF = "improper_ring.html">ring/omp</A></TD><TD WIDTH="100"><A HREF = "improper_umbrella.html">umbrella/omp</A>
</TD></TR></TABLE></DIV>
@ -655,7 +655,7 @@ package</A>.
<P>See the <A HREF = "kspace_style.html">kspace_style</A> command for an overview of
Kspace solvers. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">ewald</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">ewald/disp</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">msm</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">msm/cg</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">pppm</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm/cg</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm/disp</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm/disp/tip4p</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">pppm/tip4p</A>
@ -665,7 +665,7 @@ Kspace solvers. Click on the style itself for a full description:
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">ewald/omp</A></TD><TD ><A HREF = "kspace_style.html">msm/omp</A></TD><TD ><A HREF = "kspace_style.html">msm/cg/omp</A></TD><TD ><A HREF = "kspace_style.html">pppm/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">pppm/gpu</A></TD><TD ><A HREF = "kspace_style.html">pppm/omp</A></TD><TD ><A HREF = "kspace_style.html">pppm/cg/omp</A></TD><TD ><A HREF = "kspace_style.html">pppm/tip4p/omp</A>
</TD></TR></TABLE></DIV>

2
doc/Section_commands.txt
View File

@ -536,7 +536,7 @@ package"_Section_start.html#start_3.
"nvt/eff"_fix_nh_eff.html,
"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
"qeq/reax"_fix_qeq_reax.html,
"reax/c/bonds"_fix_reaxc_bonds.html,
"reax/c/bonds"_fix_reax_bonds.html,
"smd"_fix_smd.html,
"temp/rescale/eff"_fix_temp_rescale_eff.html :tb(c=6,ea=c)

20
doc/fix_reax_bonds.html
View File

@ -11,6 +11,8 @@
<H3>fix reax/bonds command
</H3>
<H3>fix reax/c/bonds command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID reax/bonds Nevery filename
@ -22,14 +24,18 @@
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all reax/bonds 100 bonds.tatb
<PRE>fix 1 all reax/bonds 100 bonds.tatb
fix 1 all reax/c/bonds 100 bonds.reaxc
</PRE>
<P><B>Description:</B>
</P>
<P>Write out the bond information computed by the ReaxFF potential
specified by <A HREF = "pair_reax.html">pair_style reax</A>. The bond information
specified by <A HREF = "pair_reax.html">pair_style reax</A> or
<A HREF = "pair_reax_c.html">pair_style reax/c</A> in the exact same format as
the stand-alone ReaxFF code. The bond information
is written to <I>filename</I> on timesteps that are multiples of <I>Nevery</I>,
including timestep 0.
including timestep 0. For time-averaged chemical species analysis,
please see the <A HREF = "fix_species.html">fix species</A> command.
</P>
<P>The format of the output file should be self-explantory.
</P>
@ -51,13 +57,17 @@ This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>
reax</A> be invoked. This fix is part of the REAX
package. It is only enabled if LAMMPS was built with that package,
which also requires the REAX library be built and linked with LAMMPS.
The fix reax/c/bonds command requires that the <A HREF = "pair_reax_c.html">pair_style
reax/c</A> be invoked. This fix is part of the USER-REAXC
package. It is only enabled if LAMMPS was built with that package.
See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more
info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_reax.html">pair_style reax</A>, <A HREF = "pair_reaxc_bonds.html">pair_style
reax/c/bonds</A>
<P><A HREF = "pair_reax.html">pair_style reax</A>,
<A HREF = "pair_reax_c.html">pair_style reax/c</A>,
<A HREF = "fix_species.html">fix species</A>
</P>
<P><B>Default:</B> none
</P>

19
doc/fix_reax_bonds.txt
View File

@ -7,6 +7,7 @@
:line
fix reax/bonds command :h3
fix reax/c/bonds command :h3
[Syntax:]
@ -19,14 +20,18 @@ filename = name of output file :ul
[Examples:]
fix 1 all reax/bonds 100 bonds.tatb :pre
fix 1 all reax/bonds 100 bonds.tatb
fix 1 all reax/c/bonds 100 bonds.reaxc :pre
[Description:]
Write out the bond information computed by the ReaxFF potential
specified by "pair_style reax"_pair_reax.html. The bond information
specified by "pair_style reax"_pair_reax.html or
"pair_style reax/c"_pair_reax_c.html in the exact same format as
the stand-alone ReaxFF code. The bond information
is written to {filename} on timesteps that are multiples of {Nevery},
including timestep 0.
including timestep 0. For time-averaged chemical species analysis,
please see the "fix species"_fix_species.html command.
The format of the output file should be self-explantory.
@ -48,12 +53,16 @@ The fix reax/bonds command requires that the "pair_style
reax"_pair_reax.html be invoked. This fix is part of the REAX
package. It is only enabled if LAMMPS was built with that package,
which also requires the REAX library be built and linked with LAMMPS.
The fix reax/c/bonds command requires that the "pair_style
reax/c"_pair_reax_c.html be invoked. This fix is part of the USER-REAXC
package. It is only enabled if LAMMPS was built with that package.
See the "Making LAMMPS"_Section_start.html#start_3 section for more
info.
[Related commands:]
"pair_style reax"_pair_reax.html, "pair_style
reax/c/bonds"_pair_reaxc_bonds.html
"pair_style reax"_pair_reax.html,
"pair_style reax/c"_pair_reax_c.html,
"fix species"_fix_species.html
[Default:] none

