mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3560 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
f650b52f2d
commit
2b3965902b
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@ -349,9 +349,9 @@ each style or click on the style itself for a full description:
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<TR ALIGN="center"><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD></TR>
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<TR ALIGN="center"><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_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
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<TR ALIGN="center"><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A>
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</TD></TR></TABLE></DIV>
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<P>These are compute styles contributed by users, which can be used if
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@ -478,6 +478,7 @@ each style or click on the style itself for a full description:
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"pe/atom"_compute_pe_atom.html,
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"pressure"_compute_pressure.html,
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"property/atom"_compute_property_atom.html,
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"property/local"_compute_property_local.html,
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"rdf"_compute_rdf.html,
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"reduce"_compute_reduce.html,
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"reduce/region"_compute_reduce.html,
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@ -1053,14 +1053,25 @@ command.
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</H5>
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<P>Dump file output is specified by the <A HREF = "dump.html">dump</A> and
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<A HREF = "dump_modify.html">dump_modify</A> commands. There are several
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pre-defined formats (dump atom, dump xtc, etc). There is also a <A HREF = "dump.html">dump
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custom</A> format where the user specifies what values are
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output with each atom. Pre-defined atom attributes can be specified
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(id, x, fx, etc). Three additional kinds of keywords can also be
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specified (c_ID, f_ID, v_name), where a <A HREF = "compute.html">compute</A> or
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<A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A> provides the values to be
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output. In each case, the compute, fix, or variable must generate
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per-atom values for input to the <A HREF = "dump.html">dump custom</A> command.
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pre-defined formats (dump atom, dump xtc, etc).
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</P>
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<P>There is also a <A HREF = "dump.html">dump custom</A> format where the user
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specifies what values are output with each atom. Pre-defined atom
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attributes can be specified (id, x, fx, etc). Three additional kinds
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of keywords can also be specified (c_ID, f_ID, v_name), where a
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<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A>
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provides the values to be output. In each case, the compute, fix, or
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variable must generate per-atom values for input to the <A HREF = "dump.html">dump
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custom</A> command.
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</P>
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<P>There is also a <A HREF = "dump.html">dump local</A> format where the user specifies
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what local values to output. A pre-defined index keyword can be
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specified to enumuerate the local values. Two additional kinds of
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keywords can also be specified (c_ID, f_ID), where a
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<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or <A HREF = "variable.html">variable</A>
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provides the values to be output. In each case, the compute or fix
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must generate local values for input to the <A HREF = "dump.html">dump local</A>
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command.
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</P>
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<H5><A NAME = "fixoutput"></A>Fixes that write output files
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</H5>
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@ -1124,6 +1135,12 @@ as output values which can be used as input to other output commands.
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The list of atom attributes is the same as for the <A HREF = "dump.html">dump
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custom</A> command.
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</P>
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<P>The <A HREF = "compute_property_local.html">compute property/local</A> command takes
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a list of one or more pre-defined local attributes (bond info, angle
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info, etc) and stores the values in a local vector or array. These
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are produced as output values which can be used as input to other
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output commands.
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</P>
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<H5><A NAME = "fixoutput"></A>Fixes that process output quantities
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</H5>
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<P>The <A HREF = "fix_ave_atom.html">fix ave/atom</A> command performs time-averaging
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@ -1181,6 +1198,7 @@ vector input could be a column of an array.
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<TR><TD >Command</TD><TD > Input</TD><TD > Output</TD><TD ></TD></TR>
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<TR><TD ><A HREF = "thermo_style.html">thermo_style custom</A></TD><TD > global scalars</TD><TD > screen, log file</TD><TD ></TD></TR>
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<TR><TD ><A HREF = "dump.html">dump custom</A></TD><TD > per-atom vectors</TD><TD > dump file</TD><TD ></TD></TR>
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<TR><TD ><A HREF = "dump.html">dump local</A></TD><TD > local vectors</TD><TD > dump file</TD><TD ></TD></TR>
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<TR><TD ><A HREF = "fix_print.html">fix print</A></TD><TD > global scalar from variable</TD><TD > screen, file</TD><TD ></TD></TR>
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<TR><TD ><A HREF = "print.html">print</A></TD><TD > global scalar from variable</TD><TD > screen</TD><TD ></TD></TR>
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<TR><TD ><A HREF = "compute.html">computes</A></TD><TD > N/A</TD><TD > global/per-atom/local scalar/vector/array</TD><TD ></TD></TR>
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@ -1188,6 +1206,7 @@ vector input could be a column of an array.
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<TR><TD ><A HREF = "variable.html">variables</A></TD><TD > global scalars, per-atom vectors</TD><TD > global scalar, per-atom vector</TD><TD ></TD></TR>
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<TR><TD ><A HREF = "compute_reduce.html">compute reduce</A></TD><TD > global/per-atom/local vectors</TD><TD > global scalar/vector</TD><TD ></TD></TR>
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<TR><TD ><A HREF = "compute_property_atom.html">compute property/atom</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
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<TR><TD ><A HREF = "compute_local_atom.html">compute property/local</A></TD><TD > local vectors</TD><TD > local vector/array</TD><TD ></TD></TR>
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<TR><TD ><A HREF = "fix_ave_atom.html">fix ave/atom</A></TD><TD > per-atom vectors</TD><TD > per-atom vector/array</TD><TD ></TD></TR>
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<TR><TD ><A HREF = "fix_ave_time.html">fix ave/time</A></TD><TD > global scalars/vectors</TD><TD > global scalar/vector/array, file</TD><TD ></TD></TR>
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<TR><TD ><A HREF = "fix_ave_spatial.html">fix ave/spatial</A></TD><TD > per-atom vectors</TD><TD > global array, file</TD><TD ></TD></TR>
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@ -1044,14 +1044,25 @@ Dump file output :h5,link(dump)
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Dump file output is specified by the "dump"_dump.html and
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"dump_modify"_dump_modify.html commands. There are several
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pre-defined formats (dump atom, dump xtc, etc). There is also a "dump
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custom"_dump.html format where the user specifies what values are
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output with each atom. Pre-defined atom attributes can be specified
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(id, x, fx, etc). Three additional kinds of keywords can also be
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specified (c_ID, f_ID, v_name), where a "compute"_compute.html or
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"fix"_fix.html or "variable"_variable.html provides the values to be
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output. In each case, the compute, fix, or variable must generate
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per-atom values for input to the "dump custom"_dump.html command.
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pre-defined formats (dump atom, dump xtc, etc).
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There is also a "dump custom"_dump.html format where the user
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specifies what values are output with each atom. Pre-defined atom
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attributes can be specified (id, x, fx, etc). Three additional kinds
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of keywords can also be specified (c_ID, f_ID, v_name), where a
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"compute"_compute.html or "fix"_fix.html or "variable"_variable.html
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provides the values to be output. In each case, the compute, fix, or
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variable must generate per-atom values for input to the "dump
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custom"_dump.html command.
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There is also a "dump local"_dump.html format where the user specifies
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what local values to output. A pre-defined index keyword can be
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specified to enumuerate the local values. Two additional kinds of
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keywords can also be specified (c_ID, f_ID), where a
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"compute"_compute.html or "fix"_fix.html or "variable"_variable.html
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provides the values to be output. In each case, the compute or fix
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must generate local values for input to the "dump local"_dump.html
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command.
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Fixes that write output files :h5,link(fixoutput)
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@ -1115,6 +1126,12 @@ as output values which can be used as input to other output commands.
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The list of atom attributes is the same as for the "dump
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custom"_dump.html command.
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The "compute property/local"_compute_property_local.html command takes
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a list of one or more pre-defined local attributes (bond info, angle
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info, etc) and stores the values in a local vector or array. These
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are produced as output values which can be used as input to other
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output commands.
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Fixes that process output quantities :h5,link(fixoutput)
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The "fix ave/atom"_fix_ave_atom.html command performs time-averaging
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@ -1171,6 +1188,7 @@ vector input could be a column of an array.
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Command: Input: Output:
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"thermo_style custom"_thermo_style.html: global scalars: screen, log file:
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"dump custom"_dump.html: per-atom vectors: dump file:
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"dump local"_dump.html: local vectors: dump file:
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"fix print"_fix_print.html: global scalar from variable: screen, file:
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"print"_print.html: global scalar from variable: screen:
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"computes"_compute.html: N/A: global/per-atom/local scalar/vector/array:
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@ -1178,6 +1196,7 @@ Command: Input: Output:
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"variables"_variable.html: global scalars, per-atom vectors: global scalar, per-atom vector:
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"compute reduce"_compute_reduce.html: global/per-atom/local vectors: global scalar/vector:
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"compute property/atom"_compute_property_atom.html: per-atom vectors: per-atom vector/array:
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"compute property/local"_compute_local_atom.html: local vectors: local vector/array:
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"fix ave/atom"_fix_ave_atom.html: per-atom vectors: per-atom vector/array:
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"fix ave/time"_fix_ave_time.html: global scalars/vectors: global scalar/vector/array, file:
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"fix ave/spatial"_fix_ave_spatial.html: per-atom vectors: global array, file:
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@ -112,7 +112,8 @@ variable</A>.
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<LI>Local values can be reduced by the <A HREF = "compute_reduce.html">compute
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reduce</A> command, or histogrammed by the <A HREF = "fix_ave_histo.html">fix
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ave/histo</A> command.
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ave/histo</A> command, or output by the <A HREF = "dump.html">dump
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local</A> command.
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</UL>
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<P>The results of computes that calculate global quantities can be either
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"intensive" or "extensive" values. Intensive means the value is
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@ -184,6 +185,7 @@ available in LAMMPS:
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<LI><A HREF = "compute_pe_atom.html">pe/atom</A> - potential energy for each atom
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<LI><A HREF = "compute_pressure.html">pressure</A> - total pressure and pressure tensor
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<LI><A HREF = "compute_property_atom.html">property/atom</A> - convert atom attributes to per-atom vectors/arrays
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<LI><A HREF = "compute_property_local.html">property/local</A> - convert local attributes to localvectors/arrays
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<LI><A HREF = "compute_rdf.html">rdf</A> - radial distribution function g(r) histogram of group of atoms
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<LI><A HREF = "compute_reduce.html">reduce</A> - combine per-atom quantities into a single global value
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<LI><A HREF = "compute_reduce.html">reduce/region</A> - same as compute reduce, within a region
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@ -209,7 +211,7 @@ page</A>.
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</P>
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<P><A HREF = "uncompute.html">uncompute</A>, <A HREF = "compute_modify.html">compute_modify</A>, <A HREF = "fix_ave_atom.html">fix
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ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix ave/spatial</A>,
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<A HREF = "fix_ave_time.html">fix ave/time</A>
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<A HREF = "fix_ave_time.html">fix ave/time</A>, <A HREF = "fix_ave_histo.html">fix ave/histo</A>
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</P>
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<P><B>Default:</B> none
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</P>
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@ -107,7 +107,8 @@ variable"_variable.html. :l
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Local values can be reduced by the "compute
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reduce"_compute_reduce.html command, or histogrammed by the "fix
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ave/histo"_fix_ave_histo.html command. :l,ule
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ave/histo"_fix_ave_histo.html command, or output by the "dump
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local"_dump.html command. :l,ule
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The results of computes that calculate global quantities can be either
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"intensive" or "extensive" values. Intensive means the value is
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"pe/atom"_compute_pe_atom.html - potential energy for each atom
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"pressure"_compute_pressure.html - total pressure and pressure tensor
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"property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays
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"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays
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"rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms
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"reduce"_compute_reduce.html - combine per-atom quantities into a single global value
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"reduce/region"_compute_reduce.html - same as compute reduce, within a region
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@ -204,6 +206,6 @@ page"_Section_commands.html#3_5.
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"uncompute"_uncompute.html, "compute_modify"_compute_modify.html, "fix
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ave/atom"_fix_ave_atom.html, "fix ave/spatial"_fix_ave_spatial.html,
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"fix ave/time"_fix_ave_time.html
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"fix ave/time"_fix_ave_time.html, "fix ave/histo"_fix_ave_histo.html
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[Default:] none
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q, mux, muy, muz,
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radius, omegax, omegay, omegaz,
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angmomx, angmomy, angmomz,
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quatw, quati, quatj, quatk, tqx, tqy, tqz
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id = atom ID
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quatw, quati, quatj, quatk, tqx, tqy, tqz
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</PRE>
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<PRE> id = atom ID
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mol = molecule ID
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type = atom type
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mass = atom mass
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q, mux, muy, muz,
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radius, omegax, omegay, omegaz,
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angmomx, angmomy, angmomz,
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quatw, quati, quatj, quatk, tqx, tqy, tqz
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quatw, quati, quatj, quatk, tqx, tqy, tqz :pre
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id = atom ID
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mol = molecule ID
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type = atom type
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radius, omegax, omegay, omegaz,
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angmomx, angmomy, angmomz,
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quatw, quati, quatj, quatk, tqx, tqy, tqz,
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c_ID, c_ID[N], f_ID, f_ID[N], v_name
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id = atom ID
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c_ID, c_ID[N], f_ID, f_ID[N], v_name
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</PRE>
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<PRE> id = atom ID
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mol = molecule ID
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type = atom type
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mass = atom mass
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@ -32,7 +32,8 @@ args = list of arguments for a particular style :l
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radius, omegax, omegay, omegaz,
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angmomx, angmomy, angmomz,
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quatw, quati, quatj, quatk, tqx, tqy, tqz,
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c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name
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c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
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id = atom ID
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mol = molecule ID
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type = atom type
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