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Steven J. Plimpton
2018-05-03 16:55:22 -06:00
parent b0b67ca610 eeee2d3026
commit 2b8576c7c7
3190 changed files with 620824 additions and 58680 deletions
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31
doc/src/Developer/developer.tex
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@ -449,15 +449,15 @@ Writing fixes is a flexible way of extending LAMMPS. Users can
implement many things using fixes:
\begin{itemize}
\item changing particles attributes (positions, velocities, forces, etc.).
\item changing particles attributes (positions, velocities, forces, etc.).
Example: FixFreeze.
\item reading/writing data. Example: FixRestart.
\item implementing boundary conditions. Example: FixWall.
\item saving information about particles for future use (previous positions,
\item saving information about particles for future use (previous positions,
for instance). Example: FixStoreState.
\end{itemize}
All fixes are derived from class Fix and must have constructor with the
All fixes are derived from class Fix and must have constructor with the
signature: FixMine(class LAMMPS *, int, char **).
Every fix must be registered in LAMMPS by writing the following lines
@ -478,7 +478,7 @@ included in the file "style\_fix.h". In case if you use LAMMPS make,
this file is generated automatically - all files starting with prefix
fix\_ are included, so call your header the same way. Otherwise, don<6F>t
forget to add your include into "style\_fix.h".
Let's write a simple fix which will print average velocity at the end
of each timestep. First of all, implement a constructor:
@ -487,11 +487,11 @@ of each timestep. First of all, implement a constructor:
FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
: Fix(lmp, narg, arg)
{
if (narg < 4)
if (narg < 4)
error->all(FLERR,"Illegal fix print command");
nevery = atoi(arg[3]);
if (nevery <= 0)
if (nevery <= 0)
error->all(FLERR,"Illegal fix print command");
}
\end{verbatim}
@ -545,7 +545,7 @@ void FixPrintVel::end_of_step()
{
// for add3, scale3
using namespace MathExtra;
double** v = atom->v;
int nlocal = atom->nlocal;
double localAvgVel[4]; // 4th element for particles count
@ -559,7 +559,7 @@ void FixPrintVel::end_of_step()
MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
scale3(1.0 / globalAvgVel[3], globalAvgVel);
if (comm->me == 0) {
printf("\%e, \%e, \%e\n",
printf("\%e, \%e, \%e\n",
globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
}
}
@ -607,14 +607,15 @@ this situation there are several methods which should be implemented:
\begin{itemize}
\item \verb|double memory_usage| - return how much memory fix uses
\item \verb|void grow_arrays(int)| - do reallocation of the per particle arrays
\item \verb|void grow_arrays(int)| - do reallocation of the per particle arrays
in your fix
\item \verb|void copy_arrays(int i, int j)| - copy i-th per-particle information
to j-th. Used when atoms sorting is performed
\item \verb|void copy_arrays(int i, int j, int delflag)| - copy i-th per-particle
information to j-th. Used when atoms sorting is performed. if delflag is set
and atom j owns a body, move the body information to atom i.
\item \verb|void set_arrays(int i)| - sets i-th particle related information to zero
\end{itemize}
Note, that if your class implements these methods, it must call add calls of
Note, that if your class implements these methods, it must call add calls of
add\_callback and delete\_callback to constructor and destructor:
\begin{center}
@ -654,7 +655,7 @@ void FixSavePos::grow_arrays(int nmax)
memory->grow(this->x, nmax, 3, "FixSavePos:x");
}
void FixSavePos::copy_arrays(int i, int j)
void FixSavePos::copy_arrays(int i, int j, int delflag)
{
memcpy(this->x[j], this->x[i], sizeof(double) * 3);
}
@ -670,7 +671,7 @@ int FixSavePos::pack_exchange(int i, double *buf)
buf[m++] = x[i][0];
buf[m++] = x[i][1];
buf[m++] = x[i][2];
return m;
}

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9
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@ -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}

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33
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@ -0,0 +1,33 @@
\documentclass[aps,pr,onecolumn,superscriptaddress,noshowpacs,a4paper,15pt]{revtex4}
\pdfoutput=1
\bibliographystyle{apsrev4}
\usepackage{color}
\usepackage{dcolumn} %Align table columns on decimal point
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{graphicx}
\usepackage[pdftex]{hyperref}
\hypersetup{colorlinks=true,citecolor=blue,linkcolor=red,urlcolor=blue}
\usepackage[all]{hypcap}
\newcommand{\red}{\color{red}}
\newcommand{\blue}{\color{blue}}
\definecolor{green}{rgb}{0,0.5,0}
\newcommand{\green}{\color{green}}
\newcommand{\white}{\color{white}}
%\newcommand{\cite}[1]{\hspace{-1 ex} % \nocite{#1}\citenum{#1}}
\thickmuskip=0.5\thickmuskip %shorter spaces in math
\begin{document}
\begingroup
\Large
\begin{eqnarray*}
E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\[15pt]
V_{ij} & = & {\rm Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\[15pt]
{\rm Tap}(r_{ij}) & = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
\end{eqnarray*}
\endgroup
\end{document}

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@ -0,0 +1,42 @@
\documentclass[aps,pr,onecolumn,superscriptaddress,noshowpacs,a4paper,15pt]{revtex4}
\pdfoutput=1
\bibliographystyle{apsrev4}
\usepackage{color}
\usepackage{dcolumn} %Align table columns on decimal point
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{graphicx}
\usepackage[pdftex]{hyperref}
\hypersetup{colorlinks=true,citecolor=blue,linkcolor=red,urlcolor=blue}
\usepackage[all]{hypcap}
\newcommand{\red}{\color{red}}
\newcommand{\blue}{\color{blue}}
\definecolor{green}{rgb}{0,0.5,0}
\newcommand{\green}{\color{green}}
\newcommand{\white}{\color{white}}
%\newcommand{\cite}[1]{\hspace{-1 ex} % \nocite{#1}\citenum{#1}}
\thickmuskip=0.5\thickmuskip %shorter spaces in math
%
\begin{document}
%
\begingroup
\Large
\begin{eqnarray*}
E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\[15pt]
V_{ij} & = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
\left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
\frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
\cdot \frac{C_6}{r^6_{ij}} \right \}\\[15pt]
\rho_{ij}^2 & = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\[15pt]
\rho_{ji}^2 & = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\[15pt]
f(\rho) & = & C e^{ -( \rho / \delta )^2 }\\[15pt]
{\rm Tap}(r_{ij}) & = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
\end{eqnarray*}
\endgroup
%
\end{document}
%