88
doc/fix_reaxc_bonds.html
View File

@ -1,88 +0,0 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix reax/c/bonds command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID reax/c/bonds Nevery Nrepeat Nfreq filename
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>reax/c/bonds = style name of this command
<LI>Nevery = output interval in timesteps
<LI>Nrepeat = # of times to use input values for calculating averages
<LI>Nfreq = calculate averages every this many timesteps
<LI>filename = name of output file
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all reax/c/bonds 10 10 100 bonds.reaxc
</PRE>
<P><B>Description:</B>
</P>
<P>Write out the bond information computed by the ReaxFF potential
specified by <A HREF = "pair_reax_c.html">pair_style reax/c</A>. Bond order values
are averaged and the bond information is written to <I>filename</I> on
timesteps that are multiples of <I>Nfreq</I>, including timestep 0.
</P>
<HR>
<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
timesteps the input values will be used in order to contribute to the
average. The final averaged quantities are generated on timesteps
that are a multiple of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
quantities, computed in the preceding portion of the simulation every
<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq >
(Nrepeat-1)*Nevery is required.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
timestep 200, etc.
</P>
<P>The format of the output file should be self-explanatory. When using
the same force field file with <A HREF = "pair_reax.html">pair_style reax</A> and
<A HREF = "pair_reax_c.html">pair_style reax/c</A>, the following commands generate
the same bond information:
</P>
<PRE>fix 1 all reax/bonds <I>N</I> bonds.reax
fix 1 all reax/c/bonds 1 1 <I>N</I> bonds.reaxc
</PRE>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. No parameter of this fix can
be used with the <I>start/stop</I> keywords of the <A HREF = "run.html">run</A> command.
This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P><B>Restrictions:</B>
</P>
<P>The fix reax/c/bonds requires that the <A HREF = "pair_reax_c.html">pair_style
reax/c</A> be invoked. This fix is part of the
USER-REAXC package. It is only enabled if LAMMPS was built with that
package. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section
for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_reax_c.html">pair_style reax/c</A>, <A HREF = "fix_reax_bonds.html">fix
reax/bonds</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>

83
doc/fix_reaxc_bonds.txt
View File

@ -1,83 +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,Section_commands.html#comm)
:line
fix reax/c/bonds command :h3
[Syntax:]
fix ID group-ID reax/c/bonds Nevery Nrepeat Nfreq filename :pre
ID, group-ID are documented in "fix"_fix.html command
reax/c/bonds = style name of this command
Nevery = output interval in timesteps
Nrepeat = # of times to use input values for calculating averages
Nfreq = calculate averages every this many timesteps
filename = name of output file :ul
[Examples:]
fix 1 all reax/c/bonds 10 10 100 bonds.reaxc :pre
[Description:]
Write out the bond information computed by the ReaxFF potential
specified by "pair_style reax/c"_pair_reax_c.html. Bond order values
are averaged and the bond information is written to {filename} on
timesteps that are multiples of {Nfreq}, including timestep 0.
:line
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
timesteps the input values will be used in order to contribute to the
average. The final averaged quantities are generated on timesteps
that are a multiple of {Nfreq}. The average is over {Nrepeat}
quantities, computed in the preceding portion of the simulation every
{Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and
{Nevery} must be non-zero even if {Nrepeat} is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq >
(Nrepeat-1)*Nevery is required.
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
timestep 200, etc.
The format of the output file should be self-explanatory. When using
the same force field file with "pair_style reax"_pair_reax.html and
"pair_style reax/c"_pair_reax_c.html, the following commands generate
the same bond information:
fix 1 all reax/bonds {N} bonds.reax
fix 1 all reax/c/bonds 1 1 {N} bonds.reaxc :pre
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various "output
commands"_Section_howto.html#howto_15. No parameter of this fix can
be used with the {start/stop} keywords of the "run"_run.html command.
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:]
The fix reax/c/bonds requires that the "pair_style
reax/c"_pair_reax_c.html be invoked. This fix is part of the
USER-REAXC package. It is only enabled if LAMMPS was built with that
package. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info.
[Related commands:]
"pair_style reax/c"_pair_reax_c.html, "fix
reax/bonds"_fix_reax_bonds.html
[Default:] none

