git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13686 f3b2605a-c512-4ea7-a41b-209d697bcdaa

2015-07-22 16:14:45 +00:00
parent ead2e3aeec
commit cd9d7e46ae
6 changed files with 73 additions and 5 deletions
--- a/doc/Section_commands.html
+++ b/doc/Section_commands.html
@ -436,9 +436,9 @@ package</A>.
 <TR ALIGN="center"><TD ><A HREF = "fix_adapt_fep.html">adapt/fep</A></TD><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_ave_spatial_sphere.html">ave/spatial/sphere</A></TD><TD ><A HREF = "fix_colvars.html">colvars</A></TD><TD ><A HREF = "fix_gle.html">gle</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_ipi.html">ipi</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_lb_fluid.html">lb/fluid</A></TD><TD ><A HREF = "fix_lb_momentum.html">lb/momentum</A></TD><TD ><A HREF = "fix_lb_pc.html">lb/pc</A></TD></TR>
 <TR ALIGN="center"><TD ><A HREF = "fix_lb_rigid_pc_sphere.html">lb/rigid/pc/sphere</A></TD><TD ><A HREF = "fix_lb_viscous.html">lb/viscous</A></TD><TD ><A HREF = "fix_meso.html">meso</A></TD><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></TR>
-<TR ALIGN="center"><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><TD ><A HREF = "fix_phonon.html">phonon</A></TD><TD ><A HREF = "fix_pimd.html">pimd</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_qmmm.html">qmmm</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD><TD ><A HREF = "fix_saed_vtk.html">saed/vtk</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>
-<TR ALIGN="center"><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD><TD ><A HREF = "fix_ti_spring.html">ti/spring</A></TD><TD ><A HREF = "fix_ttm.html">ttm/mod</A> 
+<TR ALIGN="center"><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><TD ><A HREF = "fix_phonon.html">phonon</A></TD><TD ><A HREF = "fix_pimd.html">pimd</A></TD><TD ><A HREF = "fix_qbmsst.html">qbmsst</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_qmmm.html">qmmm</A></TD><TD ><A HREF = "fix_qtb.html">qtb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD><TD ><A HREF = "fix_saed_vtk.html">saed/vtk</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD><TD ><A HREF = "fix_ti_spring.html">ti/spring</A></TD><TD ><A HREF = "fix_ttm.html">ttm/mod</A> 
 </TD></TR></TABLE></DIV>

 <HR>
--- a/doc/Section_packages.html
+++ b/doc/Section_packages.html
@ -136,6 +136,7 @@ on how to build LAMMPS with both kinds of auxiliary libraries.
 <TR ALIGN="center"><TD >USER-OMP</TD><TD > OpenMP threaded styles</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "accelerate_omp.html">Section accelerate</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >USER-PHONON</TD><TD > phonon dynamical matrix</TD><TD > Ling-Ti Kong (Shanghai Jiao Tong U)</TD><TD > <A HREF = "fix_phonon.html">fix phonon</A></TD><TD > USER/phonon</TD><TD > -</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >USER-QMMM</TD><TD > QM/MM coupling</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "fix_qmmm.html">fix qmmm</A></TD><TD > USER/qmmm</TD><TD > -</TD><TD > lib/qmmm</TD></TR>
+<TR ALIGN="center"><TD >USER-QTB</TD><TD > quantum nuclear effects</TD><TD > Yuan Shen (Stanford)</TD><TD > <A HREF = "fix_qtb.html">fix qtb</A> <A HREF = "fix_qbmsst.html">fix_qbmsst</A></TD><TD > qtb</TD><TD > -</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >USER-QUIP</TD><TD > QM/MM coupling</TD><TD > Albert Bartok-Partay (U Cambridge)</TD><TD > <A HREF = "fix_quip.html">fix quip</A></TD><TD > USER/quip</TD><TD > -</TD><TD > lib/quip</TD></TR>
 <TR ALIGN="center"><TD >USER-REAXC</TD><TD > C version of ReaxFF</TD><TD > Metin Aktulga (LBNL)</TD><TD > <A HREF = "pair_reax_c.html">pair_style reaxc</A></TD><TD > reax</TD><TD > -</TD><TD > -</TD></TR>
 <TR ALIGN="center"><TD >USER-SPH</TD><TD > smoothed particle hydrodynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "USER/sph/SPH_LAMMPS_userguide.pdf">userguide.pdf</A></TD><TD > USER/sph</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#sph">sph</A></TD><TD > -</TD></TR>
@ -548,6 +549,33 @@ without changes to LAMMPS itself.
 </P>
 <HR>

+<H4>USER-QTB package 
+</H4>
+<P>This package provides a self-consistent quantum treatment of the
+vibrational modes in a classical molecular dynamics simulation.  By
+coupling the MD simulation to a colored thermostat, it introduces zero
+point energy into the system, alter the energy power spectrum and the
+heat capacity towards their quantum nature. This package could be of
+interest if one wants to model systems at temperatures lower than
+their classical limits or when temperatures ramp up across the
+classical limits in the simulation.
+</P>
+<P>See these two doc pages to get started:
+</P>
+<P><A HREF = "fix_qtb.html">fix qtb</A> provides quantum nulcear correction through a
+colored thermostat and can be used with other time integration schemes
+like <A HREF = "fix_nve.html">fix nve</A> or <A HREF = "fix_nh.html">fix nph</A>.
+</P>
+<P><A HREF = "fix_qbmsst.html">fix qbmsst</A> enables quantum nuclear correction of a
+multi-scale shock technique simulation by coupling the quantum thermal
+bath with the shocked system.
+</P>
+<P>The person who created this package is Yuan Shen (sy0302 at
+stanford.edu) at Stanford University.  Contact him directly if you
+have questions.
+</P>
+<HR>
+
 <H4>USER-REAXC package 
 </H4>
 <P>This package contains a implementation for LAMMPS of the ReaxFF force
--- a/doc/Section_packages.txt
+++ b/doc/Section_packages.txt
@ -128,6 +128,7 @@ USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfi
 USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_accelerate_omp.html, -, -, -
 USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
 USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
+USER-QTB, quantum nuclear effects, Yuan Shen (Stanford), "fix qtb"_fix_qtb.html "fix_qbmsst"_fix_qbmsst.html, qtb, -, -
 USER-QUIP, QM/MM coupling, Albert Bartok-Partay (U Cambridge), "fix quip"_fix_quip.html, USER/quip, -, lib/quip
 USER-REAXC, C version of ReaxFF, Metin Aktulga (LBNL), "pair_style reaxc"_pair_reax_c.html, reax, -, -
 USER-SPH, smoothed particle hydrodynamics, Georg Ganzenmuller (EMI), "userguide.pdf"_USER/sph/SPH_LAMMPS_userguide.pdf, USER/sph, "sph"_sph, -
@ -535,6 +536,33 @@ The person who created this package is Axel Kohlmeyer at Temple U

 :line

+USER-QTB package :h4
+
+This package provides a self-consistent quantum treatment of the
+vibrational modes in a classical molecular dynamics simulation.  By
+coupling the MD simulation to a colored thermostat, it introduces zero
+point energy into the system, alter the energy power spectrum and the
+heat capacity towards their quantum nature. This package could be of
+interest if one wants to model systems at temperatures lower than
+their classical limits or when temperatures ramp up across the
+classical limits in the simulation.
+
+See these two doc pages to get started:
+
+"fix qtb"_fix_qtb.html provides quantum nulcear correction through a
+colored thermostat and can be used with other time integration schemes
+like "fix nve"_fix_nve.html or "fix nph"_fix_nh.html.
+
+"fix qbmsst"_fix_qbmsst.html enables quantum nuclear correction of a
+multi-scale shock technique simulation by coupling the quantum thermal
+bath with the shocked system.
+
+The person who created this package is Yuan Shen (sy0302 at
+stanford.edu) at Stanford University.  Contact him directly if you
+have questions.
+
+:line
+
 USER-REAXC package :h4

 This package contains a implementation for LAMMPS of the ReaxFF force
--- a/doc/compute_saed.html
+++ b/doc/compute_saed.html
@ -160,7 +160,11 @@ options.
 </P>
 <P><B>Restrictions:</B> 
 </P>
-<P>The compute_saed command does not work for triclinic cells. 
+<P>This command is part of the USER-DIFFRACTION 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>This command does not work for triclinic cells.
 </P>
 <P><B>Related commands:</B> 
 </P>
--- a/doc/compute_xrd.html
+++ b/doc/compute_xrd.html
@ -182,7 +182,11 @@ options.
 </P>
 <P><B>Restrictions:</B> 
 </P>
-<P>The compute_xrd command does not work for triclinic cells. 
+<P>This command is part of the USER-DIFFRACTION 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>This command does not work for triclinic cells. 
 </P>
 <P><B>Related commands:</B> 
 </P>
--- a/doc/fix_saed_vtk.html
+++ b/doc/fix_saed_vtk.html
@ -170,6 +170,10 @@ minimization</A>.
 </P>
 <P><B>Restrictions:</B> 
 </P>
+<P>This command is part of the USER-DIFFRACTION 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>The attributes for fix_saed_vtk must match the values assigned in the
 associated <A HREF = "compute_saed.txt">compute_saed</A> command.
 </P>