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@ -0,0 +1,33 @@
\documentclass[aps,pr,onecolumn,superscriptaddress,noshowpacs,a4paper,15pt]{revtex4}
\pdfoutput=1
\bibliographystyle{apsrev4}
\usepackage{color}
\usepackage{dcolumn} %Align table columns on decimal point
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{graphicx}
\usepackage[pdftex]{hyperref}
\hypersetup{colorlinks=true,citecolor=blue,linkcolor=red,urlcolor=blue}
\usepackage[all]{hypcap}
\newcommand{\red}{\color{red}}
\newcommand{\blue}{\color{blue}}
\definecolor{green}{rgb}{0,0.5,0}
\newcommand{\green}{\color{green}}
\newcommand{\white}{\color{white}}
%\newcommand{\cite}[1]{\hspace{-1 ex} % \nocite{#1}\citenum{#1}}
\thickmuskip=0.5\thickmuskip %shorter spaces in math
\begin{document}
\begingroup
\Large
\begin{eqnarray*}
E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\[15pt]
V_{ij} & = & e^{-\lambda (r_{ij} -z_0)} \left [ C + f(\rho_{ij}) + f(\rho_{ji}) - A \left ( \frac{r_{ij}}{z_0}\right )^{-6} \right ] \\
\rho_{ij}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{i})^2 \\[15pt]
\rho_{ji}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{j})^2 \\[15pt]
f(\rho) & = & e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { \rho/\delta }^{2n}
\end{eqnarray*}
\endgroup
\end{document}

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14
doc/src/Eqs/pair_ufm.tex Normal file
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@ -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}

16
doc/src/Manual.txt
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@ -1,9 +1,9 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="22 Sep 2017 version">
<META NAME="docnumber" CONTENT="20 Apr 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.">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
<BODY>
@ -18,12 +18,10 @@
:line
<H1></H1>
LAMMPS Documentation :c,h1
20 Apr 2018 version :c,h2
LAMMPS Documentation :c,h3
22 Sep 2017 version :c,h4
Version info: :h4
Version info: :h3
The LAMMPS "version" is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
@ -176,11 +174,11 @@ 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

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10
doc/src/Section_accelerate.txt
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@ -8,7 +8,7 @@ Section"_Section_howto.html :c
:line
5. Accelerating LAMMPS performance :h3
5. Accelerating LAMMPS performance :h2
This section describes various methods for improving LAMMPS
performance for different classes of problems running on different
@ -41,7 +41,7 @@ compute nodes, on different hardware platforms.
:line
:line
5.1 Measuring performance :h4,link(acc_1)
5.1 Measuring performance :h3,link(acc_1)
Before trying to make your simulation run faster, you should
understand how it currently performs and where the bottlenecks are.
@ -89,7 +89,7 @@ LAMMPS, to obtain synchronized timings.
:line
5.2 General strategies :h4,link(acc_2)
5.2 General strategies :h3,link(acc_2)
NOTE: this section 5.2 is still a work in progress
@ -141,7 +141,7 @@ when using a barostat.
:line
5.3 Packages with optimized styles :h4,link(acc_3)
5.3 Packages with optimized styles :h3,link(acc_3)
Accelerated versions of various "pair_style"_pair_style.html,
"fixes"_fix.html, "computes"_compute.html, and other commands have
@ -325,7 +325,7 @@ restrictions :ul
:line
5.4 Comparison of various accelerator packages :h4,link(acc_4)
5.4 Comparison of various accelerator packages :h3,link(acc_4)
NOTE: this section still needs to be re-worked with additional KOKKOS
and USER-INTEL information.

94
doc/src/Section_commands.txt
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@ -6,7 +6,7 @@
:line
3. Commands :h3
3. Commands :h2
This section describes how a LAMMPS input script is formatted and the
input script commands used to define a LAMMPS simulation.
@ -190,7 +190,7 @@ allowed, but that should be sufficient for most use cases.
:line
3.3 Input script structure :h4,link(cmd_3)
3.3 Input script structure :h3,link(cmd_3)
This section describes the structure of a typical LAMMPS input script.
The "examples" directory in the LAMMPS distribution contains many
@ -414,7 +414,7 @@ Input script control:
:line
3.5 Individual commands :h4,link(cmd_5),link(comm)
3.5 Individual commands :h3,link(cmd_5),link(comm)
This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The "previous
@ -497,6 +497,7 @@ in the command's documentation.
"region"_region.html,
"replicate"_replicate.html,
"rerun"_rerun.html,
"reset_ids"_reset_ids.html,
"reset_timestep"_reset_timestep.html,
"restart"_restart.html,
"run"_run.html,
@ -537,7 +538,7 @@ package"_Section_start.html#start_3.
:line
Fix styles :h4
Fix styles :h3
See the "fix"_fix.html command for one-line descriptions of each style
or click on the style itself for a full description. Some of the
@ -619,8 +620,9 @@ 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 +639,10 @@ 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 +670,7 @@ 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,
@ -682,15 +684,16 @@ package"_Section_start.html#start_3.
"addtorque"_fix_addtorque.html,
"atc"_fix_atc.html,
"ave/correlate/long"_fix_ave_correlate_long.html,
"bond/react"_fix_bond_react.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,
@ -710,17 +713,17 @@ package"_Section_start.html#start_3.
"mvv/dpd"_fix_mvv_dpd.html,
"mvv/edpd"_fix_mvv_dpd.html,
"mvv/tdpd"_fix_mvv_dpd.html,
"nve/dot"_fix_nve_dot.html,
"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
"nvk"_fix_nvk.html,
"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
"nph/eff"_fix_nh_eff.html,
"npt/eff"_fix_nh_eff.html,
"nve/eff"_fix_nve_eff.html,
"nvt/eff"_fix_nh_eff.html,
"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
"npt/uef"_fix_nh_uef.html,
"nve/dot"_fix_nve_dot.html,
"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
"nve/eff"_fix_nve_eff.html,
"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
"nvk"_fix_nvk.html,
"nvt/eff"_fix_nh_eff.html,
"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
"nvt/uef"_fix_nh_uef.html,
"phonon"_fix_phonon.html,
"pimd"_fix_pimd.html,
@ -728,12 +731,12 @@ 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,
@ -750,7 +753,7 @@ package"_Section_start.html#start_3.
:line
Compute styles :h4
Compute styles :h3
See the "compute"_compute.html command for one-line descriptions of
each style or click on the style itself for a full description. Some
@ -893,7 +896,7 @@ package"_Section_start.html#start_3.
:line
Pair_style potentials :h4
Pair_style potentials :h3
See the "pair_style"_pair_style.html command for an overview of pair
potentials. Click on the style itself for a full description. Many
@ -906,7 +909,7 @@ 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,
@ -920,6 +923,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"born/coul/long/cs"_pair_born.html,
"born/coul/msm (o)"_pair_born.html,
"born/coul/wolf (go)"_pair_born.html,
"born/coul/wolf/cs"_pair_born.html,
"brownian (o)"_pair_brownian.html,
"brownian/poly (o)"_pair_brownian.html,
"buck (giko)"_pair_buck.html,
@ -939,6 +943,7 @@ KOKKOS, o = USER-OMP, t = OPT.
"coul/msm"_pair_coul.html,
"coul/streitz"_pair_coul.html,
"coul/wolf (ko)"_pair_coul.html,
"coul/wolf/cs"_pair_coul.html,
"dpd (gio)"_pair_dpd.html,
"dpd/tstat (go)"_pair_dpd.html,
"dsmc"_pair_dsmc.html,
@ -975,6 +980,7 @@ 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,
@ -1008,7 +1014,7 @@ 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,
@ -1019,11 +1025,12 @@ 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
@ -1035,15 +1042,19 @@ package"_Section_start.html#start_3.
"coul/cut/soft (o)"_pair_lj_soft.html,
"coul/diel (o)"_pair_coul_diel.html,
"coul/long/soft (o)"_pair_lj_soft.html,
"coul/shield"_pair_coul_shield.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,
"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html,
"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
"lennard/mdf"_pair_mdf.html,
"list"_pair_list.html,
@ -1068,7 +1079,7 @@ 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,
@ -1085,6 +1096,7 @@ 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,
@ -1092,7 +1104,7 @@ 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,
@ -1100,7 +1112,7 @@ package"_Section_start.html#start_3.
:line
Bond_style potentials :h4
Bond_style potentials :h3
See the "bond_style"_bond_style.html command for an overview of bond
potentials. Click on the style itself for a full description. Some
@ -1134,7 +1146,7 @@ package"_Section_start.html#start_3.
:line
Angle_style potentials :h4
Angle_style potentials :h3
See the "angle_style"_angle_style.html command for an overview of
angle potentials. Click on the style itself for a full description.
@ -1170,7 +1182,7 @@ package"_Section_start.html#start_3.
:line
Dihedral_style potentials :h4
Dihedral_style potentials :h3
See the "dihedral_style"_dihedral_style.html command for an overview
of dihedral potentials. Click on the style itself for a full
@ -1204,7 +1216,7 @@ package"_Section_start.html#start_3.
:line
Improper_style potentials :h4
Improper_style potentials :h3
See the "improper_style"_improper_style.html command for an overview
of improper potentials. Click on the style itself for a full
@ -1233,7 +1245,7 @@ package"_Section_start.html#start_3.
:line
Kspace solvers :h4
Kspace solvers :h3
See the "kspace_style"_kspace_style.html command for an overview of
Kspace solvers. Click on the style itself for a full description.
@ -1247,7 +1259,7 @@ 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,

48
doc/src/Section_errors.txt
View File

@ -8,7 +8,7 @@ Section"_Section_history.html :c
:line
12. Errors :h3
12. Errors :h2
This section describes the errors you can encounter when using LAMMPS,
either conceptually, or as printed out by the program.
@ -167,7 +167,7 @@ As a last resort, you can send an email directly to the
:line
12.3 Error & warning messages :h4,link(err_3)
12.3 Error & warning messages :h3,link(err_3)
These are two alphabetic lists of the "ERROR"_#error and
"WARNING"_#warn messages LAMMPS prints out and the reason why. If the
@ -186,7 +186,7 @@ packages"_Section_start.html#start_3 are not listed here. If such an
error occurs and is not self-explanatory, you'll need to look in the
source code or contact the author of the package.
Errors: :h4,link(error)
Errors: :h3,link(error)
:dlb
@ -1565,15 +1565,6 @@ This operation is not allowed. :dd
This operation is not allowed. :dd
{Cannot use -cuda on and -kokkos on together} :dt
This is not allowed since both packages can use GPUs. :dd
{Cannot use -cuda on without USER-CUDA installed} :dt
The USER-CUDA package must be installed via "make yes-user-cuda"
before LAMMPS is built. :dd
{Cannot use -kokkos on without KOKKOS installed} :dt
Self-explanatory. :dd
@ -1597,11 +1588,6 @@ solver/pair style. :dd
This is a current restriction of this command. :dd
{Cannot use GPU package with USER-CUDA package enabled} :dt
You cannot use both the GPU and USER-CUDA packages
together. Use one or the other. :dd
{Cannot use Kokkos pair style with rRESPA inner/middle} :dt
Self-explanatory. :dd
@ -8252,12 +8238,6 @@ Self-explanatory. :dd
The package command cannot be used afer a read_data, read_restart, or
create_box command. :dd
{Package cuda command without USER-CUDA package enabled} :dt
The USER-CUDA package must be installed via "make yes-user-cuda"
before LAMMPS is built, and the "-c on" must be used to enable the
package. :dd
{Package gpu command without GPU package installed} :dt
The GPU package must be installed via "make yes-gpu" before LAMMPS is
@ -10230,22 +10210,6 @@ it in different ways. :dd
Self-explanatory. :dd
{USER-CUDA mode requires CUDA variant of min style} :dt
CUDA mode is enabled, so the min style must include a cuda suffix. :dd
{USER-CUDA mode requires CUDA variant of run style} :dt
CUDA mode is enabled, so the run style must include a cuda suffix. :dd
{USER-CUDA package does not yet support comm_style tiled} :dt
Self-explanatory. :dd
{USER-CUDA package requires a cuda enabled atom_style} :dt
Self-explanatory. :dd
{Unable to initialize accelerator for use} :dt
There was a problem initializing an accelerator for the gpu package :dd
@ -10494,10 +10458,6 @@ Must use remap v option with fix deform with this pair style. :dd
If fix deform is used, the remap v option is required. :dd
{Using suffix cuda without USER-CUDA package enabled} :dt
Self-explanatory. :dd
{Using suffix gpu without GPU package installed} :dt
Self-explanatory. :dd
@ -11037,7 +10997,7 @@ Self-explanatory. :dd
:dle
Warnings: :h4,link(warn)
Warnings: :h3,link(warn)
:dlb

6
doc/src/Section_example.txt
View File

@ -6,7 +6,7 @@
:line
7. Example problems :h3
7. Example problems :h2
The LAMMPS distribution includes an examples sub-directory with many
sample problems. Many are 2d models that run quickly are are
@ -46,7 +46,7 @@ Lists of both kinds of directories are given below.
:line
Lowercase directories :h4
Lowercase directories :h3
accelerate: run with various acceleration options (OpenMP, GPU, Phi)
airebo: polyethylene with AIREBO potential
@ -122,7 +122,7 @@ browser.
:line
Uppercase directories :h4
Uppercase directories :h3
ASPHERE: various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc
COUPLE: examples of how to use LAMMPS as a library

6
doc/src/Section_history.txt
View File

@ -8,7 +8,7 @@ Section"_Manual.html :c
:line
13. Future and history :h3
13. Future and history :h2
This section lists features we plan to add to LAMMPS, features of
previous versions of LAMMPS, and features of other parallel molecular
@ -20,7 +20,7 @@ dynamics codes our group has distributed.
:line
:line
13.1 Coming attractions :h4,link(hist_1)
13.1 Coming attractions :h3,link(hist_1)
As of summer 2016 we are using the "LAMMPS project issue tracker
on GitHub"_https://github.com/lammps/lammps/issues for keeping
@ -46,7 +46,7 @@ if you want to have your suggestion added to the list.
:line
13.2 Past versions :h4,link(hist_2)
13.2 Past versions :h3,link(hist_2)
LAMMPS development began in the mid 1990s under a cooperative research
& development agreement (CRADA) between two DOE labs (Sandia and LLNL)

184
doc/src/Section_howto.txt
View File

@ -6,7 +6,7 @@
:line
6. How-to discussions :h3
6. How-to discussions :h2
This section describes how to perform common tasks using LAMMPS.
@ -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
@ -1058,7 +1058,7 @@ Example input scripts for these kinds of models are in the body,
colloid, dipole, ellipse, line, peri, pour, and tri directories of the
"examples directory"_Section_example.html in the LAMMPS distribution.
Atom styles :h5
Atom styles :h4
There are several "atom styles"_atom_style.html that allow for
definition of finite-size particles: sphere, dipole, ellipsoid, line,
@ -1140,7 +1140,7 @@ ellipses. This means they have the same moment of inertia as the 3d
object. When temperature is computed, the correct degrees of freedom
are used for rotation in a 2d versus 3d system.
Pair potentials :h5
Pair potentials :h4
When a system with finite-size particles is defined, the particles
will only rotate and experience torque if the force field computes
@ -1168,7 +1168,7 @@ Brownian and lubrication potentials are used with spherical particles.
The line, tri, and body potentials are used with line segment,
triangular, and body particles respectively.
Time integration :h5
Time integration :h4
There are several fixes that perform time integration on finite-size
spherical particles, meaning the integrators update the rotational
@ -1204,7 +1204,7 @@ Note that for mixtures of point and finite-size particles, these
integration fixes can only be used with "groups"_group.html which
contain finite-size particles.
Computes, thermodynamics, and dump output :h5
Computes, thermodynamics, and dump output :h4
There are several computes that calculate the temperature or
rotational energy of spherical or ellipsoidal particles:
@ -1236,7 +1236,7 @@ angular momentum, the quaternion, the torque, the end-point and
corner-point coordinates (for line and tri particles), and
sub-particle attributes of body particles.
Rigid bodies composed of finite-size particles :h5
Rigid bodies composed of finite-size particles :h4
The "fix rigid"_fix_rigid.html command treats a collection of
particles as a rigid body, computes its inertia tensor, sums the total
@ -1319,7 +1319,7 @@ to output and the kind of data they operate on and produce:
"Variables that generate values to output"_#variable
"Summary table of output options and data flow between commands"_#table :ul
Global/per-atom/local data :h5,link(global)
Global/per-atom/local data :h4,link(global)
Various output-related commands work with three different styles of
data: global, per-atom, or local. A global datum is one or more
@ -1329,7 +1329,7 @@ atom. Local datums are calculated by each processor based on the
atoms it owns, but there may be zero or more per atom, e.g. a list of
bond distances.
Scalar/vector/array data :h5,link(scalar)
Scalar/vector/array data :h4,link(scalar)
Global, per-atom, and local datums can each come in three kinds: a
single scalar value, a vector of values, or a 2d array of values. The
@ -1352,7 +1352,7 @@ the dimension twice (array -> scalar). Thus a command that uses
scalar values as input can typically also process elements of a vector
or array.
Thermodynamic output :h5,link(thermo)
Thermodynamic output :h4,link(thermo)
The frequency and format of thermodynamic output is set by the
"thermo"_thermo.html, "thermo_style"_thermo_style.html, and
@ -1377,7 +1377,7 @@ intensive values; you can include a division by "natoms" in the
formula if desired, to make an extensive calculation produce an
intensive result.
Dump file output :h5,link(dump)
Dump file output :h4,link(dump)
Dump file output is specified by the "dump"_dump.html and
"dump_modify"_dump_modify.html commands. There are several
@ -1401,7 +1401,7 @@ provides the values to be output. In each case, the compute or fix
must generate local values for input to the "dump local"_dump.html
command.
Fixes that write output files :h5,link(fixoutput)
Fixes that write output files :h4,link(fixoutput)
Several fixes take various quantities as input and can write output
files: "fix ave/time"_fix_ave_time.html, "fix
@ -1455,7 +1455,7 @@ values for a specific atom. Thus the "fix print"_fix_print.html
command is a means to output a wide variety of quantities separate
from normal thermodynamic or dump file output.
Computes that process output quantities :h5,link(computeoutput)
Computes that process output quantities :h4,link(computeoutput)
The "compute reduce"_compute_reduce.html and "compute
reduce/region"_compute_reduce.html commands take one or more per-atom
@ -1481,7 +1481,7 @@ info, etc) and stores the values in a local vector or array. These
are produced as output values which can be used as input to other
output commands.
Fixes that process output quantities :h5,link(fixprocoutput)
Fixes that process output quantities :h4,link(fixprocoutput)
The "fix vector"_fix_vector.html command can create global vectors as
output from global scalars as input, accumulating them one element at
@ -1503,7 +1503,7 @@ including per-atom quantities calculated by a "compute"_compute.html,
by a "fix"_fix.html, or by an atom-style "variable"_variable.html.
The output of this fix can be used as input to other output commands.
Computes that generate values to output :h5,link(compute)
Computes that generate values to output :h4,link(compute)
Every "compute"_compute.html in LAMMPS produces either global or
per-atom or local values. The values can be scalars or vectors or
@ -1513,7 +1513,7 @@ describes what it produces. Computes that produce per-atom or local
values have the word "atom" or "local" in their style name. Computes
without the word "atom" or "local" produce global values.
Fixes that generate values to output :h5,link(fix)
Fixes that generate values to output :h4,link(fix)
Some "fixes"_fix.html in LAMMPS produces either global or per-atom or
local values which can be accessed by other commands. The values can
@ -1522,7 +1522,7 @@ using the other commands described in this section. The doc page for
each fix command tells whether it produces any output quantities and
describes them.
Variables that generate values to output :h5,link(variable)
Variables that generate values to output :h4,link(variable)
"Variables"_variable.html defined in an input script can store one or
more strings. But equal-style, vector-style, and atom-style or
@ -1534,7 +1534,7 @@ computes, fixes, and other variables. The values generated by
variables can be used as input to and thus output by the other
commands described in this section.
Summary table of output options and data flow between commands :h5,link(table)
Summary table of output options and data flow between commands :h4,link(table)
This table summarizes the various commands that can be used for
generating output from LAMMPS. Each command produces output data of
@ -1856,9 +1856,21 @@ internal LAMMPS operations. Note that LAMMPS classes are defined
within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
application.
Library.cpp contains these functions for creating and destroying an
instance of LAMMPS and sending it commands to execute. See the
documentation in the src/library.cpp file for details:
The examples/COUPLE and python/examples directories have example C++
and C and Python codes which show how a driver code can link to LAMMPS
as a library, run LAMMPS on a subset of processors, grab data from
LAMMPS, change it, and put it back into LAMMPS.
The file src/library.cpp contains the following functions for creating
and destroying an instance of LAMMPS and sending it commands to
execute. See the documentation in the src/library.cpp file for
details.
NOTE: You can write code for additional functions as needed to define
how your code talks to LAMMPS and add them to src/library.cpp and
src/library.h, as well as to the "Python
interface"_Section_python.html. The added functions can access or
change any internal LAMMPS data you wish.
void lammps_open(int, char **, MPI_Comm, void **)
void lammps_open_no_mpi(int, char **, void **)
@ -1932,11 +1944,12 @@ the library allocated previously via other function calls. See
comments in src/library.cpp file for which other functions need this
clean-up.
Library.cpp also contains these functions for extracting information
from LAMMPS and setting value within LAMMPS. Again, see the
documentation in the src/library.cpp file for details, including
The file src/library.cpp also contains these functions for extracting
information from LAMMPS and setting value within LAMMPS. Again, see
the documentation in the src/library.cpp file for details, including
which quantities can be queried by name:
int lammps_extract_setting(void *, char *)
void *lammps_extract_global(void *, char *)
void lammps_extract_box(void *, double *, double *,
double *, double *, double *, int *, int *)
@ -1945,55 +1958,77 @@ void *lammps_extract_compute(void *, char *, int, int)
void *lammps_extract_fix(void *, char *, int, int, int, int)
void *lammps_extract_variable(void *, char *, char *) :pre
void lammps_reset_box(void *, double *, double *, double, double, double)
int lammps_set_variable(void *, char *, char *) :pre
The extract_setting() function returns info on the size
of data types (e.g. 32-bit or 64-bit atom IDs) used
by the LAMMPS executable (a compile-time choice).
The other extract functions return a pointer to various global or
per-atom quantities stored in LAMMPS or to values calculated by a
compute, fix, or variable. The pointer returned by the
extract_global() function can be used as a permanent reference to a
value which may change. For the extract_atom() method, see the
extract() method in the src/atom.cpp file for a list of valid per-atom
properties. New names could easily be added if the property you want
is not listed. For the other extract functions, the underlying
storage may be reallocated as LAMMPS runs, so you need to re-call the
function to assure a current pointer or returned value(s).
double lammps_get_thermo(void *, char *)
int lammps_get_natoms(void *)
void lammps_gather_atoms(void *, double *)
void lammps_scatter_atoms(void *, double *) :pre
void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
imageint *, int) :pre
int lammps_get_natoms(void *) :pre
The extract functions return a pointer to various global or per-atom
quantities stored in LAMMPS or to values calculated by a compute, fix,
or variable. The pointer returned by the extract_global() function
can be used as a permanent reference to a value which may change. For
the extract_atom() method, see the extract() method in the
src/atom.cpp file for a list of valid per-atom properties. New names
could easily be added if the property you want is not listed. For the
other extract functions, the underlying storage may be reallocated as
LAMMPS runs, so you need to re-call the function to assure a current
pointer or returned value(s).
The lammps_reset_box() function resets the size and shape of the
simulation box, e.g. as part of restoring a previously extracted and
saved state of a simulation.
The lammps_set_variable() function can set an existing string-style
variable to a new string value, so that subsequent LAMMPS commands can
access the variable.
int lammps_set_variable(void *, char *, char *)
void lammps_reset_box(void *, double *, double *, double, double, double) :pre
The lammps_get_thermo() function returns the current value of a thermo
keyword as a double precision value.
The lammps_get_natoms() function returns the total number of atoms in
the system and can be used by the caller to allocate space for the
lammps_gather_atoms() and lammps_scatter_atoms() functions. The
gather function collects peratom info of the requested type (atom
coords, types, forces, etc) from all processors, orders them by atom
ID, and returns a full list to each calling processor. The scatter
function does the inverse. It distributes the same peratom values,
passed by the caller, to each atom owned by individual processors.
Both methods are thus a means to extract or assign (overwrite) any
peratom quantities within LAMMPS. See the extract() method in the
src/atom.cpp file for a list of valid per-atom properties. New names
could easily be added if the property you want is not listed.
A special treatment is applied for accessing image flags via the
"image" property. Image flags are stored in a packed format with all
three image flags stored in a single integer. When signaling to access
the image flags as 3 individual values per atom instead of 1, the data
is transparently packed or unpacked by the library interface.
the system and can be used by the caller to allocate memory for the
lammps_gather_atoms() and lammps_scatter_atoms() functions.
The lammps_set_variable() function can set an existing string-style
variable to a new string value, so that subsequent LAMMPS commands can
access the variable.
The lammps_reset_box() function resets the size and shape of the
simulation box, e.g. as part of restoring a previously extracted and
saved state of a simulation.
void lammps_gather_atoms(void *, char *, int, int, void *)
void lammps_gather_atoms_concat(void *, char *, int, int, void *)
void lammps_gather_atoms_subset(void *, char *, int, int, int, int *, void *)
void lammps_scatter_atoms(void *, char *, int, int, void *)
void lammps_scatter_atoms_subset(void *, char *, int, int, int, int *, void *) :pre
void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
imageint *, int) :pre
The gather functions collect peratom info of the requested type (atom
coords, atom types, forces, etc) from all processors, and returns the
same vector of values to each callling processor. The scatter
functions do the inverse. They distribute a vector of peratom values,
passed by all calling processors, to invididual atoms, which may be
owned by different processos.
The lammps_gather_atoms() function does this for all N atoms in the
system, ordered by atom ID, from 1 to N. The
lammps_gather_atoms_concat() function does it for all N atoms, but
simply concatenates the subset of atoms owned by each processor. The
resulting vector is not ordered by atom ID. Atom IDs can be requetsed
by the same function if the caller needs to know the ordering. The
lammps_gather_subset() function allows the caller to request values
for only a subset of atoms (identified by ID).
For all 3 gather function, per-atom image flags can be retrieved in 2 ways.
If the count is specified as 1, they are returned
in a packed format with all three image flags stored in a single integer.
If the count is specified as 3, the values are unpacked into xyz flags
by the library before returning them.
The lammps_scatter_atoms() function takes a list of values for all N
atoms in the system, ordered by atom ID, from 1 to N, and assigns
those values to each atom in the system. The
lammps_scatter_atoms_subset() function takes a subset of IDs as an
argument and only scatters those values to the owning atoms.
The lammps_create_atoms() function takes a list of N atoms as input
with atom types and coords (required), an optionally atom IDs and
@ -2005,17 +2040,6 @@ of a simulation. Additional properties for the new atoms can then be
assigned via the lammps_scatter_atoms() or lammps_extract_atom()
functions.
The examples/COUPLE and python directories have example C++ and C and
Python codes which show how a driver code can link to LAMMPS as a
library, run LAMMPS on a subset of processors, grab data from LAMMPS,
change it, and put it back into LAMMPS.
NOTE: You can write code for additional functions as needed to define
how your code talks to LAMMPS and add them to src/library.cpp and
src/library.h, as well as to the "Python
interface"_Section_python.html. The added functions can access or
change any LAMMPS data you wish.
:line
6.20 Calculating thermal conductivity :link(howto_20),h4
@ -2264,7 +2288,7 @@ Here, each of the 3 kinds of chunk-related commands is briefly
overviewed. Then some examples are given of how to compute different
properties with chunk commands.
Compute chunk/atom command: :h5
Compute chunk/atom command: :h4
This compute can assign atoms to chunks of various styles. Only atoms
in the specified group and optional specified region are assigned to a
@ -2303,7 +2327,7 @@ do this. You can also define a "per-atom variable"_variable.html in
the input script that uses a formula to generate a chunk ID for each
atom.
Fix ave/chunk command: :h5
Fix ave/chunk command: :h4
This fix takes the ID of a "compute
chunk/atom"_compute_chunk_atom.html command as input. For each chunk,
@ -2320,7 +2344,7 @@ values to be time-averaged in various ways, and output to a file. The
fix produces a global array as output with one row of values per
chunk.
Compute */chunk commands: :h5
Compute */chunk commands: :h4
Currently the following computes operate on chunks of atoms to produce
per-chunk values.
@ -2365,7 +2389,7 @@ variables"_variable.html, like sum() and max(). E.g. to find the
largest cluster or fastest diffusing molecule. :l
:ule
Example calculations with chunks :h5
Example calculations with chunks :h4
Here are examples using chunk commands to calculate various
properties:

47
doc/src/Section_intro.txt
View File

@ -6,7 +6,7 @@
:line
1. Introduction :h3
1. Introduction :h2
This section provides an overview of what LAMMPS can and can't do,
describes what it means for LAMMPS to be an open-source code, and
@ -97,7 +97,7 @@ favorite interatomic potential, boundary condition, or atom type, see
"Section 10"_Section_modify.html, which describes how you can add
it to LAMMPS.
General features :h5
General features :h4
runs on a single processor or in parallel
distributed-memory message-passing parallelism (MPI)
@ -114,7 +114,7 @@ General features :h5
build as library, invoke LAMMPS thru library interface or provided Python wrapper
couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
Particle and model types :h5
Particle and model types :h4
("atom style"_atom_style.html command)
atoms
@ -130,7 +130,7 @@ Particle and model types :h5
rigid collections of particles
hybrid combinations of these :ul
Force fields :h5
Force fields :h4
("pair style"_pair_style.html, "bond style"_bond_style.html,
"angle style"_angle_style.html, "dihedral style"_dihedral_style.html,
"improper style"_improper_style.html, "kspace style"_kspace_style.html
@ -169,7 +169,7 @@ commands)
potentials can be used in one simulation
overlaid potentials: superposition of multiple pair potentials :ul
Atom creation :h5
Atom creation :h4
("read_data"_read_data.html, "lattice"_lattice.html,
"create_atoms"_create_atoms.html, "delete_atoms"_delete_atoms.html,
"displace_atoms"_displace_atoms.html, "replicate"_replicate.html commands)
@ -180,7 +180,7 @@ Atom creation :h5
replicate existing atoms multiple times
displace atoms :ul
Ensembles, constraints, and boundary conditions :h5
Ensembles, constraints, and boundary conditions :h4
("fix"_fix.html command)
2d or 3d systems
@ -198,7 +198,7 @@ Ensembles, constraints, and boundary conditions :h5
non-equilibrium molecular dynamics (NEMD)
variety of additional boundary conditions and constraints :ul
Integrators :h5
Integrators :h4
("run"_run.html, "run_style"_run_style.html, "minimize"_minimize.html commands)
velocity-Verlet integrator
@ -208,11 +208,11 @@ Integrators :h5
rRESPA hierarchical timestepping
rerun command for post-processing of dump files :ul
Diagnostics :h5
Diagnostics :h4
see the various flavors of the "fix"_fix.html and "compute"_compute.html commands :ul
Output :h5
Output :h4
("dump"_dump.html, "restart"_restart.html commands)
log file of thermodynamic info
@ -225,14 +225,14 @@ Output :h5
time averaging of system-wide quantities
atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul
Multi-replica models :h5
Multi-replica models :h4
"nudged elastic band"_neb.html
"parallel replica dynamics"_prd.html
"temperature accelerated dynamics"_tad.html
"parallel tempering"_temper.html
Pre- and post-processing :h5
Pre- and post-processing :h4
Various pre- and post-processing serial tools are packaged
with LAMMPS; see these "doc pages"_Section_tools.html. :ulb,l
@ -247,7 +247,7 @@ Pizza.py WWW site"_pizza. :l
:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
:link(python,http://www.python.org)
Specialized features :h5
Specialized features :h4
LAMMPS can be built with optional packages which implement a variety
of additional capabilities. An overview of all the packages is "given
@ -468,7 +468,7 @@ encouraged. :l
:line
1.5 Acknowledgments and citations :h4,link(intro_5)
1.5 Acknowledgments and citations :h3,link(intro_5)
LAMMPS development has been funded by the "US Department of
Energy"_doe (DOE), through its CRADA, LDRD, ASCI, and Genomes-to-Life
@ -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
Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential
Mike Brown (ORNL), brownw at ornl.gov, GPU and USER-INTEL package
Greg Wagner (Sandia), gjwagne at sandia.gov, MEAM package for MEAM potential (superseded by USER-MEAMC)
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 (obsoleted by KOKKOS) 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
Christoph Kloss (JKU), Christoph.Kloss at jku.at, LIGGGHTS fork 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

2
doc/src/Section_modify.txt
View File

@ -8,7 +8,7 @@ Section"_Section_python.html :c
:line
10. Modifying & extending LAMMPS :h3
10. Modifying & extending LAMMPS :h2
This section describes how to customize LAMMPS by modifying
and extending its source code.

59
doc/src/Section_packages.txt
View File

@ -8,7 +8,7 @@ Section"_Section_accelerate.html :c
:line
4. Packages :h3
4. Packages :h2
This section gives an overview of the optional packages that extend
LAMMPS functionality with instructions on how to build LAMMPS with
@ -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)

2
doc/src/Section_perf.txt
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@ -6,7 +6,7 @@
:line
8. Performance & scalability :h3
8. Performance & scalability :h2
Current LAMMPS performance is discussed on the Benchmarks page of the
"LAMMPS WWW Site"_lws where CPU timings and parallel efficiencies are