17
doc/pair_reax_c.html
View File

@ -33,7 +33,7 @@
pair_style reax/c controlfile checkqeq no
pair_style reax/c NULL lgvdw yes
pair_style reax/c NULL safezone 1.6 mincap 100
pair_coeff * * ffield.reax 1 2 2 3
pair_coeff * * ffield.reax C H O N
</PRE>
<P><B>Description:</B>
</P>
@ -172,7 +172,7 @@ additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
</P>
<UL><LI>filename
<LI>N indices = mapping of ReaxFF elements to atom types
<LI>N indices = ReaxFF elements
</UL>
<P>The filename is the ReaxFF potential file. Unlike for the <I>reax</I>
pair style, any filename can be used.
@ -198,7 +198,7 @@ elements are ordered as C, H, O, N in the <I>ffield</I> file. If you want
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
H, you would use the following pair_coeff command:
</P>
<PRE>pair_coeff * * ffield.reax 1 1 4 2
<PRE>pair_coeff * * ffield.reax C C N H
</PRE>
<HR>
@ -297,13 +297,14 @@ appropriate units if your simulation doesn't use "real" units.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_qeq_reax.html">fix_qeq_reax</A>,
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "fix_qeq_reax.html">fix qeq/reax</A>,
<A HREF = "fix_reax_bonds.html">fix reax/c/bonds</A>,
<A HREF = "fix_species.html">fix species</A>,
<A HREF = "pair_reax.html">pair_style reax</A>
</P>
<P><B>Default:</B>
</P>
<P>The keyword defaults are checkqeq = yes, lgvdw = no, safezone = 1.2,
mincap = 50.
<P>The keyword defaults are checkqeq = yes, lgvdw = no, safezone = 1.2, mincap = 50.
</P>
<HR>
@ -314,8 +315,8 @@ Journal of Physical Chemistry A, 112, 1040-1053 (2008).
</P>
<A NAME = "Aktulga"></A>
<P><B>(Aktulga)</B> Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
245-259 (2012).
<P><B>(Aktulga)</B> Aktulga, Fogarty, Pandit, Grama, Parallel Computing, to
appear (2011).
</P>
<A NAME = "Liu_2011"></A>

17
doc/pair_reax_c.txt
View File

@ -27,7 +27,7 @@ pair_style reax/c NULL
pair_style reax/c controlfile checkqeq no
pair_style reax/c NULL lgvdw yes
pair_style reax/c NULL safezone 1.6 mincap 100
pair_coeff * * ffield.reax 1 2 2 3 :pre
pair_coeff * * ffield.reax C H O N :pre
[Description:]
@ -166,7 +166,7 @@ additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
filename
N indices = mapping of ReaxFF elements to atom types :ul
N indices = ReaxFF elements :ul
The filename is the ReaxFF potential file. Unlike for the {reax}
pair style, any filename can be used.
@ -192,7 +192,7 @@ elements are ordered as C, H, O, N in the {ffield} file. If you want
the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be
H, you would use the following pair_coeff command:
pair_coeff * * ffield.reax 1 1 4 2 :pre
pair_coeff * * ffield.reax C C N H :pre
:line
@ -291,13 +291,14 @@ appropriate units if your simulation doesn't use "real" units.
[Related commands:]
"pair_coeff"_pair_coeff.html, "fix_qeq_reax"_fix_qeq_reax.html,
"pair_coeff"_pair_coeff.html, "fix qeq/reax"_fix_qeq_reax.html,
"fix reax/c/bonds"_fix_reax_bonds.html,
"fix species"_fix_species.html,
"pair_style reax"_pair_reax.html
[Default:]
The keyword defaults are checkqeq = yes, lgvdw = no, safezone = 1.2,
mincap = 50.
The keyword defaults are checkqeq = yes, lgvdw = no, safezone = 1.2, mincap = 50.
:line
@ -306,8 +307,8 @@ mincap = 50.
Journal of Physical Chemistry A, 112, 1040-1053 (2008).
:link(Aktulga)
[(Aktulga)] Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
245-259 (2012).
[(Aktulga)] Aktulga, Fogarty, Pandit, Grama, Parallel Computing, to
appear (2011).
:link(Liu_2011)
[(Liu)] L. Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal