patch 22Feb18

Tiny update to fix latte for checking library version

cmake/CMakeLists.txt

@@ -104,7 +104,7 @@ set(OTHER_PACKAGES KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE
   USER-ATC USER-AWPMD USER-CGDNA USER-MESO
   USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
   USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
-  USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
+  USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
   USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 foreach(PKG ${DEFAULT_PACKAGES})
@@ -170,13 +170,6 @@ if(ENABLE_KSPACE)
   endif()
 endif()
 
-if(ENABLE_MISC)
-  option(LAMMPS_XDR "include XDR compatibility files for doing particle dumps in XTC format" OFF)
-  if(LAMMPS_XDR)
-    add_definitions(-DLAMMPS_XDR) # for liblammps
-  endif()
-endif()
-
 if(ENABLE_MSCG OR ENABLE_USER-ATC OR ENABLE_USER-AWPMD OR ENABLE_USER-QUIP OR ENABLE_LATTE)
   find_package(LAPACK)
   if(NOT LAPACK_FOUND)
@@ -198,14 +191,13 @@ if(ENABLE_PYTHON)
   add_definitions(-DLMP_PYTHON)
   include_directories(${PYTHON_INCLUDE_DIR})
   list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
+  if(BUILD_SHARED_LIBS)
     if(NOT PYTHON_INSTDIR)
       execute_process(COMMAND ${PYTHON_EXECUTABLE}
         -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
         OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
     endif()
     install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})
-  if(NOT BUILD_SHARED_LIBS)
-    message(FATAL_ERROR "Python package need lammps to be build shared, use -DBUILD_SHARED_LIBS=ON")
   endif()
 endif()
 
@@ -401,6 +393,10 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
       target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
     elseif(PKG_LIB STREQUAL h5md)
       target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include)
+    elseif(PKG_LIB STREQUAL colvars)
+      target_compile_options(colvars PRIVATE -DLEPTON)
+      target_include_directories(colvars PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton/include)
+      target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
     else()
       target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
     endif()
@@ -480,6 +476,8 @@ if(ENABLE_KOKKOS)
                          ${KOKKOS_PKG_SOURCES_DIR}/neigh_list_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/neigh_bond_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
                          ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
   set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
@@ -487,6 +485,17 @@ if(ENABLE_KOKKOS)
   # detects styles which have KOKKOS version
   RegisterStylesExt(${KOKKOS_PKG_SOURCES_DIR} kokkos KOKKOS_PKG_SOURCES)
 
+  # register kokkos-only styles
+  RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
+  RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
+
+  if(ENABLE_USER-DPD)
+    get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
+    list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
+    RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
+    set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
+  endif()
+
   get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
 
   list(APPEND LIB_SOURCES ${KOKKOS_PKG_SOURCES})

cmake/Modules/StyleHeaderUtils.cmake

@@ -11,6 +11,12 @@ function(FindStyleHeaders path style_class file_pattern headers)
     set_property(GLOBAL PROPERTY ${headers} "${hlist}")
 endfunction(FindStyleHeaders)
 
+function(AddStyleHeader path headers)
+    get_property(hlist GLOBAL PROPERTY ${headers})
+    list(APPEND hlist ${path})
+    set_property(GLOBAL PROPERTY ${headers} "${hlist}")
+endfunction(AddStyleHeader)
+
 function(FindStyleHeadersExt path style_class extension headers sources)
     get_property(hlist GLOBAL PROPERTY ${headers})
     get_property(slist GLOBAL PROPERTY ${sources})
@@ -62,6 +68,22 @@ function(GenerateStyleHeader path property style)
     CreateStyleHeader("${path}" "style_${style}.h" ${files})
 endfunction(GenerateStyleHeader)
 
+function(RegisterNBinStyles search_path)
+    FindStyleHeaders(${search_path} NBIN_CLASS      nbin_      NBIN      ) # nbin      ) # neighbor
+endfunction(RegisterNBinStyles)
+
+function(RegisterNPairStyles search_path)
+    FindStyleHeaders(${search_path} NPAIR_CLASS     npair_     NPAIR     ) # npair     ) # neighbor
+endfunction(RegisterNPairStyles)
+
+function(RegisterNBinStyle path)
+    AddStyleHeader(${path} NBIN)
+endfunction(RegisterNBinStyle)
+
+function(RegisterNPairStyle path)
+    AddStyleHeader(${path} NPAIR)
+endfunction(RegisterNPairStyle)
+
 function(RegisterStyles search_path)
     FindStyleHeaders(${search_path} ANGLE_CLASS     angle_     ANGLE     ) # angle     ) # force
     FindStyleHeaders(${search_path} ATOM_CLASS      atom_vec_  ATOM_VEC  ) # atom      ) # atom      atom_vec_hybrid

doc/Makefile

@@ -20,7 +20,8 @@ ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0)
 HAS_VIRTUALENV = YES
 endif
 
-SOURCES=$(wildcard src/*.txt)
+SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
+SOURCES=$(filter-out src/lammps_commands.txt src/lammps_tutorials.txt,$(wildcard src/*.txt))
 OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
 
 .PHONY: help clean-all clean epub html pdf old venv spelling anchor_check
@@ -55,7 +56,7 @@ html: $(OBJECTS) $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
 		cp -r src/* $(RSTDIR)/ ;\
-		sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
+		sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		echo "############################################" ;\
 		doc_anchor_check src/*.txt ;\
 		echo "############################################" ;\
@@ -91,7 +92,7 @@ epub: $(OBJECTS)
 	@(\
 		. $(VENV)/bin/activate ;\
 		cp -r src/* $(RSTDIR)/ ;\
-		sphinx-build -j 8 -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
+		sphinx-build $(SPHINXEXTRA) -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
 		deactivate ;\
 	)
 	@mv  epub/LAMMPS.epub .
@@ -159,7 +160,7 @@ $(VENV):
 	@( \
 		virtualenv -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
-		pip install Sphinx==1.5.6; \
+		pip install Sphinx; \
 		pip install sphinxcontrib-images; \
 		deactivate;\
 	)

doc/src/Eqs/pair_buck6d.txt

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+  E = A e^{-\kappa r} - \frac{C}{r^6} \cdot \frac{1}{1 + D r^{14}} \qquad r < r_c \\
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/pair_ufm.tex

@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+$$
+	E = -\varepsilon\, \ln{\left[1-\exp{\left(-r^{2}/\sigma^{2}\right)}\right]} \qquad  r < r_c
+$$
+
+$$
+  \varepsilon = p\,k_B\,T
+$$
+
+\end{document}
+

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="23 Oct 2017 version">
+<META NAME="docnumber" CONTENT="22 Feb 2018 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 <H1></H1>
 
 LAMMPS Documentation :c,h3
-23 Oct 2017 version :c,h4
+22 Feb 2018 version :c,h4
 
 Version info: :h4
 
@@ -176,11 +176,11 @@ END_RST -->
   5.1 "Measuring performance"_acc_1 :ulb,b
   5.2 "Algorithms and code options to boost performace"_acc_2 :b
   5.3 "Accelerator packages with optimized styles"_acc_3 :b
-    5.3.1 "GPU package"_accelerate_gpu.html :ulb,b
+    5.3.1 "GPU package"_accelerate_gpu.html :b
     5.3.2 "USER-INTEL package"_accelerate_intel.html :b
     5.3.3 "KOKKOS package"_accelerate_kokkos.html :b
     5.3.4 "USER-OMP package"_accelerate_omp.html :b
-    5.3.5 "OPT package"_accelerate_opt.html :ule,b
+    5.3.5 "OPT package"_accelerate_opt.html :b
   5.4 "Comparison of various accelerator packages"_acc_4 :ule,b
 "How-to discussions"_Section_howto.html :l
   6.1 "Restarting a simulation"_howto_1 :ulb,b

doc/src/Section_commands.txt

@@ -619,8 +619,9 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "pour"_fix_pour.html,
 "press/berendsen"_fix_press_berendsen.html,
 "print"_fix_print.html,
-"property/atom"_fix_property_atom.html,
-"python"_fix_python.html,
+"property/atom (k)"_fix_property_atom.html,
+"python/invoke"_fix_python_invoke.html,
+"python/move"_fix_python_move.html,
 "qeq/comb (o)"_fix_qeq_comb.html,
 "qeq/dynamic"_fix_qeq.html,
 "qeq/fire"_fix_qeq.html,
@@ -637,10 +638,10 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "rigid/nve (o)"_fix_rigid.html,
 "rigid/nvt (o)"_fix_rigid.html,
 "rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph (o)"_fix_rigid.html,
-"rigid/small/npt (o)"_fix_rigid.html,
-"rigid/small/nve (o)"_fix_rigid.html,
-"rigid/small/nvt (o)"_fix_rigid.html,
+"rigid/small/nph"_fix_rigid.html,
+"rigid/small/npt"_fix_rigid.html,
+"rigid/small/nve"_fix_rigid.html,
+"rigid/small/nvt"_fix_rigid.html,
 "setforce (k)"_fix_setforce.html,
 "shake"_fix_shake.html,
 "spring"_fix_spring.html,
@@ -668,7 +669,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "wall/harmonic"_fix_wall.html,
 "wall/lj1043"_fix_wall.html,
 "wall/lj126"_fix_wall.html,
-"wall/lj93"_fix_wall.html,
+"wall/lj93 (k)"_fix_wall.html,
 "wall/piston"_fix_wall_piston.html,
 "wall/reflect (k)"_fix_wall_reflect.html,
 "wall/region"_fix_wall_region.html,
@@ -683,14 +684,14 @@ package"_Section_start.html#start_3.
 "atc"_fix_atc.html,
 "ave/correlate/long"_fix_ave_correlate_long.html,
 "colvars"_fix_colvars.html,
-"dpd/energy"_fix_dpd_energy.html,
+"dpd/energy (k)"_fix_dpd_energy.html,
 "drude"_fix_drude.html,
 "drude/transform/direct"_fix_drude_transform.html,
 "drude/transform/reverse"_fix_drude_transform.html,
 "edpd/source"_fix_dpd_source.html,
 "eos/cv"_fix_eos_cv.html,
 "eos/table"_fix_eos_table.html,
-"eos/table/rx"_fix_eos_table_rx.html,
+"eos/table/rx (k)"_fix_eos_table_rx.html,
 "filter/corotate"_fix_filter_corotate.html,
 "flow/gauss"_fix_flow_gauss.html,
 "gle"_fix_gle.html,
@@ -728,12 +729,12 @@ package"_Section_start.html#start_3.
 "qeq/reax (ko)"_fix_qeq_reax.html,
 "qmmm"_fix_qmmm.html,
 "qtb"_fix_qtb.html,
-"reax/c/bonds"_fix_reax_bonds.html,
-"reax/c/species"_fix_reaxc_species.html,
+"reax/c/bonds (k)"_fix_reax_bonds.html,
+"reax/c/species (k)"_fix_reaxc_species.html,
 "rhok"_fix_rhok.html,
-"rx"_fix_rx.html,
+"rx (k)"_fix_rx.html,
 "saed/vtk"_fix_saed_vtk.html,
-"shardlow"_fix_shardlow.html,
+"shardlow (k)"_fix_shardlow.html,
 "smd"_fix_smd.html,
 "smd/adjust/dt"_fix_smd_adjust_dt.html,
 "smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
@@ -906,7 +907,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "none"_pair_none.html,
 "zero"_pair_zero.html,
 "hybrid"_pair_hybrid.html,
-"hybrid/overlay"_pair_hybrid.html,
+"hybrid/overlay (k)"_pair_hybrid.html,
 "adp (o)"_pair_adp.html,
 "airebo (oi)"_pair_airebo.html,
 "airebo/morse (oi)"_pair_airebo.html,
@@ -977,6 +978,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "lj/cut/coul/long (gikot)"_pair_lj.html,
 "lj/cut/coul/long/cs"_pair_lj.html,
 "lj/cut/coul/msm (go)"_pair_lj.html,
+"lj/cut/coul/wolf (o)"_pair_lj.html,
 "lj/cut/dipole/cut (go)"_pair_dipole.html,
 "lj/cut/dipole/long"_pair_dipole.html,
 "lj/cut/tip4p/cut (o)"_pair_lj.html,
@@ -1010,7 +1012,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "reax"_pair_reax.html,
 "rebo (oi)"_pair_airebo.html,
 "resquared (go)"_pair_resquared.html,
-"snap"_pair_snap.html,
+"snap (k)"_pair_snap.html,
 "soft (go)"_pair_soft.html,
 "sw (giko)"_pair_sw.html,
 "table (gko)"_pair_table.html,
@@ -1021,11 +1023,12 @@ KOKKOS, o = USER-OMP, t = OPT.
 "tip4p/cut (o)"_pair_coul.html,
 "tip4p/long (o)"_pair_coul.html,
 "tri/lj"_pair_tri_lj.html,
+"ufm (got)"_pair_ufm.html,
 "vashishta (ko)"_pair_vashishta.html,
 "vashishta/table (o)"_pair_vashishta.html,
-"yukawa (go)"_pair_yukawa.html,
+"yukawa (gok)"_pair_yukawa.html,
 "yukawa/colloid (go)"_pair_yukawa_colloid.html,
-"zbl (go)"_pair_zbl.html :tb(c=4,ea=c)
+"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c)
 
 These are additional pair styles in USER packages, which can be used
 if "LAMMPS is built with the appropriate
@@ -1038,13 +1041,14 @@ package"_Section_start.html#start_3.
 "coul/diel (o)"_pair_coul_diel.html,
 "coul/long/soft (o)"_pair_lj_soft.html,
 "dpd/fdt"_pair_dpd_fdt.html,
-"dpd/fdt/energy"_pair_dpd_fdt.html,
+"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
 "eam/cd (o)"_pair_eam.html,
 "edip (o)"_pair_edip.html,
 "edip/multi"_pair_edip.html,
 "edpd"_pair_meso.html,
 "eff/cut"_pair_eff.html,
-"exp6/rx"_pair_exp6_rx.html,
+"exp6/rx (k)"_pair_exp6_rx.html,
+"extep"_pair_extep.html,
 "gauss/cut"_pair_gauss.html,
 "kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
 "lennard/mdf"_pair_mdf.html,
@@ -1070,7 +1074,7 @@ package"_Section_start.html#start_3.
 "morse/smooth/linear"_pair_morse.html,
 "morse/soft"_pair_morse.html,
 "multi/lucy"_pair_multi_lucy.html,
-"multi/lucy/rx"_pair_multi_lucy_rx.html,
+"multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
 "oxdna/coaxstk"_pair_oxdna.html,
 "oxdna/excv"_pair_oxdna.html,
 "oxdna/hbond"_pair_oxdna.html,
@@ -1087,6 +1091,7 @@ package"_Section_start.html#start_3.
 "smd/triangulated/surface"_pair_smd_triangulated_surface.html,
 "smd/ulsph"_pair_smd_ulsph.html,
 "smtbq"_pair_smtbq.html,
+"snap (k)"_pair_snap.html,
 "sph/heatconduction"_pair_sph_heatconduction.html,
 "sph/idealgas"_pair_sph_idealgas.html,
 "sph/lj"_pair_sph_lj.html,
@@ -1094,7 +1099,7 @@ package"_Section_start.html#start_3.
 "sph/taitwater"_pair_sph_taitwater.html,
 "sph/taitwater/morris"_pair_sph_taitwater_morris.html,
 "srp"_pair_srp.html,
-"table/rx"_pair_table_rx.html,
+"table/rx (k)"_pair_table_rx.html,
 "tdpd"_pair_meso.html,
 "tersoff/table (o)"_pair_tersoff.html,
 "thole"_pair_thole.html,
@@ -1249,7 +1254,7 @@ USER-OMP, t = OPT.
 "ewald/disp"_kspace_style.html,
 "msm (o)"_kspace_style.html,
 "msm/cg (o)"_kspace_style.html,
-"pppm (go)"_kspace_style.html,
+"pppm (gok)"_kspace_style.html,
 "pppm/cg (o)"_kspace_style.html,
 "pppm/disp (i)"_kspace_style.html,
 "pppm/disp/tip4p"_kspace_style.html,

doc/src/Section_howto.txt

@@ -454,7 +454,7 @@ NOTE: By default, for 2d systems, granular particles are still modeled
 as 3d spheres, not 2d discs (circles), meaning their moment of inertia
 will be the same as in 3d.  If you wish to model granular particles in
 2d as 2d discs, see the note on this topic in "Section
-6.2"_Section_howto.html#howto_2, where 2d simulations are disussed.
+6.2"_Section_howto.html#howto_2, where 2d simulations are discussed.
 
 :line
 

doc/src/Section_intro.txt

@@ -507,11 +507,15 @@ we'll be pleased to add them to the
 "Movies"_http://lammps.sandia.gov/movies.html pages of the LAMMPS WWW
 site.
 
-The core group of LAMMPS developers is at Sandia National Labs:
+The primary LAMMPS developers are at Sandia National Labs and Temple University:
 
 Steve Plimpton, sjplimp at sandia.gov
 Aidan Thompson, athomps at sandia.gov
-Paul Crozier, pscrozi at sandia.gov :ul
+Stan Moore, stamoor at sandia.gov
+Axel Kohlmeyer, akohlmey at gmail.com :ul
+
+Past primary developers include Paul Crozier and Mark Stevens,
+both at Sandia, and Ray Shan, now at Materials Design.
 
 The following folks are responsible for significant contributions to
 the code, or other aspects of the LAMMPS development effort.  Many of
@@ -519,19 +523,20 @@ the packages they have written are somewhat unique to LAMMPS and the
 code would not be as general-purpose as it is without their expertise
 and efforts.
 
-Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK and USER-OMP packages
+Axel Kohlmeyer (Temple U), akohlmey at gmail.com, SVN and Git repositories, indefatigable mail list responder, USER-CGSDK, USER-OMP, USER-COLVARS, USER-MOLFILE, USER-QMMM, USER-TALLY, and COMPRESS packages
 Roy Pollock (LLNL), Ewald and PPPM solvers
-Mike Brown (ORNL), brownw at ornl.gov, GPU package
+Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL package
 Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
 Mike Parks (Sandia), mlparks at sandia.gov, PERI package for Peridynamics
 Rudra Mukherjee (JPL), Rudranarayan.M.Mukherjee at jpl.nasa.gov, POEMS package for articulated rigid body motion
 Reese Jones (Sandia) and collaborators, rjones at sandia.gov, USER-ATC package for atom/continuum coupling
 Ilya Valuev (JIHT), valuev at physik.hu-berlin.de, USER-AWPMD package for wave-packet MD
-Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA package
+Christian Trott (U Tech Ilmenau), christian.trott at tu-ilmenau.de, USER-CUDA and KOKKOS packages
 Andres Jaramillo-Botero (Caltech), ajaramil at wag.caltech.edu, USER-EFF package for electron force field
 Christoph Kloss (JKU), Christoph.Kloss at jku.at, USER-LIGGGHTS package for granular models and granular/fluid coupling
 Metin Aktulga (LBL), hmaktulga at lbl.gov, USER-REAXC package for C version of ReaxFF
-Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SPH package :ul
+Georg Gunzenmuller (EMI), georg.ganzenmueller at emi.fhg.de, USER-SMD and USER-SPH packages
+Colin Denniston (U Western Ontario), cdennist at uwo.ca, USER-LB package :ul
 
 As discussed in "Section 13"_Section_history.html, LAMMPS
 originated as a cooperative project between DOE labs and industrial

doc/src/Section_packages.txt

@@ -138,6 +138,7 @@ Package, Description, Doc page, Example, Library
 "USER-MESO"_#USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, -
 "USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, -
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
+"USER-MOFFF"_#USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, -
 "USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
 "USER-NETCDF"_#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
 "USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
@@ -243,7 +244,7 @@ COLLOID package :link(COLLOID),h4
 
 [Contents:]
 
-Coarse-grained finite-size colloidal particles.  Pair stayle and fix
+Coarse-grained finite-size colloidal particles.  Pair styles and fix
 wall styles for colloidal interactions.  Includes the Fast Lubrication
 Dynamics (FLD) method for hydrodynamic interactions, which is a
 simplified approximation to Stokesian dynamics.
@@ -732,9 +733,9 @@ make lib-latte args="-b -m gfortran"    # download and build in lib/latte and
 :pre
 
 Note that 3 symbolic (soft) links, "includelink" and "liblink" and
-"filelink", are created in lib/latte to point into the LATTE home dir.
+"filelink.o", are created in lib/latte to point into the LATTE home dir.
 When LAMMPS builds in src it will use these links.  You should 
-also check that the Makefile.lammps file you create is apporpriate
+also check that the Makefile.lammps file you create is appropriate
 for the compiler you use on your system to build LATTE.
 
 You can then install/un-install the package and build LAMMPS in the
@@ -984,7 +985,7 @@ MSCG package :link(mscg),h4
 [Contents:]
 
 A "fix mscg"_fix_mscg.html command which can parameterize a
-Mulit-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
+Multi-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
 library"_mscg_home.
 
 :link(mscg_home,https://github.com/uchicago-voth/MSCG-release)
@@ -1781,7 +1782,7 @@ coarse-grained DPD-based models for energetic, reactive molecular
 crystalline materials.  It includes many pair styles specific to these
 systems, including for reactive DPD, where each particle has internal
 state for multiple species and a coupled set of chemical reaction ODEs
-are integrated each timestep.  Highly accurate time intergrators for
+are integrated each timestep.  Highly accurate time integrators for
 isothermal, isoenergetic, isobaric and isenthalpic conditions are
 included.  These enable long timesteps via the Shardlow splitting
 algorithm.
@@ -2231,7 +2232,7 @@ Several extensions of the the dissipative particle dynamics (DPD)
 method.  Specifically, energy-conserving DPD (eDPD) that can model
 non-isothermal processes, many-body DPD (mDPD) for simulating
 vapor-liquid coexistence, and transport DPD (tDPD) for modeling
-advection-diffuion-reaction systems. The equations of motion of these
+advection-diffusion-reaction systems. The equations of motion of these
 DPD extensions are integrated through a modified velocity-Verlet (MVV)
 algorithm.
 
@@ -2259,6 +2260,44 @@ http://lammps.sandia.gov/movies.html#mesodpd :ul
 
 :line
 
+USER-MOFFF package :link(USER-MOFFF),h4
+
+[Contents:]
+
+Pair, angle and improper styles needed to employ the MOF-FF
+force field by Schmid and coworkers with LAMMPS. 
+MOF-FF is a first principles derived force field with the primary aim
+to simulate MOFs and related porous framework materials, using spherical 
+Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B
+2013, 250, 1128-1141.
+For the usage of MOF-FF see the example in the example directory as 
+well as the "MOF+"_MOFplus website.
+
+:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
+
+[Author:] Hendrik Heenen (Technical U of Munich), 
+Rochus Schmid (Ruhr-University Bochum).
+
+[Install or un-install:]
+
+make yes-user-mofff
+make machine :pre
+
+make no-user-mofff
+make machine :pre
+
+[Supporting info:]
+
+src/USER-MOFFF: filenames -> commands
+src/USER-MOFFF/README
+"pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html
+"angle_style class2"_angle_class2.html
+"angle_style cosine/buck6d"_angle_cosine_buck6d.html
+"improper_style inversion/harmonic"_improper_inversion_harmonic.html
+examples/USER/mofff :ul
+
+:line
+
 USER-MOLFILE package :link(USER-MOLFILE),h4
 
 [Contents:]
@@ -2495,7 +2534,7 @@ make machine :pre
 
 NOTE: The LAMMPS executable these steps produce is not yet functional
 for a QM/MM simulation.  You must also build Quantum ESPRESSO and
-create a new executable which links LAMMPS and Quanutm ESPRESSO
+create a new executable which links LAMMPS and Quantum ESPRESSO
 together.  These are steps 3 and 4 described in the lib/qmmm/README
 file.
 
@@ -2554,7 +2593,7 @@ developed by the Cambridge University group.
 
 :link(quip,https://github.com/libAtoms/QUIP)
 
-To use this package you must have the QUIP libAatoms library available
+To use this package you must have the QUIP libAtoms library available
 on your system.
 
 [Author:] Albert Bartok (Cambridge University)
@@ -2809,7 +2848,7 @@ USER-VTK package :link(USER-VTK),h4
 
 A "dump vtk"_dump_vtk.html command which outputs snapshot info in the
 "VTK format"_vtk, enabling visualization by "Paraview"_paraview or
-other visuzlization packages.
+other visualization packages.
 
 :link(vtk,http://www.vtk.org)
 :link(paraview,http://www.paraview.org)

doc/src/Section_python.txt

@@ -123,7 +123,7 @@ code directly from an input script:
 
 "python"_python.html
 "variable python"_variable.html
-"fix python"_fix_python.html
+"fix python/invoke"_fix_python_invoke.html
 "pair_style python"_pair_python.html :ul
 
 The "python"_python.html command which can be used to define and
@@ -165,7 +165,7 @@ doc page for its python-style variables for more info, including
 examples of Python code you can write for both pure Python operations
 and callbacks to LAMMPS.
 
-The "fix python"_fix_python.html command can execute
+The "fix python/invoke"_fix_python_invoke.html command can execute
 Python code at selected timesteps during a simulation run.
 
 The "pair_style python"_pair_python command allows you to define

doc/src/Section_start.txt

@@ -79,7 +79,7 @@ This section has the following sub-sections:
 
 Read this first :h5,link(start_2_1)
 
-If you want to avoid building LAMMPS yourself, read the preceeding
+If you want to avoid building LAMMPS yourself, read the preceding
 section about options available for downloading and installing
 executables.  Details are discussed on the "download"_download page.
 
@@ -252,14 +252,13 @@ re-compile, after typing "make clean" (which will describe different
 clean options).
 
 The LMP_INC variable is used to include options that turn on ifdefs
-within the LAMMPS code.  The options that are currently recogized are:
+within the LAMMPS code.  The options that are currently recognized are:
 
 -DLAMMPS_GZIP
 -DLAMMPS_JPEG
 -DLAMMPS_PNG
 -DLAMMPS_FFMPEG
 -DLAMMPS_MEMALIGN
--DLAMMPS_XDR
 -DLAMMPS_SMALLBIG
 -DLAMMPS_BIGBIG
 -DLAMMPS_SMALLSMALL
@@ -308,11 +307,6 @@ has to be aligned on larger than default byte boundaries (e.g. 16
 bytes instead of 8 bytes on x86 type platforms) for optimal
 performance.
 
-If you use -DLAMMPS_XDR, the build will include XDR compatibility
-files for doing particle dumps in XTC format.  This is only necessary
-if your platform does have its own XDR files available.  See the
-Restrictions section of the "dump"_dump.html command for details.
-
 Use at most one of the -DLAMMPS_SMALLBIG, -DLAMMPS_BIGBIG,
 -DLAMMPS_SMALLSMALL settings.  The default is -DLAMMPS_SMALLBIG. These
 settings refer to use of 4-byte (small) vs 8-byte (big) integers
@@ -363,7 +357,7 @@ installed on your platform.  If MPI is installed on your system in the
 usual place (under /usr/local), you also may not need to specify these
 3 variables, assuming /usr/local is in your path.  On some large
 parallel machines which use "modules" for their compile/link
-environements, you may simply need to include the correct module in
+environments, you may simply need to include the correct module in
 your build environment, before building LAMMPS.  Or the parallel
 machine may have a vendor-provided MPI which the compiler has no
 trouble finding.
@@ -431,7 +425,7 @@ use the KISS library described above.
 You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
 so the compiler and linker can find the needed FFT header and library
 files.  Note that on some large parallel machines which use "modules"
-for their compile/link environements, you may simply need to include
+for their compile/link environments, you may simply need to include
 the correct module in your build environment.  Or the parallel machine
 may have a vendor-provided FFT library which the compiler has no
 trouble finding.  See the src/MAKE/OPTIONS/Makefile.fftw file for an
@@ -470,7 +464,7 @@ precision.
 
 The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
 use single-precision FFTs with PPPM, which can speed-up long-range
-calulations, particularly in parallel or on GPUs.  Fourier transform
+calculations, particularly in parallel or on GPUs.  Fourier transform
 and related PPPM operations are somewhat insensitive to floating point
 truncation errors and thus do not always need to be performed in
 double precision.  Using the -DFFT_SINGLE setting trades off a little
@@ -483,7 +477,7 @@ with support for single-precision, as explained above.  For FFTW3 you
 also need to include -lfftw3f with the FFT_LIB setting, in addition to
 -lfftw3.  For FFTW2, you also need to specify -DFFT_SIZE with the
 FFT_INC setting and -lsfftw with the FFT_LIB setting (in place of
--lfftw).  Similarly, if FFTW2 has been preinstalled with an explicit
+-lfftw).  Similarly, if FFTW2 has been pre-installed with an explicit
 double-precision library (libdfftw.a and not the default libfftw.a),
 then you can specify -DFFT_SIZE (and not -DFFT_SINGLE), and specify
 -ldfftw to use double-precision FFTs.
@@ -714,7 +708,7 @@ list various make commands that can be used to manage packages.
 If you use a command in a LAMMPS input script that is part of a
 package, you must have built LAMMPS with that package, else you will
 get an error that the style is invalid or the command is unknown.
-Every command's doc page specfies if it is part of a package.  You can
+Every command's doc page specifies if it is part of a package.  You can
 type
 
 lmp_machine -h :pre
@@ -859,7 +853,7 @@ details for each package.
 [External libraries:]
 
 Packages in the tables "Section 4"_Section_packages.html with an "ext"
-in the last column link to exernal libraries whose source code is not
+in the last column link to external libraries whose source code is not
 included with LAMMPS.  You must first download and install the library
 before building LAMMPS with that package installed.  E.g. the voronoi
 package links to the freely available "Voro++ library"_voro_home2.  You
@@ -963,7 +957,7 @@ src/MAKE/Makefile.foo and perform the build in the directory
 Obj_shared_foo.  This is so that each file can be compiled with the
 -fPIC flag which is required for inclusion in a shared library.  The
 build will create the file liblammps_foo.so which another application
-can link to dyamically.  It will also create a soft link liblammps.so,
+can link to dynamically.  It will also create a soft link liblammps.so,
 which will point to the most recently built shared library.  This is
 the file the Python wrapper loads by default.
 
@@ -1329,8 +1323,8 @@ LAMMPS is compiled with CUDA=yes.
 numa Nm :pre
 
 This option is only relevant when using pthreads with hwloc support.
-In this case Nm defines the number of NUMA regions (typicaly sockets)
-on a node which will be utilizied by a single MPI rank.  By default Nm
+In this case Nm defines the number of NUMA regions (typically sockets)
+on a node which will be utilized by a single MPI rank.  By default Nm
 = 1.  If this option is used the total number of worker-threads per
 MPI rank is threads*numa.  Currently it is always almost better to
 assign at least one MPI rank per NUMA region, and leave numa set to
@@ -1394,7 +1388,7 @@ replica runs on on one or a few processors.  Note that with MPI
 installed on a machine (e.g. your desktop), you can run on more
 (virtual) processors than you have physical processors.
 
-To run multiple independent simulatoins from one input script, using
+To run multiple independent simulations from one input script, using
 multiple partitions, see "Section 6.4"_Section_howto.html#howto_4
 of the manual.  World- and universe-style "variables"_variable.html
 are useful in this context.
@@ -1673,7 +1667,7 @@ The first section provides a global loop timing summary. The {loop time}
 is the total wall time for the section.  The {Performance} line is
 provided for convenience to help predicting the number of loop
 continuations required and for comparing performance with other,
-similar MD codes.  The {CPU use} line provides the CPU utilzation per
+similar MD codes.  The {CPU use} line provides the CPU utilization per
 MPI task; it should be close to 100% times the number of OpenMP
 threads (or 1 of no OpenMP). Lower numbers correspond to delays due
 to file I/O or insufficient thread utilization.

doc/src/Section_tools.txt

@@ -48,6 +48,7 @@ own sub-directories with their own Makefiles and/or README files.
 "chain"_#chain
 "colvars"_#colvars
 "createatoms"_#createatoms
+"doxygen"_#doxygen
 "drude"_#drude
 "eam database"_#eamdb
 "eam generate"_#eamgn
@@ -110,14 +111,21 @@ back-and-forth between the CHARMM MD code and LAMMPS.
 They are intended to make it easy to use CHARMM as a builder and as a
 post-processor for LAMMPS. Using charmm2lammps.pl, you can convert a
 PDB file with associated CHARMM info, including CHARMM force field
-data, into its LAMMPS equivalent.  Using lammps2pdb.pl you can convert
-LAMMPS atom dumps into PDB files.
+data, into its LAMMPS equivalent. Support for the CMAP correction of
+CHARMM22 and later is available as an option. This tool can also add
+solvent water molecules and Na+ or Cl- ions to the system.
+Using lammps2pdb.pl you can convert LAMMPS atom dumps into PDB files.
 
 See the README file in the ch2lmp sub-directory for more information.
 
 These tools were created by Pieter in't Veld (pjintve at sandia.gov)
 and Paul Crozier (pscrozi at sandia.gov) at Sandia.
 
+CMAP support added and tested by Xiaohu Hu (hux2 at ornl.gov) and
+Robert A. Latour (latourr at clemson.edu), David Hyde-Volpe, and
+Tigran Abramyan, (Clemson University) and
+Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
+
 :line
 
 chain tool :h4,link(chain)
@@ -172,6 +180,18 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
 
 :line
 
+doxygen tool :h4,link(doxygen)
+
+The tools/doxygen directory contains a shell script called
+doxygen.sh which can generate a call graph and API lists using
+the "Doxygen software"_http://doxygen.org.
+
+See the included README file for details.
+
+The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
+
+:line
+
 drude tool :h4,link(drude)
 
 The tools/drude directory contains a Python script called

doc/src/USER/atc/man_add_molecule.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_add_molecule">fix_modify AtC add_molecule </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_add_molecule">fix_modify AtC add_molecule </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify_AtC add_molecule &lt;small|large&gt; &lt;TAG&gt; &lt;GROUP_NAME&gt; <br/>
 </p>
 <ul>
@@ -35,21 +33,21 @@ syntax</a></h2>
 <li>&lt;GROUP_NAME&gt; = name of group that tracking will be applied to <br/>
  </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> group WATERGROUP type 1 2 </code> <br/>
  <code> fix_modify AtC add_molecule small water WATERGROUP </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Associates a tag with all molecules corresponding to a specified group. <br/>
  </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>No defaults for this command. </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_add_species.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_add_species">fix_modify AtC add_species </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_add_species">fix_modify AtC add_species </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify_AtC add_species &lt;TAG&gt; &lt;group|type&gt; &lt;ID&gt; <br/>
 </p>
 <ul>
@@ -35,21 +33,21 @@ syntax</a></h2>
 <li>&lt;ID&gt; = name of group or type number <br/>
  </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC add_species gold type 1 </code> <br/>
  <code> group GOLDGROUP type 1 </code> <br/>
  <code> fix_modify AtC add_species gold group GOLDGROUP </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Associates a tag with all atoms of a specified type or within a specified group. <br/>
  </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>No defaults for this command. </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_atom_element_map.html

@@ -7,42 +7,40 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_atom_element_map">fix_modify AtC atom_element_map </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_atom_element_map">fix_modify AtC atom_element_map </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC atom_element_map &lt;eulerian|lagrangian&gt; &lt;frequency&gt; <br/>
 </p>
 <ul>
 <li>frequency (int) : frequency of updating atom-to-continuum maps based on the current configuration - only for eulerian </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc atom_element_map eulerian 100 </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Changes frame of reference from eulerian to lagrangian and sets the frequency for which the map from atoms to elements is reformed and all the attendant data is recalculated. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>Cannot change map type after initialization. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>lagrangian </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_atom_weight.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_atom_weight">fix_modify AtC atom_weight </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_atom_weight">fix_modify AtC atom_weight </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC atom_weight &lt;method&gt; &lt;arguments&gt;</p>
 <ul>
 <li>&lt;method&gt; = <br/>
@@ -36,22 +34,22 @@ syntax</a></h2>
  read_in: list of values for atoms are read-in from specified file <br/>
  </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc atom_weight constant myatoms 11.8 </code> <br/>
  <code> fix_modify atc atom_weight lattice </code> <br/>
  <code> fix_modify atc atom_weight read-in atm_wt_file.txt </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Command for assigning the value of atomic weights used for atomic integration in atom-continuum coupled simulations. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>Use of lattice option requires a lattice type and parameter is already specified. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>lattice </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_atomic_charge.html

@@ -7,41 +7,39 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_atomic_charge">fix_modify AtC atomic_charge </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_atomic_charge">fix_modify AtC atomic_charge </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC &lt;include | omit&gt; atomic_charge</p>
 <ul>
 <li>&lt;include | omit&gt; = switch to activiate/deactiviate inclusion of intrinsic atomic charge in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc compute include atomic_charge </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Determines whether AtC tracks the total charge as a finite element field </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>Required for: electrostatics </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>if the atom charge is defined, default is on, otherwise default is off </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_boundary.html

@@ -7,38 +7,36 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_boundary">fix_modify AtC boundary </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_boundary">fix_modify AtC boundary </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC boundary type &lt;atom-type-id&gt;</p>
 <ul>
 <li>&lt;atom-type-id&gt; = type id for atoms that represent a ficticious boundary internal to the FE mesh </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC boundary type ghost_atoms </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Command to define the atoms that represent the ficticious boundary internal to the FE mesh. For fully overlapped MD/FE domains with periodic boundary conditions no boundary atoms should be defined. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_boundary_dynamics.html

@@ -7,36 +7,34 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_boundary_dynamics">fix_modify AtC boundary_dynamics </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_boundary_dynamics">fix_modify AtC boundary_dynamics </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC boundary_dynamics &lt; on | damped_harmonic | prescribed | coupled | none &gt; [args] <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Sets different schemes for controlling boundary atoms. On will integrate the boundary atoms using the velocity-verlet algorithm. Damped harmonic uses a mass/spring/dashpot for the boundary atoms with added arguments of the damping and spring constants followed by the ratio of the boundary type mass to the desired mass. Prescribed forces the boundary atoms to follow the finite element displacement. Coupled does the same. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>Boundary atoms must be specified. When using swaps between internal and boundary atoms, the initial configuration must have already correctly partitioned the two. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>prescribed on </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_boundary_faceset.html

@@ -7,38 +7,36 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_boundary_faceset">fix_modify AtC boundary_faceset </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_boundary_faceset">fix_modify AtC boundary_faceset </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC boundary_faceset &lt;is | add&gt; [args] </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p>fix_modify AtC boundary_faceset is obndy </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>This command species the faceset name when using a faceset to compute the MD/FE boundary fluxes. The faceset must already exist. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>This is only valid when fe_md_boundary is set to faceset. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
 <a href="http://www.doxygen.org/index.html">

doc/src/USER/atc/man_boundary_integral.html

@@ -7,43 +7,41 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_boundary_integral">fix_modify AtC output boundary_integral </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_boundary_integral">fix_modify AtC output boundary_integral </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC output boundary_integral [field] faceset [name]</p>
 <ul>
 <li>field (string) : name of hardy field</li>
 <li>name (string) : name of faceset </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC output boundary_integral stress faceset loop1 </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_consistent_fe_initialization.html

@@ -7,41 +7,39 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_consistent_fe_initialization">fix_modify AtC consistent_fe_initialization </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_consistent_fe_initialization">fix_modify AtC consistent_fe_initialization </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC consistent_fe_initialization &lt;on | off&gt;</p>
 <ul>
 <li>&lt;on|off&gt; = switch to activiate/deactiviate the initial setting of FE intrinsic field to match the projected MD field </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc consistent_fe_initialization on </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Determines whether AtC initializes FE intrinsic fields (e.g., temperature) to match the projected MD values. This is particularly useful for fully overlapping simulations. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>Can be used with: thermal, two_temperature. Cannot be used with time filtering on. Does not include boundary nodes. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>Default is off </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_contour_integral.html

@@ -7,44 +7,42 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_contour_integral">fix_modify AtC output contour_integral </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_contour_integral">fix_modify AtC output contour_integral </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC output contour_integral [field] faceset [name] &lt;axis [x | y | z ]&gt;</p>
 <ul>
 <li>field (string) : name of hardy field</li>
 <li>name (string) : name of faceset</li>
 <li>axis (string) : x or y or z </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC output contour_integral stress faceset loop1 </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Calculates a surface integral of the given field dotted with the outward normal of the faces and puts output in the "GLOBALS" file </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_control.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_control">fix_modify AtC control </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_control">fix_modify AtC control </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC control &lt;physics_type&gt; &lt;solution_parameter&gt; </p>
 <p><br/>
 </p>
@@ -46,22 +44,22 @@ syntax</a></h2>
 <li>tolerance (float) = relative tolerance to which matrix equations will be solved<br/>
 </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC control thermal max_iterations 10 </code> <br/>
  <code> fix_modify AtC control momentum tolerance 1.e-5 </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Sets the numerical parameters for the matrix solvers used in the specified control algorithm. Many solution approaches require iterative solvers, and these methods enable users to provide the maximum number of iterations and the relative tolerance. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>only for be used with specific controllers : thermal, momentum <br/>
  They are ignored if a lumped solution is requested </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>max_iterations is the number of rows in the matrix<br/>
  tolerance is 1.e-10 </p>
 </div>

doc/src/USER/atc/man_control_momentum.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_control_momentum">fix_modify AtC control momentum </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_control_momentum">fix_modify AtC control momentum </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC control momentum none <br/>
 </p>
 <p>fix_modify AtC control momentum rescale &lt;frequency&gt;<br/>
@@ -44,21 +42,21 @@ syntax</a></h2>
 <li>face_set_id (string) = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation<br/>
  </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p>fix_modify AtC control momentum glc_velocity <br/>
  fix_modify AtC control momentum flux faceset bndy_faces <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>only to be used with specific transfers : elastic <br/>
  rescale not valid with time filtering activated </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_control_thermal.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_control_thermal">fix_modify AtC control thermal </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_control_thermal">fix_modify AtC control thermal </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC control thermal &lt;control_type&gt; &lt;optional_args&gt;</p>
 <ul>
 <li>control_type (string) = none | rescale | hoover | flux<br/>
@@ -46,25 +44,25 @@ syntax</a></h2>
 <li>face_set_id (string), optional = id of boundary face set, if not specified (or not possible when the atomic domain does not line up with mesh boundaries) defaults to an atomic-quadrature approximate evaulation, does not work with interpolate<br/>
  </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC control thermal none </code> <br/>
  <code> fix_modify AtC control thermal rescale 10 </code> <br/>
  <code> fix_modify AtC control thermal hoover </code> <br/>
  <code> fix_modify AtC control thermal flux </code> <br/>
  <code> fix_modify AtC control thermal flux faceset bndy_faces </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Sets the energy exchange mechansim from the finite elements to the atoms, managed through a control algorithm. Rescale computes a scale factor for each atom to match the finite element temperature. Hoover is a Gaussian least-constraint isokinetic thermostat enforces that the nodal restricted atomic temperature matches the finite element temperature. Flux is a similar mode, but rather adds energy to the atoms based on conservation of energy. Hoover and flux allows the prescription of sources or fixed temperatures on the atoms. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>only for be used with specific transfers : thermal (rescale, hoover, flux), two_temperature (flux) <br/>
  rescale not valid with time filtering activated </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none<br/>
  rescale frequency is 1<br/>
  flux boundary_integration_type is interpolate </p>

doc/src/USER/atc/man_control_thermal_correction_max_iterations.html

@@ -7,43 +7,41 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_control_thermal_correction_max_iterations">fix_modify AtC control thermal correction_max_iterations </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_control_thermal_correction_max_iterations">fix_modify AtC control thermal correction_max_iterations </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC control thermal correction_max_iterations &lt;max_iterations&gt;</p>
 <ul>
 <li>max_iterations (int) = maximum number of iterations that will be used by iterative matrix solvers<br/>
 </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC control thermal correction_max_iterations 10 </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Sets the maximum number of iterations to compute the 2nd order in time correction term for lambda with the fractional step method. The method uses the same tolerance as the controller's matrix solver. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>only for use with thermal physics using the fractional step method. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>correction_max_iterations is 20 </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_decomposition.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_decomposition">fix_modify AtC decomposition </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_decomposition">fix_modify AtC decomposition </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC decomposition &lt;type&gt;</p>
 <ul>
 <li>&lt;type&gt; = <br/>
@@ -32,20 +30,20 @@ syntax</a></h2>
  distributed_memory: only owned nodal information on processor <br/>
  </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc decomposition distributed_memory </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Command for assigning the distribution of work and memory for parallel runs. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>replicated_memory is appropriate for simulations were the number of nodes &lt;&lt; number of atoms </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>replicated_memory </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_electron_integration.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_electron_integration">fix_modify AtC extrinsic electron_integration </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_electron_integration">fix_modify AtC extrinsic electron_integration </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC extrinsic electron_integration &lt;integration_type&gt; &lt;num_subcyle_steps(optional)&gt; <br/>
 </p>
 <ul>
@@ -32,20 +30,20 @@ syntax</a></h2>
 </li>
 <li>num_subcycle_steps (int), optional = number of subcycle steps for the electron time integration</li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC extrinsic electron_integration implicit </code> <br/>
  <code> fix_modify AtC extrinsic electron_integration explicit 100 </code> <br/>
 </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Switches between integration scheme for the electron temperature. The number of subcyling steps used to integrate the electron temperature 1 LAMMPS timestep can be manually adjusted to capture fast electron dynamics.</p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>For use only with two_temperature type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <br/>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<p>For use only with two_temperature type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) <br/>
  </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>implicit<br/>
  subcycle_steps = 1 </p>
 </div>

doc/src/USER/atc/man_equilibrium_start.html

@@ -7,40 +7,38 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_equilibrium_start">fix_modify AtC equilibrium_start </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_equilibrium_start">fix_modify AtC equilibrium_start </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC equilibrium_start &lt;on|off&gt;</p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc equilibrium_start on </code> <br/>
 </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Starts filtered calculations assuming they start in equilibrium, i.e. perfect finite element force balance.</p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>only needed before filtering is begun</p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p>see <a class="el" href="man_time_filter.html">fix_modify AtC filter</a></p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>on </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_extrinsic_exchange.html

@@ -7,40 +7,38 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_extrinsic_exchange">fix_modify AtC extrinsic exchange </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_extrinsic_exchange">fix_modify AtC extrinsic exchange </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC extrinsic exchange &lt;on|off&gt;</p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC extrinsic exchange on </code> <br/>
 </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Switches energy exchange between the MD system and electron system on and off</p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>Only valid for use with two_temperature type of AtC fix.</p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<p>see <a class="el" href="man_fix_atc.html">fix atc command</a></p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<p>see <a class="el" href="../../fix_atc.html">fix atc command</a></p>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>on </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_fe_md_boundary.html

@@ -7,40 +7,38 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_fe_md_boundary">fix_modify AtC fe_md_boundary </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_fe_md_boundary">fix_modify AtC fe_md_boundary </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC fe_md_boundary &lt;faceset | interpolate | no_boundary&gt; [args] </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc fe_md_boundary interpolate </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Specifies different methods for computing fluxes between between the MD and FE integration regions. Faceset defines a faceset separating the MD and FE regions and uses finite element face quadrature to compute the flux. Interpolate uses a reconstruction scheme to approximate the flux, which is more robust but less accurate if the MD/FE boundary does correspond to a faceset. No boundary results in no fluxes between the systems being computed. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>If faceset is used, all the AtC non-boundary atoms must lie within and completely fill the domain enclosed by the faceset. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p>see  for how to specify the faceset name. </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>Interpolate. </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_fem_mesh.html

@@ -1,24 +1,45 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
 <title>ATC: fix_modify AtC fem create mesh</title>
-<link href="doxygen.css" rel="stylesheet" type="text/css">
-</head><body>
-<!-- Generated by Doxygen 1.3.9.1 -->
-<h1><a class="anchor" name="man_fem_mesh">fix_modify AtC fem create mesh</a></h1><h2><a class="anchor" name="syntax">
-syntax</a></h2>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<link href="doxygen.css" rel="stylesheet" type="text/css"/>
+</head>
+<body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
+<!-- Generated by Doxygen 1.6.1 -->
+<div class="contents">
+
+<h3><a class="anchor" id="man_fem_mesh">fix_modify AtC fem create mesh</a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 fix_modify AtC fem create mesh &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;<ul>
 <li>nx ny nz = number of elements in x, y, z</li><li>region-id = id of region that is to be meshed</li><li>f p p = perioidicity flags for x, y, z </li></ul>
-<h2><a class="anchor" name="examples">
-examples</a></h2>
-<code> fix_modify AtC fem create mesh 10 1 1 feRegion p p p </code> <h2><a class="anchor" name="description">
-description</a></h2>
-Creates a uniform mesh in a rectangular region <h2><a class="anchor" name="restrictions">
-restrictions</a></h2>
-creates only uniform rectangular grids in a rectangular region <h2><a class="anchor" name="related">
-related</a></h2>
-<h2><a class="anchor" name="default">
-default</a></h2>
-none <hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by&nbsp;
+<h4><a class="anchor" id="examples">
+examples</a></h4>
+<p><code> fix_modify AtC fem create mesh 10 1 1 feRegion p p p </code> <br/>
+</p>
+<h4><a class="anchor" id="description">
+description</a></h4>
+<p>Creates a uniform mesh in a rectangular region</p>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<p>creates only uniform rectangular grids in a rectangular region</p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
+none
+<hr size="1"><address style="align: right;"><small>Generated on Mon Aug 17 09:35:16 2009 for ATC by&nbsp;
 <a href="http://www.doxygen.org/index.html">
 <img src="doxygen.png" alt="doxygen" align="middle" border="0"></a> 1.3.9.1 </small></address>
 </body>

doc/src/USER/atc/man_filter_scale.html

@@ -7,45 +7,43 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_filter_scale">fix_modify AtC filter scale </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_filter_scale">fix_modify AtC filter scale </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC filter scale &lt;scale&gt; <br/>
 </p>
 <ul>
 <li>scale (real) = characteristic time scale of the filter <br/>
 </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC filter scale 10.0 </code> <br/>
 </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>only for be used with specific transfers: thermal, two_temperature</p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p><a class="el" href="man_time_filter.html">fix_modify AtC filter</a> <a class="el" href="man_filter_type.html">fix_modify AtC filter type</a></p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>0. </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_filter_type.html

@@ -7,41 +7,39 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_filter_type">fix_modify AtC filter type </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_filter_type">fix_modify AtC filter type </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC filter type &lt;exponential | step | no_filter&gt; <br/>
 </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC filter type exponential </code> <br/>
 </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Specifies the type of time filter used. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>only for be used with specific transfers: thermal, two_temperature</p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p><a class="el" href="man_time_filter.html">fix_modify AtC filter</a> <a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a></p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>No default. </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_fix_atc.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_fix_atc">fix atc command </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_fix_atc">fix atc command </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix &lt;fixID&gt; &lt;group&gt; atc &lt;type&gt; &lt;parameter_file&gt;</p>
 <ul>
 <li>fixID = name of fix</li>
@@ -38,15 +36,15 @@ syntax</a></h2>
 <li>parameter_file = name of the file with material parameters. <br/>
  note: Neither hardy nor field requires a parameter file </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix AtC internal atc thermal Ar_thermal.dat </code> <br/>
  <code> fix AtC internal atc two_temperature Ar_ttm.mat </code> <br/>
  <code> fix AtC internal atc hardy </code> <br/>
  <code> fix AtC internal atc field </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the /post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.</p>
 <p>The following coupling example is typical, but non-exhaustive:<br/>
 </p>
@@ -134,16 +132,16 @@ description</a></h2>
 </li>
 </ul>
 <p>Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes <em> The finite element method </em>, Dover 2003, for the basics of FE simulation.</p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.</p>
 <p>Currently,</p>
 <ul>
 <li>the coupling is restricted to thermal physics</li>
 <li>the FE computations are done in serial on each processor.</li>
 </ul>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p>fix_modify commands for setup: <br/>
 </p>
 <ul>
@@ -243,8 +241,8 @@ related</a></h2>
 <li><a class="el" href="man_remove_molecule.html">fix_modify AtC remove_molecule</a></li>
 </ul>
 <p>Note: a set of example input files with the attendant material files are included with this package </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_fix_flux.html

@@ -7,44 +7,42 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_fix_flux">fix_modify AtC fix_flux </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_fix_flux">fix_modify AtC fix_flux </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC fix_flux &lt;field&gt; &lt;face_set&gt; &lt;value | function&gt;</p>
 <ul>
 <li>&lt;field&gt; = field name valid for type of physics, temperature | electron_temperature</li>
 <li>&lt;face_set&gt; = name of set of element faces </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc fix_flux temperature faceSet 10.0 </code> <br/>
 </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Command for fixing normal fluxes e.g. heat_flux. This command only prescribes the normal component of the physical flux, e.g. heat (energy) flux. The units are in AtC units, i.e. derived from the LAMMPS length, time, and mass scales. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>Only normal fluxes (Neumann data) can be prescribed. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p>see <a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
 <a href="http://www.doxygen.org/index.html">

doc/src/USER/atc/man_fix_nodes.html

@@ -7,46 +7,44 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_fix_nodes">fix_modify AtC fix </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_fix_nodes">fix_modify AtC fix </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC fix &lt;field&gt; &lt;nodeset&gt; &lt;constant | function&gt;</p>
 <ul>
 <li>&lt;field&gt; = field name valid for type of physics</li>
 <li>&lt;nodeset&gt; = name of set of nodes to apply boundary condition</li>
 <li>&lt;constant | function&gt; = value or name of function followed by its parameters </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC fix temperature groupNAME 10. </code> <br/>
  <code> fix_modify AtC fix temperature groupNAME 0 0 0 10.0 0 0 1.0 </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Creates a constraint on the values of the specified field at specified nodes. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>keyword 'all' reserved in nodeset name </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p>see <a class="el" href="man_unfix_nodes.html">fix_modify AtC unfix</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_hardy_computes.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_hardy_computes">fix_modify AtC computes </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_hardy_computes">fix_modify AtC computes </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC computes &lt;add | delete&gt; [per-atom compute id] &lt;volume | number&gt; <br/>
 </p>
 <ul>
@@ -35,8 +33,8 @@ syntax</a></h2>
 <li>volume | number (keyword) = field created is a per-unit-volume quantity or a per-atom quantity as weighted by kernel functions <br/>
 </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> compute virial all stress/atom </code> <br/>
  <code> fix_modify AtC computes add virial volume </code> <br/>
  <code> fix_modify AtC computes delete virial </code> <br/>
@@ -44,20 +42,20 @@ examples</a></h2>
  <code> compute centrosymmetry all centro/atom </code> <br/>
  <code> fix_modify AtC computes add centrosymmetry number </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Calculates continuum fields corresponding to specified per-atom computes created by LAMMPS <br/>
  </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) <br/>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) <br/>
  Per-atom compute must be specified before corresponding continuum field can be requested <br/>
  </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p>See manual page for compute </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>No defaults exist for this command </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_hardy_fields.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_hardy_fields">fix_modify AtC fields </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_hardy_fields">fix_modify AtC fields </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC fields &lt;all | none&gt; <br/>
  fix_modify AtC fields &lt;add | delete&gt; &lt;list_of_fields&gt; <br/>
 </p>
@@ -56,24 +54,24 @@ syntax</a></h2>
  type_concentration: volume fraction of a specific atom type <br/>
  </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC fields add velocity temperature </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Allows modification of the fields calculated and output by the transfer class. The commands are cumulative, e.g.<br/>
  <code> fix_modify AtC fields none </code> <br/>
  followed by <br/>
  <code> fix_modify AtC fields add velocity temperature </code> <br/>
  will only output the velocity and temperature fields. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>Must be used with the hardy/field type of AtC fix, see <a class="el" href="man_fix_atc.html">fix atc command</a>. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<p>Must be used with the hardy/field type of AtC fix, see <a class="el" href="../../fix_atc.html">fix atc command</a>. Currently, the stress and heat flux formulas are only correct for central force potentials, e.g. Lennard-Jones and EAM but not Stillinger-Weber. </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p>See <a class="el" href="man_hardy_gradients.html">fix_modify AtC gradients</a> , <a class="el" href="man_hardy_rates.html">fix_modify AtC rates</a> and <a class="el" href="man_hardy_computes.html">fix_modify AtC computes</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>By default, no fields are output </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_hardy_gradients.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_hardy_gradients">fix_modify AtC gradients </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_hardy_gradients">fix_modify AtC gradients </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC gradients &lt;add | delete&gt; &lt;list_of_fields&gt; <br/>
 </p>
 <ul>
@@ -33,21 +31,21 @@ syntax</a></h2>
 <li>fields (keyword) = <br/>
  gradients can be calculated for all fields listed in <a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC gradients add temperature velocity stress </code> <br/>
  <code> fix_modify AtC gradients delete velocity </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Requests calculation and ouput of gradients of the fields from the transfer class. These gradients will be with regard to spatial or material coordinate for eulerian or lagrangian analysis, respectively, as specified by atom_element_map (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ) </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>No gradients are calculated by default </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_hardy_kernel.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_hardy_kernel">fix_modify AtC kernel </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_hardy_kernel">fix_modify AtC kernel </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC kernel &lt;type&gt; &lt;parameters&gt;</p>
 <ul>
 <li>type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere <br/>
@@ -40,22 +38,22 @@ syntax</a></h2>
  quartic_sphere = radius (double) <br/>
  </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC kernel cell 1.0 1.0 1.0 </code> <br/>
  <code> fix_modify AtC kernel quartic_sphere 10.0 </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>Must be used with the hardy AtC fix <br/>
  For bar kernel types, half-width oriented along x-direction <br/>
  For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/>
- ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+ ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>No default </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_hardy_on_the_fly.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_hardy_on_the_fly">fix_modify AtC on_the_fly </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_hardy_on_the_fly">fix_modify AtC on_the_fly </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC on_the_fly &lt;bond | kernel&gt; &lt;optional on | off&gt; <br/>
  - bond | kernel (keyword) = specifies on-the-fly calculation of bond or kernel matrix elements <br/>
 </p>
@@ -32,24 +30,24 @@ syntax</a></h2>
 <li>on | off (keyword) = activate or discontinue on-the-fly mode <br/>
  </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC on_the_fly bond on </code> <br/>
  <code> fix_modify AtC on_the_fly kernel </code> <br/>
  <code> fix_modify AtC on_the_fly kernel off </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Overrides normal mode of pre-calculating and storing bond pair-to-node a nd kernel atom-to-node matrices. If activated, will calculate elements of t hese matrices during repeated calls of field computations (i.e. "on-the-fly") and not store them for future use. <br/>
  on flag is optional - if omitted, on_the_fly will be activated for the s pecified matrix. Can be deactivated using off flag. <br/>
  </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>By default, on-the-fly calculation is not active (i.e. off). However, code does a memory allocation check to determine if it can store all needed bond and kernel matrix ele ments. If this allocation fails, on-the-fly is activated. <br/>
  </p>
 </div>

doc/src/USER/atc/man_hardy_rates.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_hardy_rates">fix_modify AtC rates </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_hardy_rates">fix_modify AtC rates </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC rates &lt;add | delete&gt; &lt;list_of_fields&gt; <br/>
 </p>
 <ul>
@@ -33,22 +31,22 @@ syntax</a></h2>
 <li>fields (keyword) = <br/>
  rates can be calculated for all fields listed in <a class="el" href="man_hardy_fields.html">fix_modify AtC fields</a></li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC rates add temperature velocity stress </code> <br/>
  <code> fix_modify AtC rates delete stress </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Requests calculation and ouput of rates (time derivatives) of the fields from the transfer class. For eulerian analysis (see <a class="el" href="man_atom_element_map.html">fix_modify AtC atom_element_map</a> ), these rates are the partial time derivatives of the nodal fields, not the full (material) time derivatives. <br/>
  </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>No rates are calculated by default </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_initial.html

@@ -7,41 +7,39 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_initial">fix_modify AtC initial </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_initial">fix_modify AtC initial </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC initial &lt;field&gt; &lt;nodeset&gt; &lt;constant | function&gt;</p>
 <ul>
 <li>&lt;field&gt; = field name valid for type of physics, temperature | electron_temperature</li>
 <li>&lt;nodeset&gt; = name of set of nodes to apply initial condition</li>
 <li>&lt;constant | function&gt; = value or name of function followed by its parameters </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc initial temperature groupNAME 10. </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Sets the initial values for the specified field at the specified nodes. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>keyword 'all' reserved in nodeset name </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_internal_atom_integrate.html

@@ -7,30 +7,28 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_internal_atom_integrate">fix_modify AtC internal_atom_integrate </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_internal_atom_integrate">fix_modify AtC internal_atom_integrate </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC internal_atom_integrate &lt;on | off&gt; <code> fix_modify AtC internal_atom_integrate on </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Has AtC perform time integration for the atoms in the group on which it operates. This does not include boundary atoms. </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>on for coupling methods, off for post-processors off </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_internal_element_set.html

@@ -7,42 +7,40 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_internal_element_set">fix_modify AtC internal_element_set </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_internal_element_set">fix_modify AtC internal_element_set </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC internal_element_set &lt;element-set-name&gt;</p>
 <ul>
 <li>&lt;element-set-name&gt; = name of element set defining internal region, or off </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC internal_element_set myElementSet </code> <code> fix_modify AtC internal_element_set off </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Enables AtC to base the region for internal atoms to be an element set. If no ghost atoms are used, all the AtC atoms must be constrained to remain in this element set by the user, e.g., with walls. If boundary atoms are used in conjunction with Eulerian atom maps AtC will partition all atoms of a boundary or internal type to be of type internal if they are in the internal region or to be of type boundary otherwise. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>If boundary atoms are used in conjunction with Eulerian atom maps, the Eulerian reset frequency must be an integer multiple of the Lammps reneighbor frequency </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p>see atom_element_map_type and boundary </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>off </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_internal_quadrature.html

@@ -7,40 +7,38 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_internal_quadrature">fix_modify AtC internal_quadrature </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_internal_quadrature">fix_modify AtC internal_quadrature </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify atc internal_quadrature &lt;on | off&gt; [region] </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc internal_quadrature off </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Command to use or not use atomic quadrature on internal elements fully filled with atoms. By turning the internal quadrature off these elements do not contribute to the governing PDE and the fields at the internal nodes follow the weighted averages of the atomic data. </p>
-<h2><a class="anchor" id="optional">
-optional</a></h2>
+<h4><a class="anchor" id="optional">
+optional</a></h4>
 <p>Optional region tag specifies which finite element nodes will be treated as being within the MD region. This option is only valid with internal_quadrature off. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>on </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_kernel_function.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_kernel_function">fix_modify AtC kernel </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_kernel_function">fix_modify AtC kernel </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC kernel &lt;type&gt; &lt;parameters&gt;</p>
 <ul>
 <li>type (keyword) = step, cell, cubic_bar, cubic_cylinder, cubic_sphere, quartic_bar, quartic_cylinder, quartic_sphere <br/>
@@ -40,21 +38,21 @@ syntax</a></h2>
  quartic_sphere = radius (double) <br/>
  </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p>fix_modify AtC kernel cell 1.0 1.0 1.0 fix_modify AtC kernel quartic_sphere 10.0 </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>Must be used with the hardy AtC fix <br/>
  For bar kernel types, half-width oriented along x-direction <br/>
  For cylinder kernel types, cylindrical axis is assumed to be in z-direction <br/>
- ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+ ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>No default </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_localized_lambda.html

@@ -7,38 +7,36 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_localized_lambda">fix_modify AtC control localized_lambda </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_localized_lambda">fix_modify AtC control localized_lambda </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC control localized_lambda &lt;on|off&gt; </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc control localized_lambda on </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Turns on localization algorithms for control algorithms to restrict the influence of FE coupling or boundary conditions to a region near the boundary of the MD region. Control algorithms will not affect atoms in elements not possessing faces on the boundary of the region. Flux-based control is localized via row-sum lumping while quantity control is done by solving a truncated matrix equation. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>Default is off. </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_lumped_lambda_solve.html

@@ -7,38 +7,36 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_lumped_lambda_solve">fix_modify AtC control lumped_lambda_solve </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_lumped_lambda_solve">fix_modify AtC control lumped_lambda_solve </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC control lumped_lambda_solve &lt;on|off&gt; </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc control lumped_lambda_solve on </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Command to use or not use lumped matrix for lambda solve </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
 <a href="http://www.doxygen.org/index.html">

doc/src/USER/atc/man_mask_direction.html

@@ -7,38 +7,36 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_mask_direction">fix_modify AtC control mask_direction </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mask_direction">fix_modify AtC control mask_direction </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC control mask_direction &lt;direction&gt; &lt;on|off&gt; </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc control mask_direction 0 on </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Command to mask out certain dimensions from the atomic regulator </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
 <a href="http://www.doxygen.org/index.html">

doc/src/USER/atc/man_mass_matrix.html

@@ -7,41 +7,39 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_mass_matrix">fix_modify AtC mass_matrix </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mass_matrix">fix_modify AtC mass_matrix </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC mass_matrix &lt;fe | md_fe&gt;</p>
 <ul>
 <li>&lt;fe | md_fe&gt; = activiate/deactiviate using the FE mass matrix in the MD region </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc mass_matrix fe </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Determines whether AtC uses the FE mass matrix based on Gaussian quadrature or based on atomic quadrature in the MD region. This is useful for fully overlapping simulations to improve efficiency. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>Should not be used unless the FE region is contained within the MD region, otherwise the method will be unstable and inaccurate </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>Default is off </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_material.html

@@ -7,39 +7,37 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_material">fix_modify AtC material </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_material">fix_modify AtC material </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC material [elementset_name] [material_id] <br/>
  </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC material gap_region 2</code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Sets the material model in elementset_name to be of type material_id. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>The element set must already be created and the material must be specified in the material file given the the atc fix on construction </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>All elements default to the first material in the material file. </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_mesh_add_to_nodeset.html

@@ -7,41 +7,39 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_mesh_add_to_nodeset">fix_modify AtC mesh add_to_nodeset </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_add_to_nodeset">fix_modify AtC mesh add_to_nodeset </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC mesh add_to_nodeset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p>
 <ul>
 <li>&lt;id&gt; = id of FE nodeset to be added to</li>
 <li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains the desired nodes to be added </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC mesh add_to_nodeset lbc -11.9 -11 -12 12 -12 12 </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Command to add nodes to an already existing FE nodeset. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>Coordinates are assumed to be in lattice units. </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_mesh_create.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_mesh_create">fix_modify AtC mesh create </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_create">fix_modify AtC mesh create </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC mesh create &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt; <br/>
 </p>
 <ul>
@@ -32,21 +30,21 @@ syntax</a></h2>
 <li>region-id = id of region that is to be meshed</li>
 <li>f p p = periodicity flags for x, y, z </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC mesh create 10 1 1 feRegion p p p </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Creates a uniform mesh in a rectangular region </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>Creates only uniform rectangular grids in a rectangular region </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p><a class="el" href="man_mesh_quadrature.html">fix_modify AtC mesh quadrature</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>When created, mesh defaults to gauss2 (2-point Gaussian) quadrature. Use "mesh quadrature" command to change quadrature style. </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_mesh_create_elementset.html

@@ -7,42 +7,40 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_mesh_create_elementset">fix_modify AtC mesh create_elementset </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_create_elementset">fix_modify AtC mesh create_elementset </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC create_elementset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p>
 <ul>
 <li>&lt;id&gt; = id to assign to the collection of FE element</li>
 <li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains only the desired elements </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC mesh create_elementset middle -4.1 4.1 -100 100 -100 1100 </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Command to assign an id to a set of FE elements to be used subsequently in defining material and mesh-based operations. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>Only viable for rectangular grids. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>Coordinates are assumed to be in lattice units. </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_mesh_create_faceset_box.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_mesh_create_faceset_box">fix_modify AtC mesh create_faceset box </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_create_faceset_box">fix_modify AtC mesh create_faceset box </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC mesh create_faceset &lt;id&gt; box &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; &lt;in|out&gt; [units]</p>
 <ul>
 <li>&lt;id&gt; = id to assign to the collection of FE faces</li>
@@ -32,19 +30,19 @@ syntax</a></h2>
 <li>&lt;in|out&gt; = "in" gives inner faces to the box, "out" gives the outer faces to the box</li>
 <li>units = option to specify real as opposed to lattice units </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC mesh create_faceset obndy box -4.0 4.0 -12 12 -12 12 out </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Command to assign an id to a set of FE faces. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>Only viable for rectangular grids. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>The default options are units = lattice and the use of outer faces </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_mesh_create_faceset_plane.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_mesh_create_faceset_plane">fix_modify AtC mesh create_faceset plane </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_create_faceset_plane">fix_modify AtC mesh create_faceset plane </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC mesh create_faceset &lt;id&gt; plane &lt;x|y|z&gt; &lt;val1&gt; &lt;x|y|z&gt; &lt;lval2&gt; &lt;uval2&gt; [units]</p>
 <ul>
 <li>&lt;id&gt; = id to assign to the collection of FE faces</li>
@@ -32,19 +30,19 @@ syntax</a></h2>
 <li>&lt;val1&gt;,&lt;lval2&gt;,&lt;uval2&gt; = plane is specified as the x|y|z=val1 plane bounded by the segments x|y|z = [lval2,uval2]</li>
 <li>units = option to specify real as opposed to lattice units </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC mesh create_faceset xyplane plane y 0 x -4 0 </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Command to assign an id to a set of FE faces. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>Only viable for rectangular grids. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>The default option is units = lattice. </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_mesh_create_nodeset.html

@@ -7,41 +7,39 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_mesh_create_nodeset">fix_modify AtC mesh create_nodeset </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_create_nodeset">fix_modify AtC mesh create_nodeset </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC mesh create_nodeset &lt;id&gt; &lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt;</p>
 <ul>
 <li>&lt;id&gt; = id to assign to the collection of FE nodes</li>
 <li>&lt;xmin&gt; &lt;xmax&gt; &lt;ymin&gt; &lt;ymax&gt; &lt;zmin&gt; &lt;zmax&gt; = coordinates of the bounding box that contains only the desired nodes </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -12 12 -12 12 </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Command to assign an id to a set of FE nodes to be used subsequently in defining boundary conditions. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>Coordinates are assumed to be in lattice units. </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_mesh_delete_elements.html

@@ -7,40 +7,38 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_mesh_delete_elements">fix_modify AtC mesh delete_elements </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_delete_elements">fix_modify AtC mesh delete_elements </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC mesh delete_elements &lt;element_set&gt;</p>
 <ul>
 <li>&lt;element_set&gt; = name of an element set </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC delete_elements gap </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Deletes a group of elements from the mesh. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_mesh_nodeset_to_elementset.html

@@ -7,43 +7,41 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_mesh_nodeset_to_elementset">fix_modify AtC mesh nodeset_to_elementset </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_nodeset_to_elementset">fix_modify AtC mesh nodeset_to_elementset </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC nodeset_to_elementset &lt;nodeset_id&gt; &lt;elementset_id&gt; &lt;max/min&gt;</p>
 <ul>
 <li>&lt;nodeset_id&gt; = id of desired nodeset from which to create elementset</li>
 <li>&lt;elementset_id&gt; = id to assign to the collection of FE element</li>
 <li>&lt;max/min&gt; = flag to choose either the maximal or minimal elementset </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC mesh nodeset_to_elementset myNodeset myElementset min </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Command to create an elementset from an existing nodeset. Either the minimal element set of elements with all nodes in the set, or maximal element set with all elements with at least one node in the set, can be created </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>None. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>Unless specified, the maximal element set is created </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_mesh_output.html

@@ -7,39 +7,37 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_mesh_output">fix_modify AtC mesh output </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_output">fix_modify AtC mesh output </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC mesh output &lt;file_prefix&gt; </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC mesh output meshData </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Command to output mesh and associated data: nodesets, facesets, and elementsets. This data is only output once upon initialization since currently the mesh is static. Creates (binary, "gold" format) Ensight output of mesh data. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>none </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_mesh_quadrature.html

@@ -7,41 +7,39 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_mesh_quadrature">fix_modify AtC mesh quadrature </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_quadrature">fix_modify AtC mesh quadrature </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC mesh quadrature &lt;quad&gt;</p>
 <ul>
 <li>quad = one of &lt;nodal|gauss1|gauss2|gauss3|face&gt; --- when a mesh is created it defaults to gauss2, use this call to change it after the fact </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC mesh quadrature face </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>(Re-)assigns the quadrature style for the existing mesh. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p><a class="el" href="man_mesh_create.html">fix_modify AtC mesh create</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_mesh_read.html

@@ -7,42 +7,40 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_mesh_read">fix_modify AtC mesh read </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_read">fix_modify AtC mesh read </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC mesh read &lt;filename&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;</p>
 <ul>
 <li>filename = name of file containing mesh to be read</li>
 <li>f p p = periodicity flags for x, y, z </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC mesh read myComponent.mesh p p p </code> <br/>
  <code> fix_modify AtC mesh read myOtherComponent.exo </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Reads a mesh from a text or exodus file, and assigns periodic boundary conditions if needed. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>periodicity flags are false by default </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_mesh_write.html

@@ -7,41 +7,39 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_mesh_write">fix_modify AtC mesh write </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_mesh_write">fix_modify AtC mesh write </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC mesh write &lt;filename&gt;</p>
 <ul>
 <li>filename = name of file to write mesh </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC mesh write myMesh.mesh </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Writes a mesh to a text file. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
 <a href="http://www.doxygen.org/index.html">

doc/src/USER/atc/man_momentum_time_integration.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_momentum_time_integration">fix_modify AtC time_integration (momentum) </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_momentum_time_integration">fix_modify AtC time_integration (momentum) </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC time_integration &lt;descriptor&gt; <br/>
 </p>
 <ul>
@@ -33,24 +31,24 @@ syntax</a></h2>
 </ul>
 <p>various time integration methods for the finite elements<br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>verlet - atomic velocity update with 2nd order Verlet, nodal temperature update with 2nd order Verlet, kinetostats based on controlling force <br/>
  fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal momentum update, 2nd order Verlet for continuum and exact 2nd order Verlet for atomic contributions, kinetostats based on controlling discrete momentum changes<br/>
  gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, kinetostats based on controlling power <br/>
  </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc time_integration verlet </code> <br/>
  <code> fix_modify atc time_integration fractional_step </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_output.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_output">fix_modify AtC output </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_output">fix_modify AtC output </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC output &lt;filename_prefix&gt; &lt;frequency&gt; [text | full_text | binary | vector_components | tensor_components ] fix_modify AtC output index [step | time ]</p>
 <ul>
 <li>filename_prefix (string) = prefix for data files</li>
@@ -37,23 +35,23 @@ syntax</a></h2>
  tensor_components = outputs tensor as scalar components (use this for Paraview)<br/>
 </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC output heatFE 100 </code> <br/>
  <code> fix_modify AtC output hardyFE 1 text tensor_components </code> <br/>
  <code> fix_modify AtC output hardyFE 10 text binary tensor_components </code> <br/>
  <code> fix_modify AtC output index step </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Creates text and/or binary (Ensight, "gold" format) output of nodal/mesh data which is transfer/physics specific. Output indexed by step or time is possible. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>no default format output indexed by time </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_output_elementset.html

@@ -7,44 +7,42 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_output_elementset">fix_modify AtC output elementset </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_output_elementset">fix_modify AtC output elementset </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC output volume_integral &lt;eset_name&gt; &lt;field&gt; {`</p>
 <ul>
 <li>set_name (string) = name of elementset to be integrated over</li>
 <li>fieldname (string) = name of field to integrate csum = creates nodal sum over nodes in specified nodeset <br/>
  </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC output eset1 mass_density </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Performs volume integration of specified field over elementset and outputs resulting variable values to GLOBALS file. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_output_nodeset.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_output_nodeset">fix_modify AtC output nodeset </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_output_nodeset">fix_modify AtC output nodeset </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC output nodeset &lt;nodeset_name&gt; &lt;operation&gt;</p>
 <ul>
 <li>nodeset_name (string) = name of nodeset to be operated on</li>
@@ -32,20 +30,20 @@ syntax</a></h2>
  sum = creates nodal sum over nodes in specified nodeset <br/>
  </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC output nodeset nset1 sum </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Performs operation over the nodes belonging to specified nodeset and outputs resulting variable values to GLOBALS file. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_pair_interactions.html

@@ -7,40 +7,38 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_pair_interactions">fix_modify AtC pair_interactions/bond_interactions </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_pair_interactions">fix_modify AtC pair_interactions/bond_interactions </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC pair_interactions &lt;on|off&gt; <br/>
  fix_modify AtC bond_interactions &lt;on|off&gt; <br/>
 </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC bond_interactions on </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>include bonds and/or pairs in the stress and heat flux computations </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>pair interactions: on, bond interactions: off </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_poisson_solver.html

@@ -7,43 +7,41 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_poisson_solver">fix_modify AtC poisson_solver </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_poisson_solver">fix_modify AtC poisson_solver </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC poisson_solver mesh create &lt;nx&gt; &lt;ny&gt; &lt;nz&gt; &lt;region-id&gt; &lt;f|p&gt; &lt;f|p&gt; &lt;f|p&gt;</p>
 <ul>
 <li>nx ny nz = number of elements in x, y, z</li>
 <li>region-id = id of region that is to be meshed</li>
 <li>f p p = perioidicity flags for x, y, z </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC poisson_solver mesh create 10 1 1 feRegion p p p </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Creates a uniform mesh in a rectangular region </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>creates only uniform rectangular grids in a rectangular region </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_read_restart.html

@@ -7,41 +7,39 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_read_restart">fix_modify AtC read_restart </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_read_restart">fix_modify AtC read_restart </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC read_restart [file_name] <br/>
  </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC read_restart ATC_state </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Reads the current state of the fields from a named text-based restart file. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p>see write_restart <a class="el" href="man_write_restart.html">fix_modify AtC write_restart</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_remove_molecule.html

@@ -7,44 +7,42 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_remove_molecule">fix_modify AtC remove_molecule </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_remove_molecule">fix_modify AtC remove_molecule </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify_AtC remove_molecule &lt;TAG&gt; <br/>
 </p>
 <ul>
 <li>&lt;TAG&gt; = tag for tracking a molecule type <br/>
  </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC remove_molecule water </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Removes tag designated for tracking a specified set of molecules. <br/>
  </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>No defaults for this command. </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_remove_source.html

@@ -7,43 +7,41 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_remove_source">fix_modify AtC remove_source </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_remove_source">fix_modify AtC remove_source </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC remove_source &lt;field&gt; &lt;element_set&gt;</p>
 <ul>
 <li>&lt;field&gt; = field name valid for type of physics</li>
 <li>&lt;element_set&gt; = name of set of elements </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc remove_source temperature groupNAME </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Remove a domain source. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>keyword 'all' reserved in element_set name </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p>see <a class="el" href="man_source.html">fix_modify AtC source</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
 <a href="http://www.doxygen.org/index.html">

doc/src/USER/atc/man_remove_species.html

@@ -7,44 +7,42 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_remove_species">fix_modify AtC remove_species </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_remove_species">fix_modify AtC remove_species </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify_AtC delete_species &lt;TAG&gt; <br/>
 </p>
 <ul>
 <li>&lt;TAG&gt; = tag for tracking a species <br/>
  </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC remove_species gold </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Removes tag designated for tracking a specified species. <br/>
  </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>No defaults for this command. </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_reset_atomic_reference_positions.html

@@ -7,39 +7,37 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_reset_atomic_reference_positions">fix_modify AtC reset_atomic_reference_positions </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_reset_atomic_reference_positions">fix_modify AtC reset_atomic_reference_positions </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC reset_atomic_reference_positions </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc reset_atomic_reference_positions </code></p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p><code> Resets the atomic positions <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> uses to perform point to field operations. In can be used to use perfect lattice sites in <a class="el" href="namespaceATC.html" title="owned field/s: MASS_DENSITY">ATC</a> but a thermalized or deformed lattice in LAMMPS. </code></p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p><code> </code></p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p><code> </code></p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p><code> Default is off </code></p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_reset_time.html

@@ -7,55 +7,53 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_reset_time">fix_modify AtC reset_time </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_reset_time">fix_modify AtC reset_time </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC reset_time </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc reset_time 0.0 </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Resets the simulation time counter. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
-<h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
+<h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC kernel_bandwidth </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc reset_time 8 </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Sets a maximum parallel bandwidth for the kernel functions during parallel communication. If the command is not issued, the default will be to assume the bandwidth of the kernel matrix corresponds to the number of sampling locations. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>Only is used if kernel functions are being used. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>Number of sample locations. </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_sample_frequency.html

@@ -7,42 +7,40 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_sample_frequency">fix_modify AtC sample_frequency </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_sample_frequency">fix_modify AtC sample_frequency </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC sample_frequency [freq]</p>
 <ul>
 <li>freq (int) : frequency to sample field in number of steps </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC sample_frequency 10 </code></p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p><code> Specifies a frequency at which fields are computed for the case where time filters are being applied. </code></p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p><code> Must be used with the hardy/field AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) and is only relevant when time filters are being used. </code></p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<p><code> Must be used with the hardy/field AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) and is only relevant when time filters are being used. </code></p>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p><code> </code></p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p><code> none </code></p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_set.html

@@ -7,46 +7,44 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_set">fix_modify AtC set </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_set">fix_modify AtC set </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC set reference_potential_energy &lt;value_or_filename(optional)&gt;</p>
 <ul>
 <li>value (double) : optional user specified zero point for PE in native LAMMPS energy units <br/>
 </li>
 <li>filename (string) : optional user specified string for file of nodal PE values to be read-in </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC set reference_potential_energy </code> <br/>
  <code> fix_modify AtC set reference_potential_energy -0.05 </code> <br/>
  <code> fix_modify AtC set reference_potential_energy myPEvalues </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Used to set various quantities for the post-processing algorithms. It sets the zero point for the potential energy density using the value provided for all nodes, or from the current configuration of the lattice if no value is provided, or values provided within the specified filename. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="man_fix_atc.html">fix atc command</a> ) </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<p>Must be used with the hardy/field type of AtC fix ( see <a class="el" href="../../fix_atc.html">fix atc command</a> ) </p>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>Defaults to lammps zero point i.e. isolated atoms </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_source.html

@@ -7,43 +7,41 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_source">fix_modify AtC source </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_source">fix_modify AtC source </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC source &lt;field&gt; &lt;element_set&gt; &lt;value | function&gt;</p>
 <ul>
 <li>&lt;field&gt; = field name valid for type of physics</li>
 <li>&lt;element_set&gt; = name of set of elements </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc source temperature middle temporal_ramp 10. 0. </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Add domain sources to the mesh. The units are consistent with LAMMPS's units for mass, length and time and are defined by the PDE being solved, e.g. for thermal transfer the balance equation is for energy and source is energy per time. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>keyword 'all' reserved in element_set name </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p>see <a class="el" href="man_remove_source.html">fix_modify AtC remove_source</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_source_integration.html

@@ -7,36 +7,34 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_source_integration">fix_modify AtC source_integration </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_source_integration">fix_modify AtC source_integration </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC source_integration &lt; fe | atom&gt; </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc source_integration atom </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>Default is fe </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_temperature_definition.html

@@ -7,37 +7,35 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_temperature_definition">fix_modify AtC temperature_definition </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_temperature_definition">fix_modify AtC temperature_definition </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC temperature_definition &lt;kinetic|total&gt;</p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc temperature_definition kinetic </code> <br/>
 </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Change the definition for the atomic temperature used to create the finite element temperature. The kinetic option is based only on the kinetic energy of the atoms while the total option uses the total energy (kinetic + potential) of an atom.</p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>This command is only valid when using thermal coupling. Also, while not a formal restriction, the user should ensure that associating a potential energy with each atom makes physical sense for the total option to be meaningful.</p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>kinetic </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_thermal_time_integration.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_thermal_time_integration">fix_modify AtC time_integration (thermal) </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_thermal_time_integration">fix_modify AtC time_integration (thermal) </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC time_integration &lt;descriptor&gt; <br/>
 </p>
 <ul>
@@ -33,23 +31,23 @@ syntax</a></h2>
 </ul>
 <p>various time integration methods for the finite elements<br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>gear - atomic velocity update with 2nd order Verlet, nodal temperature update with 3rd or 4th order Gear, thermostats based on controlling power <br/>
  fractional_step - atomic velocity update with 2nd order Verlet, mixed nodal temperature update, 3/4 Gear for continuum and 2 Verlet for atomic contributions, thermostats based on controlling discrete energy changes<br/>
  </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc time_integration gear </code> <br/>
  <code> fix_modify atc time_integration fractional_step </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<p>see <a class="el" href="man_fix_atc.html">fix atc command</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<p>see <a class="el" href="../../fix_atc.html">fix atc command</a> </p>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_time_filter.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_time_filter">fix_modify AtC filter </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_time_filter">fix_modify AtC filter </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC filter &lt;on | off | equilibrate&gt; <br/>
 </p>
 <ul>
@@ -32,22 +30,22 @@ syntax</a></h2>
 </li>
 <li>equilibrate = runs dynamics without filtering but initializes filtered quantities </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc transfer filter on </code> <br/>
 </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Filters the MD dynamics to construct a more appropriate continuous field. Equilibrating first filters the time derivatives without changing the dynamics to provide a better initial condition to the filtered dynamics</p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>only for be used with specific transfers: thermal, two_temperature</p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p><a class="el" href="man_filter_scale.html">fix_modify AtC filter scale</a> <br/>
  <a class="el" href="man_equilibrium_start.html">fix_modify AtC equilibrium_start</a></p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>off </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_track_displacement.html

@@ -7,38 +7,36 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_track_displacement">fix_modify AtC track_displacement </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_track_displacement">fix_modify AtC track_displacement </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC track_displacement &lt;on/off&gt; <br/>
  </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc track_displacement on </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Determines whether displacement is tracked or not. For solids problems this is a useful quantity, but for fluids it is not relevant. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>Some constitutive models require the displacement field </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>on </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_unfix_flux.html

@@ -7,43 +7,41 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_unfix_flux">fix_modify AtC unfix_flux </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_unfix_flux">fix_modify AtC unfix_flux </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC fix_flux &lt;field&gt; &lt;face_set&gt; &lt;value | function&gt;</p>
 <ul>
 <li>&lt;field&gt; = field name valid for type of physics, temperature | electron_temperature</li>
 <li>&lt;face_set&gt; = name of set of element faces </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc unfix_flux temperature faceSet </code> <br/>
 </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Command for removing prescribed normal fluxes e.g. heat_flux, stress. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p>see <a class="el" href="man_unfix_flux.html">fix_modify AtC unfix_flux</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
 <a href="http://www.doxygen.org/index.html">

doc/src/USER/atc/man_unfix_nodes.html

@@ -7,43 +7,41 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_unfix_nodes">fix_modify AtC unfix </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_unfix_nodes">fix_modify AtC unfix </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC unfix &lt;field&gt; &lt;nodeset&gt;</p>
 <ul>
 <li>&lt;field&gt; = field name valid for type of physics</li>
 <li>&lt;nodeset&gt; = name of set of nodes </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC unfix temperature groupNAME </code> </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Removes constraint on field values for specified nodes. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>keyword 'all' reserved in nodeset name </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p>see <a class="el" href="man_fix_nodes.html">fix_modify AtC fix</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/USER/atc/man_write_atom_weights.html

@@ -7,24 +7,22 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_write_atom_weights">fix_modify AtC write_atom_weights </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_write_atom_weights">fix_modify AtC write_atom_weights </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC write_atom_weights &lt;filename&gt; &lt;frequency&gt;</p>
 <ul>
 <li>&lt;filename&gt; = name of file that atomic weights are written to <br/>
@@ -32,19 +30,19 @@ syntax</a></h2>
 <li>&lt;frequency&gt; = how often writes will occur <br/>
  </li>
 </ul>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify atc write_atom_weights atm_wt_file.txt 10 </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Command for writing the values of atomic weights to a specified file. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
-<h2><a class="anchor" id="related">
-related</a></h2>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
+<h4><a class="anchor" id="related">
+related</a></h4>
+<h4><a class="anchor" id="default">
+default</a></h4>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;
 <a href="http://www.doxygen.org/index.html">

doc/src/USER/atc/man_write_restart.html

@@ -7,41 +7,39 @@
 <link href="doxygen.css" rel="stylesheet" type="text/css"/>
 </head>
 <body>
+<center>
+  <a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
+  <a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
+  <a href="../../fix_atc.html">USER-AtC Manual</a> &nbsp; &nbsp;
+  <a href="../../Section_commands.html#comm">Commands</a>
+</center>
+
+<hr>
+
+
 <!-- Generated by Doxygen 1.6.1 -->
-<div class="navigation" id="top">
-  <div class="tabs">
-    <ul>
-      <li><a href="index.html"><span>Main&nbsp;Page</span></a></li>
-      <li class="current"><a href="pages.html"><span>Related&nbsp;Pages</span></a></li>
-      <li><a href="namespaces.html"><span>Namespaces</span></a></li>
-      <li><a href="annotated.html"><span>Classes</span></a></li>
-      <li><a href="files.html"><span>Files</span></a></li>
-      <li><a href="dirs.html"><span>Directories</span></a></li>
-    </ul>
-  </div>
-</div>
 <div class="contents">
 
 
-<h1><a class="anchor" id="man_write_restart">fix_modify AtC write_restart </a></h1><h2><a class="anchor" id="syntax">
-syntax</a></h2>
+<h3><a class="anchor" id="man_write_restart">fix_modify AtC write_restart </a></h3><h4><a class="anchor" id="syntax">
+syntax</a></h4>
 <p>fix_modify AtC write_restart [file_name] <br/>
  </p>
-<h2><a class="anchor" id="examples">
-examples</a></h2>
+<h4><a class="anchor" id="examples">
+examples</a></h4>
 <p><code> fix_modify AtC write_restart restart.mydata </code> <br/>
  </p>
-<h2><a class="anchor" id="description">
-description</a></h2>
+<h4><a class="anchor" id="description">
+description</a></h4>
 <p>Dumps the current state of the fields to a named text-based restart file. This done when the command is invoked and not repeated, unlike the similar lammps command. </p>
-<h2><a class="anchor" id="restrictions">
-restrictions</a></h2>
+<h4><a class="anchor" id="restrictions">
+restrictions</a></h4>
 <p>The restart file only contains fields and their time derivatives. The reference positions of the atoms and the commands that initialize the fix are not saved e.g. an identical mesh containing the same atoms will have to be recreated. </p>
-<h2><a class="anchor" id="related">
-related</a></h2>
+<h4><a class="anchor" id="related">
+related</a></h4>
 <p>see read_restart <a class="el" href="man_read_restart.html">fix_modify AtC read_restart</a> </p>
-<h2><a class="anchor" id="default">
-default</a></h2>
+<h4><a class="anchor" id="default">
+default</a></h4>
 <p>none </p>
 </div>
 <hr size="1"/><address style="text-align: right;"><small>Generated on 21 Aug 2013 for ATC by&nbsp;

doc/src/accelerate_intel.txt

@@ -78,7 +78,7 @@ order of operations compared to LAMMPS without acceleration:
 Neighbor lists can be created in a different order :ulb,l
 Bins used for sorting atoms can be oriented differently :l
 The default stencil order for PPPM is 7. By default, LAMMPS will
-calculate other PPPM parameters to fit the desired acuracy with
+calculate other PPPM parameters to fit the desired accuracy with
 this order :l
 The {newton} setting applies to all atoms, not just atoms shared
 between MPI tasks :l

doc/src/accelerate_kokkos.txt

@@ -11,336 +11,346 @@
 
 5.3.3 KOKKOS package :h5
 
-The KOKKOS package was developed primarily by Christian Trott (Sandia)
-with contributions of various styles by others, including Sikandar
-Mashayak (UIUC), Stan Moore (Sandia), and Ray Shan (Sandia).  The
-underlying Kokkos library was written primarily by Carter Edwards,
+Kokkos is a templated C++ library that provides abstractions to allow
+a single implementation of an application kernel (e.g. a pair style) to run efficiently on
+different kinds of hardware, such as GPUs, Intel Xeon Phis, or many-core
+CPUs. Kokkos maps the C++ kernel onto different backend languages such as CUDA, OpenMP, or Pthreads.
+The Kokkos library also provides data abstractions to adjust (at
+compile time) the memory layout of data structures like 2d and
+3d arrays to optimize performance on different hardware. For more information on Kokkos, see
+"Github"_https://github.com/kokkos/kokkos. Kokkos is part of
+"Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos library was written primarily by Carter Edwards,
 Christian Trott, and Dan Sunderland (all Sandia).
 
-The KOKKOS package contains versions of pair, fix, and atom styles
+The LAMMPS KOKKOS package contains versions of pair, fix, and atom styles
 that use data structures and macros provided by the Kokkos library,
-which is included with LAMMPS in lib/kokkos.
-
-The Kokkos library is part of
-"Trilinos"_http://trilinos.sandia.gov/packages/kokkos and can also be
-downloaded from "Github"_https://github.com/kokkos/kokkos. Kokkos is a
-templated C++ library that provides two key abstractions for an
-application like LAMMPS.  First, it allows a single implementation of
-an application kernel (e.g. a pair style) to run efficiently on
-different kinds of hardware, such as a GPU, Intel Phi, or many-core
-CPU.
-
-The Kokkos library also provides data abstractions to adjust (at
-compile time) the memory layout of basic data structures like 2d and
-3d arrays and allow the transparent utilization of special hardware
-load and store operations.  Such data structures are used in LAMMPS to
-store atom coordinates or forces or neighbor lists.  The layout is
-chosen to optimize performance on different platforms.  Again this
-functionality is hidden from the developer, and does not affect how
-the kernel is coded.
-
-These abstractions are set at build time, when LAMMPS is compiled with
-the KOKKOS package installed.  All Kokkos operations occur within the
-context of an individual MPI task running on a single node of the
-machine.  The total number of MPI tasks used by LAMMPS (one or
-multiple per compute node) is set in the usual manner via the mpirun
-or mpiexec commands, and is independent of Kokkos.
+which is included with LAMMPS in /lib/kokkos. The KOKKOS package was developed primarily by Christian Trott (Sandia)
+and Stan Moore (Sandia) with contributions of various styles by others, including Sikandar
+Mashayak (UIUC), Ray Shan (Sandia), and Dan Ibanez (Sandia). For more information on developing using Kokkos abstractions
+see the Kokkos programmers' guide at /lib/kokkos/doc/Kokkos_PG.pdf.
 
 Kokkos currently provides support for 3 modes of execution (per MPI
-task).  These are OpenMP (for many-core CPUs), Cuda (for NVIDIA GPUs),
-and OpenMP (for Intel Phi).  Note that the KOKKOS package supports
-running on the Phi in native mode, not offload mode like the
-USER-INTEL package supports.  You choose the mode at build time to
+task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP (threading
+for many-core CPUs and Intel Phi), and CUDA (for NVIDIA GPUs). You choose the mode at build time to
 produce an executable compatible with specific hardware.
 
-Here is a quick overview of how to use the KOKKOS package
-for CPU acceleration, assuming one or more 16-core nodes.
-More details follow.
+[Building LAMMPS with the KOKKOS package:]
 
-use a C++11 compatible compiler
+NOTE: Kokkos support within LAMMPS must be built with a C++11 compatible
+compiler. This means GCC version 4.7.2 or later, Intel 14.0.4 or later, or
+Clang 3.5.2 or later is required.
+
+The recommended method of building the KOKKOS package is to start with the provided Kokkos
+Makefiles in /src/MAKE/OPTIONS/. You may need to modify the KOKKOS_ARCH variable in the Makefile
+to match your specific hardware. For example:
+
+for Sandy Bridge CPUs, set KOKKOS_ARCH=SNB
+for Broadwell CPUs, set KOKKOS_ARCH=BWD
+for K80 GPUs, set KOKKOS_ARCH=Kepler37
+for P100 GPUs and Power8 CPUs, set KOKKOS_ARCH=Pascal60,Power8 :ul
+
+See the [Advanced Kokkos Options] section below for a listing of all KOKKOS_ARCH options.
+
+[Compile for CPU-only (MPI only, no threading):]
+
+use a C++11 compatible compiler and set KOKKOS_ARCH variable in
+/src/MAKE/OPTIONS/Makefile.kokkos_mpi_only as described above. Then do the
+following:
+
+cd lammps/src
 make yes-kokkos
-make mpi KOKKOS_DEVICES=OpenMP                 # build with the KOKKOS package
-make kokkos_omp                                # or Makefile.kokkos_omp already has variable set :pre
+make kokkos_mpi_only :pre
 
-mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj              # 1 node, 16 MPI tasks/node, no threads
-mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj   # 2 nodes, 1 MPI task/node, 16 threads/task
-mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj           # 1 node, 2 MPI tasks/node, 8 threads/task
-mpirun -np 32 -ppn 4 lmp_mpi -k on t 4 -sf kk -in in.lj   # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
+[Compile for CPU-only (MPI plus OpenMP threading):]
 
-specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support
-include the KOKKOS package and build LAMMPS
-enable the KOKKOS package and its hardware options via the "-k on" command-line switch use KOKKOS styles in your input script :ul
-
-Here is a quick overview of how to use the KOKKOS package for GPUs,
-assuming one or more nodes, each with 16 cores and a GPU.  More
-details follow.
-
-discuss use of NVCC, which Makefiles to examine
-
-use a C++11 compatible compiler
-KOKKOS_DEVICES = Cuda, OpenMP
-KOKKOS_ARCH = Kepler35
-make yes-kokkos
-make machine :pre
-
-mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj          # one MPI task, 6 threads on CPU
-mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj   # ditto on 4 nodes :pre
-
-mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj           # two MPI tasks, 8 threads per CPU
-mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj   # ditto on 16 nodes :pre
-
-Here is a quick overview of how to use the KOKKOS package
-for the Intel Phi:
-
-use a C++11 compatible compiler
-KOKKOS_DEVICES = OpenMP
-KOKKOS_ARCH = KNC
-make yes-kokkos
-make machine :pre
-
-host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
-mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj           # 1 MPI task on 1 Phi, 1*240 = 240
-mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj            # 30 MPI tasks on 1 Phi, 30*8 = 240
-mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj           # 12 MPI tasks on 1 Phi, 12*20 = 240
-mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj   # ditto on 8 Phis :pre
-
-[Required hardware/software:]
-
-Kokkos support within LAMMPS must be built with a C++11 compatible
-compiler.  If using gcc, version 4.7.2 or later is required.
-
-To build with Kokkos support for CPUs, your compiler must support the
+NOTE: To build with Kokkos support for OpenMP threading, your compiler must support the
 OpenMP interface. You should have one or more multi-core CPUs so that
 multiple threads can be launched by each MPI task running on a CPU.
 
-To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA software
+use a C++11 compatible compiler and set KOKKOS_ARCH variable in
+/src/MAKE/OPTIONS/Makefile.kokkos_omp as described above.  Then do the
+following:
+
+cd lammps/src
+make yes-kokkos
+make kokkos_omp :pre
+
+[Compile for Intel KNL Xeon Phi (Intel Compiler, OpenMPI):]
+
+use a C++11 compatible compiler and do the following:
+
+cd lammps/src
+make yes-kokkos
+make kokkos_phi :pre
+
+[Compile for CPUs and GPUs (with OpenMPI or MPICH):]
+
+NOTE: To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA software
 version 7.5 or later must be installed on your system. See the
 discussion for the "GPU"_accelerate_gpu.html package for details of
 how to check and do this.
 
+use a C++11 compatible compiler and set KOKKOS_ARCH variable in
+/src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi for both GPU and CPU as described
+above.  Then do the following:
+
+cd lammps/src
+make yes-kokkos
+make kokkos_cuda_mpi :pre
+
+[Alternative Methods of Compiling:]
+
+Alternatively, the KOKKOS package can be built by specifying Kokkos variables
+on the make command line. For example:
+
+make mpi KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=SNB     # set the KOKKOS_DEVICES and KOKKOS_ARCH variable explicitly
+make kokkos_cuda_mpi KOKKOS_ARCH=Pascal60,Power8   # set the KOKKOS_ARCH variable explicitly :pre
+
+Setting the KOKKOS_DEVICES and KOKKOS_ARCH variables on the
+make command line requires a GNU-compatible make command. Try
+"gmake" if your system's standard make complains.
+
+NOTE: If you build using make line variables and re-build LAMMPS twice
+with different KOKKOS options and the *same* target, then you *must* perform a "make clean-all"
+or "make clean-machine" before each build. This is to force all the
+KOKKOS-dependent files to be re-compiled with the new options.
+
+[Running LAMMPS with the KOKKOS package:]
+
+All Kokkos operations occur within the
+context of an individual MPI task running on a single node of the
+machine. The total number of MPI tasks used by LAMMPS (one or
+multiple per compute node) is set in the usual manner via the mpirun
+or mpiexec commands, and is independent of Kokkos. E.g. the mpirun
+command in OpenMPI does this via its
+-np and -npernode switches. Ditto for MPICH via -np and -ppn.
+
+[Running on a multi-core CPU:]
+
+Here is a quick overview of how to use the KOKKOS package
+for CPU acceleration, assuming one or more 16-core nodes.
+
+mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -in in.lj        # 1 node, 16 MPI tasks/node, no multi-threading
+mpirun -np 2 -ppn 1 lmp_kokkos_omp -k on t 16 -sf kk -in in.lj  # 2 nodes, 1 MPI task/node, 16 threads/task
+mpirun -np 2 lmp_kokkos_omp -k on t 8 -sf kk -in in.lj          # 1 node,  2 MPI tasks/node, 8 threads/task
+mpirun -np 32 -ppn 4 lmp_kokkos_omp -k on t 4 -sf kk -in in.lj  # 8 nodes, 4 MPI tasks/node, 4 threads/task :pre
+
+To run using the KOKKOS package, use the "-k on", "-sf kk" and "-pk kokkos" "command-line switches"_Section_start.html#start_7 in your mpirun command.
+You must use the "-k on" "command-line
+switch"_Section_start.html#start_7 to enable the KOKKOS package. It
+takes additional arguments for hardware settings appropriate to your
+system. Those arguments are "documented
+here"_Section_start.html#start_7. For OpenMP use:
+
+-k on t Nt :pre
+
+The "t Nt" option specifies how many OpenMP threads per MPI
+task to use with a node. The default is Nt = 1, which is MPI-only mode.
+Note that the product of MPI tasks * OpenMP
+threads/task should not exceed the physical number of cores (on a
+node), otherwise performance will suffer. If hyperthreading is enabled, then
+the product of MPI tasks * OpenMP threads/task should not exceed the
+physical number of cores * hardware threads.
+The "-k on" switch also issues a "package kokkos" command (with no
+additional arguments) which sets various KOKKOS options to default
+values, as discussed on the "package"_package.html command doc page.
+
+The "-sf kk" "command-line switch"_Section_start.html#start_7
+will automatically append the "/kk" suffix to styles that support it.
+In this manner no modification to the input script is needed. Alternatively,
+one can run with the KOKKOS package by editing the input script as described below.
+
+NOTE: The default for the "package kokkos"_package.html command is
+to use "full" neighbor lists and set the Newton flag to "off" for both
+pairwise and bonded interactions. However, when running on CPUs, it
+will typically be faster to use "half" neighbor lists and set the
+Newton flag to "on", just as is the case for non-accelerated pair
+styles. It can also be faster to use non-threaded communication.
+Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
+change the default "package kokkos"_package.html
+options. See its doc page for details and default settings. Experimenting with
+its options can provide a speed-up for specific calculations. For example:
+
+mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half comm no -in in.lj       # Newton on, Half neighbor list, non-threaded comm :pre
+
+If the "newton"_newton.html command is used in the input
+script, it can also override the Newton flag defaults.
+
+[Core and Thread Affinity:]
+
+When using multi-threading, it is important for
+performance to bind both MPI tasks to physical cores, and threads to
+physical cores, so they do not migrate during a simulation.
+
+If you are not certain MPI tasks are being bound (check the defaults
+for your MPI installation), binding can be forced with these flags:
+
+OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
+Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ... :pre
+
+For binding threads with KOKKOS OpenMP, use thread affinity
+environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
+later, intel 12 or later) setting the environment variable
+OMP_PROC_BIND=true should be sufficient. In general, for best performance
+with OpenMP 4.0 or better set OMP_PROC_BIND=spread and OMP_PLACES=threads.
+For binding threads with the
+KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option
+as described below.
+
+[Running on Knight's Landing (KNL) Intel Xeon Phi:]
+
+Here is a quick overview of how to use the KOKKOS package
+for the Intel Knight's Landing (KNL) Xeon Phi:
+
+KNL Intel Phi chips have 68 physical cores. Typically 1 to 4 cores
+are reserved for the OS, and only 64 or 66 cores are used. Each core
+has 4 hyperthreads,so there are effectively N = 256 (4*64) or
+N = 264 (4*66) cores to run on. The product of MPI tasks * OpenMP threads/task should not exceed this limit,
+otherwise performance will suffer. Note that with the KOKKOS package you do not need to
+specify how many KNLs there are per node; each
+KNL is simply treated as running some number of MPI tasks.
+
+Examples of mpirun commands that follow these rules are shown below.
+
+Intel KNL node with 68 cores (272 threads/node via 4x hardware threading):
+mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj      # 1 node, 64 MPI tasks/node, 4 threads/task
+mpirun -np 66 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj      # 1 node, 66 MPI tasks/node, 4 threads/task
+mpirun -np 32 lmp_kokkos_phi -k on t 8 -sf kk -in in.lj      # 1 node, 32 MPI tasks/node, 8 threads/task
+mpirun -np 512 -ppn 64 lmp_kokkos_phi -k on t 4 -sf kk -in in.lj  # 8 nodes, 64 MPI tasks/node, 4 threads/task :pre
+
+The -np setting of the mpirun command sets the number of MPI
+tasks/node. The "-k on t Nt" command-line switch sets the number of
+threads/task as Nt. The product of these two values should be N, i.e.
+256 or 264.
+
+NOTE: The default for the "package kokkos"_package.html command is
+to use "full" neighbor lists and set the Newton flag to "off" for both
+pairwise and bonded interactions. When running on KNL, this
+will typically be best for pair-wise potentials. For manybody potentials,
+using "half" neighbor lists and setting the
+Newton flag to "on" may be faster. It can also be faster to use non-threaded communication.
+Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
+change the default "package kokkos"_package.html
+options. See its doc page for details and default settings. Experimenting with
+its options can provide a speed-up for specific calculations. For example:
+
+mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos comm no -in in.lj      #  Newton off, full neighbor list, non-threaded comm
+mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half comm no -in in.reax      # Newton on, half neighbor list, non-threaded comm :pre
+
+NOTE: MPI tasks and threads should be bound to cores as described above for CPUs.
+
+NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors such as Knight's Corner (KNC), your
+system must be configured to use them in "native" mode, not "offload"
+mode like the USER-INTEL package supports.
+
+[Running on GPUs:]
+
+Use the "-k" "command-line switch"_Section_commands.html#start_7 to
+specify the number of GPUs per node. Typically the -np setting
+of the mpirun command should set the number of MPI
+tasks/node to be equal to the # of physical GPUs on the node.
+You can assign multiple MPI tasks to the same GPU with the
+KOKKOS package, but this is usually only faster if significant portions
+of the input script have not been ported to use Kokkos. Using CUDA MPS
+is recommended in this scenario. As above for multi-core CPUs (and no GPU), if N is the number
+of physical cores/node, then the number of MPI tasks/node should not exceed N.
+
+-k on g Ng :pre
+
+Here are examples of how to use the KOKKOS package for GPUs,
+assuming one or more nodes, each with two GPUs:
+
+mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj          # 1 node,   2 MPI tasks/node, 2 GPUs/node
+mpirun -np 32 -ppn 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -in in.lj  # 16 nodes, 2 MPI tasks/node, 2 GPUs/node (32 GPUs total) :pre
+
+NOTE: The default for the "package kokkos"_package.html command is
+to use "full" neighbor lists and set the Newton flag to "off" for both
+pairwise and bonded interactions, along with threaded communication.
+When running on Maxwell or Kepler GPUs, this will typically be best. For Pascal GPUs,
+using "half" neighbor lists and setting the
+Newton flag to "on" may be faster. For many pair styles, setting the neighbor binsize
+equal to the ghost atom cutoff will give speedup.
+Use the "-pk kokkos" "command-line switch"_Section_start.html#start_7 to
+change the default "package kokkos"_package.html
+options. See its doc page for details and default settings. Experimenting with
+its options can provide a speed-up for specific calculations. For example:
+
+mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos binsize 2.8 -in in.lj      # Set binsize = neighbor ghost cutoff
+mpirun -np 2 lmp_kokkos_cuda_openmpi -k on g 2 -sf kk -pk kokkos newton on neigh half binsize 2.8 -in in.lj      # Newton on, half neighborlist, set binsize = neighbor ghost cutoff :pre
+
 NOTE: For good performance of the KOKKOS package on GPUs, you must
 have Kepler generation GPUs (or later). The Kokkos library exploits
 texture cache options not supported by Telsa generation GPUs (or
 older).
 
-To build with Kokkos support for Intel Xeon Phi coprocessors, your
-sysmte must be configured to use them in "native" mode, not "offload"
-mode like the USER-INTEL package supports.
+NOTE: When using a GPU, you will achieve the best performance if your
+input script does not use fix or compute styles which are not yet
+Kokkos-enabled. This allows data to stay on the GPU for multiple
+timesteps, without being copied back to the host CPU. Invoking a
+non-Kokkos fix or compute, or performing I/O for
+"thermo"_thermo_style.html or "dump"_dump.html output will cause data
+to be copied back to the CPU incurring a performance penalty.
 
-[Building LAMMPS with the KOKKOS package:]
+NOTE: To get an accurate timing breakdown between time spend in pair,
+kspace, etc., you must set the environment variable CUDA_LAUNCH_BLOCKING=1.
+However, this will reduce performance and is not recommended for production runs.
 
-You must choose at build time whether to build for CPUs (OpenMP),
-GPUs, or Phi.
+[Run with the KOKKOS package by editing an input script:]
 
-You can do any of these in one line, using the suitable make command
-line flags as described in "Section 4"_Section_packages.html of the
-manual. If run from the src directory, these
-commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda_mpi, and
-lmp_kokkos_phi.  Note that the OMP and PHI options use
-src/MAKE/Makefile.mpi as the starting Makefile.machine.  The CUDA
-option uses src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi.
-
-The latter two steps can be done using the "-k on", "-pk kokkos" and
-"-sf kk" "command-line switches"_Section_start.html#start_6
-respectively.  Or the effect of the "-pk" or "-sf" switches can be
+Alternatively the effect of the "-sf" or "-pk" switches can be
 duplicated by adding the "package kokkos"_package.html or "suffix
-kk"_suffix.html commands respectively to your input script.
+kk"_suffix.html commands to your input script.
 
-
-Or you can follow these steps:
-
-CPU-only (run all-MPI or with OpenMP threading):
-
-cd lammps/src
-make yes-kokkos
-make kokkos_omp :pre
-
-CPU-only (only MPI, no threading):
-
-cd lammps/src
-make yes-kokkos
-make kokkos_mpi_only :pre
-
-Intel Xeon Phi (Intel Compiler, Intel MPI):
-
-cd lammps/src
-make yes-kokkos
-make kokkos_phi :pre
-
-CPUs and GPUs (with MPICH or OpenMPI):
-
-cd lammps/src
-make yes-kokkos
-make kokkos_cuda_mpi :pre
-
-These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
-make command line which requires a GNU-compatible make command.  Try
-"gmake" if your system's standard make complains.
-
-NOTE: If you build using make line variables and re-build LAMMPS twice
-with different KOKKOS options and the *same* target, e.g. g++ in the
-first two examples above, then you *must* perform a "make clean-all"
-or "make clean-machine" before each build.  This is to force all the
-KOKKOS-dependent files to be re-compiled with the new options.
-
-NOTE: Currently, there are no precision options with the KOKKOS
-package.  All compilation and computation is performed in double
-precision.
-
-There are other allowed options when building with the KOKKOS package.
-As above, they can be set either as variables on the make command line
-or in Makefile.machine.  This is the full list of options, including
-those discussed above, Each takes a value shown below.  The
-default value is listed, which is set in the
-lib/kokkos/Makefile.kokkos file.
-
-#Default settings specific options
-#Options: force_uvm,use_ldg,rdc
-
-KOKKOS_DEVICES, values = {OpenMP}, {Serial}, {Pthreads}, {Cuda}, default = {OpenMP}
-KOKKOS_ARCH, values = {KNC}, {SNB}, {HSW}, {Kepler}, {Kepler30}, {Kepler32}, {Kepler35}, {Kepler37}, {Maxwell}, {Maxwell50}, {Maxwell52}, {Maxwell53}, {ARMv8}, {BGQ}, {Power7}, {Power8}, default = {none}
-KOKKOS_DEBUG, values = {yes}, {no}, default = {no}
-KOKKOS_USE_TPLS, values = {hwloc}, {librt}, default = {none}
-KOKKOS_CUDA_OPTIONS, values = {force_uvm}, {use_ldg}, {rdc} :ul
-
-KOKKOS_DEVICE sets the parallelization method used for Kokkos code
-(within LAMMPS).  KOKKOS_DEVICES=OpenMP means that OpenMP will be
-used.  KOKKOS_DEVICES=Pthreads means that pthreads will be used.
-KOKKOS_DEVICES=Cuda means an NVIDIA GPU running CUDA will be used.
-
-If KOKKOS_DEVICES=Cuda, then the lo-level Makefile in the src/MAKE
-directory must use "nvcc" as its compiler, via its CC setting.  For
-best performance its CCFLAGS setting should use -O3 and have a
-KOKKOS_ARCH setting that matches the compute capability of your NVIDIA
-hardware and software installation, e.g. KOKKOS_ARCH=Kepler30.  Note
-the minimal required compute capability is 2.0, but this will give
-significantly reduced performance compared to Kepler generation GPUs
-with compute capability 3.x.  For the LINK setting, "nvcc" should not
-be used; instead use g++ or another compiler suitable for linking C++
-applications.  Often you will want to use your MPI compiler wrapper
-for this setting (i.e. mpicxx).  Finally, the lo-level Makefile must
-also have a "Compilation rule" for creating *.o files from *.cu files.
-See src/Makefile.cuda for an example of a lo-level Makefile with all
-of these settings.
-
-KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not
-migrate during a simulation.  KOKKOS_USE_TPLS=hwloc should always be
-used if running with KOKKOS_DEVICES=Pthreads for pthreads.  It is not
-necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
-provides alternative methods via environment variables for binding
-threads to hardware cores.  More info on binding threads to cores is
-given in "Section 5.3"_Section_accelerate.html#acc_3.
-
-KOKKOS_ARCH=KNC enables compiler switches needed when compiling for an
-Intel Phi processor.
-
-KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
-on most Unix platforms.  This library is not available on all
-platforms.
-
-KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style
-within LAMMPS.  KOKKOS_DEBUG=yes enables printing of run-time
-debugging information that can be useful.  It also enables runtime
-bounds checking on Kokkos data structures.
-
-KOKKOS_CUDA_OPTIONS are additional options for CUDA.
-
-For more information on Kokkos see the Kokkos programmers' guide here:
-/lib/kokkos/doc/Kokkos_PG.pdf.
-
-[Run with the KOKKOS package from the command line:]
-
-The mpirun or mpiexec command sets the total number of MPI tasks used
-by LAMMPS (one or multiple per compute node) and the number of MPI
-tasks used per node.  E.g. the mpirun command in MPICH does this via
-its -np and -ppn switches.  Ditto for OpenMPI via -np and -npernode.
-
-When using KOKKOS built with host=OMP, you need to choose how many
-OpenMP threads per MPI task will be used (via the "-k" command-line
-switch discussed below).  Note that the product of MPI tasks * OpenMP
-threads/task should not exceed the physical number of cores (on a
-node), otherwise performance will suffer.
-
-When using the KOKKOS package built with device=CUDA, you must use
-exactly one MPI task per physical GPU.
-
-When using the KOKKOS package built with host=MIC for Intel Xeon Phi
-coprocessor support you need to insure there are one or more MPI tasks
-per coprocessor, and choose the number of coprocessor threads to use
-per MPI task (via the "-k" command-line switch discussed below).  The
-product of MPI tasks * coprocessor threads/task should not exceed the
-maximum number of threads the coprocessor is designed to run,
-otherwise performance will suffer.  This value is 240 for current
-generation Xeon Phi(TM) chips, which is 60 physical cores * 4
-threads/core.  Note that with the KOKKOS package you do not need to
-specify how many Phi coprocessors there are per node; each
-coprocessors is simply treated as running some number of MPI tasks.
-
-You must use the "-k on" "command-line
-switch"_Section_start.html#start_6 to enable the KOKKOS package.  It
-takes additional arguments for hardware settings appropriate to your
-system.  Those arguments are "documented
-here"_Section_start.html#start_6.  The two most commonly used
-options are:
-
--k on t Nt g Ng :pre
-
-The "t Nt" option applies to host=OMP (even if device=CUDA) and
-host=MIC.  For host=OMP, it specifies how many OpenMP threads per MPI
-task to use with a node.  For host=MIC, it specifies how many Xeon Phi
-threads per MPI task to use within a node.  The default is Nt = 1.
-Note that for host=OMP this is effectively MPI-only mode which may be
-fine.  But for host=MIC you will typically end up using far less than
-all the 240 available threads, which could give very poor performance.
-
-The "g Ng" option applies to device=CUDA.  It specifies how many GPUs
-per compute node to use.  The default is 1, so this only needs to be
-specified is you have 2 or more GPUs per compute node.
-
-The "-k on" switch also issues a "package kokkos" command (with no
-additional arguments) which sets various KOKKOS options to default
-values, as discussed on the "package"_package.html command doc page.
-
-Use the "-sf kk" "command-line switch"_Section_start.html#start_6,
-which will automatically append "kk" to styles that support it.  Use
-the "-pk kokkos" "command-line switch"_Section_start.html#start_6 if
-you wish to change any of the default "package kokkos"_package.html
-optionns set by the "-k on" "command-line
-switch"_Section_start.html#start_6.
-
-
-
-Note that the default for the "package kokkos"_package.html command is
-to use "full" neighbor lists and set the Newton flag to "off" for both
-pairwise and bonded interactions.  This typically gives fastest
-performance.  If the "newton"_newton.html command is used in the input
-script, it can override the Newton flag defaults.
-
-However, when running in MPI-only mode with 1 thread per MPI task, it
-will typically be faster to use "half" neighbor lists and set the
-Newton flag to "on", just as is the case for non-accelerated pair
-styles.  You can do this with the "-pk" "command-line
-switch"_Section_start.html#start_6.
-
-[Or run with the KOKKOS package by editing an input script:]
-
-The discussion above for the mpirun/mpiexec command and setting
-appropriate thread and GPU values for host=OMP or host=MIC or
-device=CUDA are the same.
+The discussion above for building LAMMPS with the KOKKOS package, the mpirun/mpiexec command, and setting
+appropriate thread are the same.
 
 You must still use the "-k on" "command-line
-switch"_Section_start.html#start_6 to enable the KOKKOS package, and
+switch"_Section_start.html#start_7 to enable the KOKKOS package, and
 specify its additional arguments for hardware options appropriate to
 your system, as documented above.
 
-Use the "suffix kk"_suffix.html command, or you can explicitly add a
+You can use the "suffix kk"_suffix.html command, or you can explicitly add a
 "kk" suffix to individual styles in your input script, e.g.
 
 pair_style lj/cut/kk 2.5 :pre
 
 You only need to use the "package kokkos"_package.html command if you
 wish to change any of its option defaults, as set by the "-k on"
-"command-line switch"_Section_start.html#start_6.
+"command-line switch"_Section_start.html#start_7.
+
+[Using OpenMP threading and CUDA together (experimental):]
+
+With the KOKKOS package, both OpenMP multi-threading and GPUs can be used
+together in a few special cases. In the Makefile, the KOKKOS_DEVICES variable must
+include both "Cuda" and "OpenMP", as is the case for /src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
+
+KOKKOS_DEVICES=Cuda,OpenMP :pre
+
+The suffix "/kk" is equivalent to "/kk/device", and for Kokkos CUDA,
+using the "-sf kk" in the command line gives the default CUDA version everywhere.
+However, if the "/kk/host" suffix is added to a specific style in the input
+script, the Kokkos OpenMP (CPU) version of that specific style will be used instead.
+Set the number of OpenMP threads as "t Nt" and the number of GPUs as "g Ng"
+
+-k on t Nt g Ng :pre
+
+For example, the command to run with 1 GPU and 8 OpenMP threads is then:
+
+mpiexec -np 1 lmp_kokkos_cuda_openmpi -in in.lj -k on g 1 t 8 -sf kk :pre
+
+Conversely, if the "-sf kk/host" is used in the command line and then the
+"/kk" or "/kk/device" suffix is added to a specific style in your input script,
+then only that specific style will run on the GPU while everything else will
+run on the CPU in OpenMP mode. Note that the execution of the CPU and GPU
+styles will NOT overlap, except for a special case:
+
+A kspace style and/or molecular topology (bonds, angles, etc.) running on
+the host CPU can overlap with a pair style running on the GPU. First compile
+with "--default-stream per-thread" added to CCFLAGS in the Kokkos CUDA Makefile.
+Then explicitly use the "/kk/host" suffix for kspace and bonds, angles, etc.
+in the input file and the "kk" suffix (equal to "kk/device") on the command line.
+Also make sure the environment variable CUDA_LAUNCH_BLOCKING is not set to "1"
+so CPU/GPU overlap can occur.
 
 [Speed-ups to expect:]
 
@@ -363,7 +373,7 @@ package. :l
 When running large number of atoms per GPU, KOKKOS is typically faster
 than the GPU package. :l
 
-When running on Intel Xeon Phi, KOKKOS is not as fast as
+When running on Intel hardware, KOKKOS is not as fast as
 the USER-INTEL package, which is optimized for that hardware. :l
 :ule
 
@@ -371,123 +381,78 @@ See the "Benchmark page"_http://lammps.sandia.gov/bench.html of the
 LAMMPS web site for performance of the KOKKOS package on different
 hardware.
 
-[Guidelines for best performance:]
+[Advanced Kokkos options:]
 
-Here are guidline for using the KOKKOS package on the different
-hardware configurations listed above.
+There are other allowed options when building with the KOKKOS package.
+As above, they can be set either as variables on the make command line
+or in Makefile.machine. This is the full list of options, including
+those discussed above. Each takes a value shown below. The
+default value is listed, which is set in the
+/lib/kokkos/Makefile.kokkos file.
 
-Many of the guidelines use the "package kokkos"_package.html command
-See its doc page for details and default settings.  Experimenting with
-its options can provide a speed-up for specific calculations.
+KOKKOS_DEVICES, values = {Serial}, {OpenMP}, {Pthreads}, {Cuda}, default = {OpenMP}
+KOKKOS_ARCH, values = {KNC}, {SNB}, {HSW}, {Kepler30}, {Kepler32}, {Kepler35}, {Kepler37}, {Maxwell50}, {Maxwell52}, {Maxwell53}, {Pascal60}, {Pascal61}, {ARMv80}, {ARMv81}, {ARMv81}, {ARMv8-ThunderX}, {BGQ}, {Power7}, {Power8}, {Power9}, {KNL}, {BDW}, {SKX}, default = {none}
+KOKKOS_DEBUG, values = {yes}, {no}, default = {no}
+KOKKOS_USE_TPLS, values = {hwloc}, {librt}, {experimental_memkind}, default = {none}
+KOKKOS_CXX_STANDARD, values = {c++11}, {c++1z}, default = {c++11}
+KOKKOS_OPTIONS, values = {aggressive_vectorization}, {disable_profiling}, default = {none}
+KOKKOS_CUDA_OPTIONS, values = {force_uvm}, {use_ldg}, {rdc}, {enable_lambda}, default = {enable_lambda} :ul
 
-[Running on a multi-core CPU:]
+KOKKOS_DEVICES sets the parallelization method used for Kokkos code
+(within LAMMPS). KOKKOS_DEVICES=Serial means that no threading will be used.
+KOKKOS_DEVICES=OpenMP means that OpenMP threading will be
+used. KOKKOS_DEVICES=Pthreads means that pthreads will be used.
+KOKKOS_DEVICES=Cuda means an NVIDIA GPU running CUDA will be used.
 
-If N is the number of physical cores/node, then the number of MPI
-tasks/node * number of threads/task should not exceed N, and should
-typically equal N.  Note that the default threads/task is 1, as set by
-the "t" keyword of the "-k" "command-line
-switch"_Section_start.html#start_6.  If you do not change this, no
-additional parallelism (beyond MPI) will be invoked on the host
-CPU(s).
+KOKKOS_ARCH enables compiler switches needed when compiling for a
+specific hardware:
 
-You can compare the performance running in different modes:
+ARMv80 = ARMv8.0 Compatible CPU
+ARMv81 = ARMv8.1 Compatible CPU
+ARMv8-ThunderX = ARMv8 Cavium ThunderX CPU
+SNB = Intel Sandy/Ivy Bridge CPUs
+HSW = Intel Haswell CPUs
+BDW = Intel Broadwell Xeon E-class CPUs
+SKX = Intel Sky Lake Xeon E-class HPC CPUs (AVX512)
+KNC = Intel Knights Corner Xeon Phi
+KNL = Intel Knights Landing Xeon Phi
+Kepler30 = NVIDIA Kepler generation CC 3.0
+Kepler32 = NVIDIA Kepler generation CC 3.2
+Kepler35 = NVIDIA Kepler generation CC 3.5
+Kepler37 = NVIDIA Kepler generation CC 3.7
+Maxwell50 = NVIDIA Maxwell generation CC 5.0
+Maxwell52 = NVIDIA Maxwell generation CC 5.2
+Maxwell53 = NVIDIA Maxwell generation CC 5.3
+Pascal60 = NVIDIA Pascal generation CC 6.0
+Pascal61 = NVIDIA Pascal generation CC 6.1
+BGQ = IBM Blue Gene/Q CPUs
+Power8 = IBM POWER8 CPUs
+Power9 = IBM POWER9 CPUs :ul
 
-run with 1 MPI task/node and N threads/task
-run with N MPI tasks/node and 1 thread/task
-run with settings in between these extremes :ul
+KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not
+migrate during a simulation. KOKKOS_USE_TPLS=hwloc should always be
+used if running with KOKKOS_DEVICES=Pthreads for pthreads. It is not
+necessary for KOKKOS_DEVICES=OpenMP for OpenMP, because OpenMP
+provides alternative methods via environment variables for binding
+threads to hardware cores. More info on binding threads to cores is
+given in "Section 5.3"_Section_accelerate.html#acc_3.
 
-Examples of mpirun commands in these modes are shown above.
+KOKKOS_USE_TPLS=librt enables use of a more accurate timer mechanism
+on most Unix platforms. This library is not available on all
+platforms.
 
-When using KOKKOS to perform multi-threading, it is important for
-performance to bind both MPI tasks to physical cores, and threads to
-physical cores, so they do not migrate during a simulation.
+KOKKOS_DEBUG is only useful when developing a Kokkos-enabled style
+within LAMMPS. KOKKOS_DEBUG=yes enables printing of run-time
+debugging information that can be useful. It also enables runtime
+bounds checking on Kokkos data structures.
 
-If you are not certain MPI tasks are being bound (check the defaults
-for your MPI installation), binding can be forced with these flags:
+KOKKOS_CXX_STANDARD and KOKKOS_OPTIONS are typically not changed when building LAMMPS.
 
-OpenMPI 1.8: mpirun -np 2 -bind-to socket -map-by socket ./lmp_openmpi ...
-Mvapich2 2.0: mpiexec -np 2 -bind-to socket -map-by socket ./lmp_mvapich ... :pre
-
-For binding threads with the KOKKOS OMP option, use thread affinity
-environment variables to force binding.  With OpenMP 3.1 (gcc 4.7 or
-later, intel 12 or later) setting the environment variable
-OMP_PROC_BIND=true should be sufficient.  For binding threads with the
-KOKKOS pthreads option, compile LAMMPS the KOKKOS HWLOC=yes option
-(see "this section"_Section_packages.html#KOKKOS of the manual for
-details).
-
-[Running on GPUs:]
-
-Insure the -arch setting in the machine makefile you are using,
-e.g. src/MAKE/Makefile.cuda, is correct for your GPU hardware/software.
-(see "this section"_Section_packages.html#KOKKOS of the manual for
-details).
-
-The -np setting of the mpirun command should set the number of MPI
-tasks/node to be equal to the # of physical GPUs on the node.
-
-Use the "-k" "command-line switch"_Section_commands.html#start_6 to
-specify the number of GPUs per node, and the number of threads per MPI
-task.  As above for multi-core CPUs (and no GPU), if N is the number
-of physical cores/node, then the number of MPI tasks/node * number of
-threads/task should not exceed N.  With one GPU (and one MPI task) it
-may be faster to use less than all the available cores, by setting
-threads/task to a smaller value.  This is because using all the cores
-on a dual-socket node will incur extra cost to copy memory from the
-2nd socket to the GPU.
-
-Examples of mpirun commands that follow these rules are shown above.
-
-NOTE: When using a GPU, you will achieve the best performance if your
-input script does not use any fix or compute styles which are not yet
-Kokkos-enabled.  This allows data to stay on the GPU for multiple
-timesteps, without being copied back to the host CPU.  Invoking a
-non-Kokkos fix or compute, or performing I/O for
-"thermo"_thermo_style.html or "dump"_dump.html output will cause data
-to be copied back to the CPU.
-
-You cannot yet assign multiple MPI tasks to the same GPU with the
-KOKKOS package.  We plan to support this in the future, similar to the
-GPU package in LAMMPS.
-
-You cannot yet use both the host (multi-threaded) and device (GPU)
-together to compute pairwise interactions with the KOKKOS package.  We
-hope to support this in the future, similar to the GPU package in
-LAMMPS.
-
-[Running on an Intel Phi:]
-
-Kokkos only uses Intel Phi processors in their "native" mode, i.e.
-not hosted by a CPU.
-
-As illustrated above, build LAMMPS with OMP=yes (the default) and
-MIC=yes.  The latter insures code is correctly compiled for the Intel
-Phi.  The OMP setting means OpenMP will be used for parallelization on
-the Phi, which is currently the best option within Kokkos.  In the
-future, other options may be added.
-
-Current-generation Intel Phi chips have either 61 or 57 cores.  One
-core should be excluded for running the OS, leaving 60 or 56 cores.
-Each core is hyperthreaded, so there are effectively N = 240 (4*60) or
-N = 224 (4*56) cores to run on.
-
-The -np setting of the mpirun command sets the number of MPI
-tasks/node.  The "-k on t Nt" command-line switch sets the number of
-threads/task as Nt.  The product of these 2 values should be N, i.e.
-240 or 224.  Also, the number of threads/task should be a multiple of
-4 so that logical threads from more than one MPI task do not run on
-the same physical core.
-
-Examples of mpirun commands that follow these rules are shown above.
+KOKKOS_CUDA_OPTIONS are additional options for CUDA. The LAMMPS KOKKOS package must be compiled
+with the {enable_lambda} option when using GPUs.
 
 [Restrictions:]
 
-As noted above, if using GPUs, the number of MPI tasks per compute
-node should equal to the number of GPUs per compute node.  In the
-future Kokkos will support assigning multiple MPI tasks to a single
-GPU.
-
-Currently Kokkos does not support AMD GPUs due to limits in the
-available backend programming models.  Specifically, Kokkos requires
-extensive C++ support from the Kernel language.  This is expected to
-change in the future.
+Currently, there are no precision options with the KOKKOS
+package. All compilation and computation is performed in double
+precision.

doc/src/angle_class2.txt

@@ -9,6 +9,7 @@
 angle_style class2 command :h3
 angle_style class2/omp command :h3
 angle_style class2/kk command :h3
+angle_style class2/p6 command :h3
 
 [Syntax:]
 
@@ -102,11 +103,29 @@ more instructions on how to use the accelerated styles effectively.
 
 :line
 
+The {class2/p6} angle style uses the {class2} potential expanded to sixth order:
+
+:c,image(Eqs/angle_class2_p6.jpg)
+
+In this expanded term 6 coefficients for the Ea formula need to be set:
+
+theta0 (degrees)
+K2 (energy/radian^2)
+K3 (energy/radian^3)
+K4 (energy/radian^4)
+K5 (energy/radian^5)
+K6 (energy/radian^6) :ul
+
+The bond-bond and bond-angle terms remain unchanged.
+
+:line
+
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the CLASS2
-package.  See the "Making LAMMPS"_Section_start.html#start_3 section
-for more info on packages.
+package.  For the {class2/p6} style LAMMPS needs to be built with the
+USER-MOFFF package.  See the "Making LAMMPS"_Section_start.html#start_3 
+section for more info on packages.
 
 [Related commands:]