131
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@ -6,7 +6,7 @@
:line
11. Python interface to LAMMPS :h3
11. Python interface to LAMMPS :h2
LAMMPS can work together with Python in three ways. First, Python can
wrap LAMMPS through the "LAMMPS library
@ -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
@ -443,7 +443,7 @@ If an error occurs, carefully go thru the steps in "Section
library and about insuring Python can find the necessary two files
it needs.
[Test LAMMPS and Python in serial:] :h5
[Test LAMMPS and Python in serial:] :h4
To run a LAMMPS test in serial, type these lines into Python
interactively from the bench directory:
@ -462,7 +462,7 @@ typed something like:
lmp_g++ -in in.lj :pre
[Test LAMMPS and Python in parallel:] :h5
[Test LAMMPS and Python in parallel:] :h4
To run LAMMPS in parallel, assuming you have installed the
"PyPar"_https://github.com/daleroberts/pypar package as discussed
@ -510,7 +510,7 @@ described in the PyPar documentation. The last line of your Python
script should be pypar.finalize(), to insure MPI is shut down
correctly.
[Running Python scripts:] :h5
[Running Python scripts:] :h4
Note that any Python script (not just for LAMMPS) can be invoked in
one of several ways:
@ -551,11 +551,14 @@ Python script, as follows:
from lammps import lammps :pre
These are the methods defined by the lammps module. If you look at
the files src/library.cpp and src/library.h you will see that they
the files src/library.cpp and src/library.h you will see they
correspond one-to-one with calls you can make to the LAMMPS library
from a C++ or C or Fortran program, and which are described in
"Section 6.19"_Section_howto.html#howto_19 of the manual.
The python/examples directory has Python scripts which show how Python
can run LAMMPS, grab data, change it, and put it back into LAMMPS.
lmp = lammps() # create a LAMMPS object using the default liblammps.so library
# 4 optional args are allowed: name, cmdargs, ptr, comm
lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
@ -565,18 +568,22 @@ lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line args, e.g. li
lmp.close() # destroy a LAMMPS object :pre
version = lmp.version() # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902
version = lmp.version() # return the numerical version id, e.g. LAMMPS 2 Sep 2015 -> 20150902 :pre
lmp.file(file) # run an entire input script, file = "in.lj"
lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" :pre
lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100"
lmp.commands_list(cmdlist) # invoke commands in cmdlist = ["run 10", "run 20"]
lmp.commands_string(multicmd) # invoke commands in multicmd = "run 10\nrun 20"
lmp.commands_string(multicmd) # invoke commands in multicmd = "run 10\nrun 20" :pre
size = lmp.extract_setting(name) # return data type info :pre
xlo = lmp.extract_global(name,type) # extract a global quantity
# name = "boxxlo", "nlocal", etc
# type = 0 = int
# 1 = double :pre
boxlo,boxhi,xy,yz,xz,periodicity,box_change = lmp.extract_box() # extract box info :pre
coords = lmp.extract_atom(name,type) # extract a per-atom quantity
# name = "x", "type", etc
# type = 0 = vector of ints
@ -601,16 +608,23 @@ var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable
# flag = 0 = equal-style variable
# 1 = atom-style variable :pre
flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful
value = lmp.get_thermo(name) # return current value of a thermo keyword
natoms = lmp.get_natoms() # total # of atoms as int :pre
flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful
lmp.reset_box(boxlo,boxhi,xy,yz,xz) # reset the simulation box size :pre
natoms = lmp.get_natoms() # total # of atoms as int
data = lmp.gather_atoms(name,type,count) # return per-atom property of all atoms gathered into data, ordered by atom ID
# name = "x", "charge", "type", etc
# count = # of per-atom values, 1 or 3, etc
data = lmp.gather_atoms_concat(name,type,count) # ditto, but concatenated atom values from each proc (unordered)
data = lmp.gather_atoms_subset(name,type,count,ndata,ids) # ditto, but for subset of Ndata atoms with IDs :pre
lmp.scatter_atoms(name,type,count,data) # scatter per-atom property to all atoms from data, ordered by atom ID
# name = "x", "charge", "type", etc
# count = # of per-atom values, 1 or 3, etc :pre
lmp.scatter_atoms_subset(name,type,count,ndata,ids,data) # ditto, but for subset of Ndata atoms with IDs :pre
lmp.create_atoms(n,ids,types,x,v,image,shrinkexceed) # create N atoms with IDs, types, x, v, and image flags :pre
:line
@ -655,9 +669,10 @@ The file(), command(), commands_list(), commands_string() methods
allow an input script, a single command, or multiple commands to be
invoked.
The extract_global(), extract_atom(), extract_compute(),
extract_fix(), and extract_variable() methods return values or
pointers to data structures internal to LAMMPS.
The extract_setting(), extract_global(), extract_box(),
extract_atom(), extract_compute(), extract_fix(), and
extract_variable() methods return values or pointers to data
structures internal to LAMMPS.
For extract_global() see the src/library.cpp file for the list of
valid names. New names could easily be added. A double or integer is
@ -697,60 +712,46 @@ doubles is returned, one value per atom, which you can use via normal
Python subscripting. The values will be zero for atoms not in the
specified group.
The get_thermo() method returns returns the current value of a thermo
keyword as a float.
The get_natoms() method returns the total number of atoms in the
simulation, as an int.
The gather_atoms() method allows any per-atom property (coordinates,
velocities, etc) to be extracted from LAMMPS. It returns a ctypes
vector of ints or doubles as specified by type, of length
count*natoms, for the named property for all atoms in the simulation.
The data is ordered by count and then by atom ID. See the extract()
method in the src/atom.cpp file for a list of valid names. Again, new
names could easily be added if the property you want is missing. The
vector can be used via normal Python subscripting. If atom IDs are
not consecutively ordered within LAMMPS, a None is returned as
indication of an error. A special treatment is applied for image flags
stored in the "image" property. All three image flags are stored in
a packed format in a single integer, so count would be 1 to retrieve
that integer, however also a count value of 3 can be used and then
the image flags will be unpacked into 3 individual integers, ordered
in a similar fashion as coordinates.
The set_variable() methosd sets an existing string-style variable to a
new string value, so that subsequent LAMMPS commands can access the
variable.
Note that the data structure gather_atoms("x") returns is different
from the data structure returned by extract_atom("x") in four ways.
(1) Gather_atoms() returns a vector which you index as x\[i\];
extract_atom() returns an array which you index as x\[i\]\[j\]. (2)
Gather_atoms() orders the atoms by atom ID while extract_atom() does
not. (3) Gathert_atoms() returns a list of all atoms in the
simulation; extract_atoms() returns just the atoms local to each
processor. (4) Finally, the gather_atoms() data structure is a copy
of the atom coords stored internally in LAMMPS, whereas extract_atom()
returns an array that effectively points directly to the internal
data. This means you can change values inside LAMMPS from Python by
assigning a new values to the extract_atom() array. To do this with
the gather_atoms() vector, you need to change values in the vector,
then invoke the scatter_atoms() method.
The reset_box() emthods resets the size and shape of the simulation
box, e.g. as part of restoring a previously extracted and saved state
of a simulation.
The scatter_atoms() method allows any per-atom property (coordinates,
velocities, etc) to be inserted into LAMMPS, overwriting the current
property. It takes a vector of ints or doubles as specified by type,
of length count*natoms, for the named property for all atoms in the
simulation. The data should be ordered by count and then by atom ID.
See the extract() method in the src/atom.cpp file for a list of valid
names. Again, new names could easily be added if the property you
want is missing. It uses the vector of data to overwrite the
corresponding properties for each atom inside LAMMPS. This requires
LAMMPS to have its "map" option enabled; see the
"atom_modify"_atom_modify.html command for details. If it is not, or
if atom IDs are not consecutively ordered, no coordinates are reset.
Similar as for gather_atoms() a special treatment is applied for image
flags, which can be provided in packed (count = 1) or unpacked (count = 3)
format and in the latter case, they will be packed before applied to
atoms.
The gather methods collect peratom info of the requested type (atom
coords, atom types, forces, etc) from all processors, and returns the
same vector of values to each callling processor. The scatter
functions do the inverse. They distribute a vector of peratom values,
passed by all calling processors, to invididual atoms, which may be
owned by different processos.
The array of coordinates passed to scatter_atoms() must be a ctypes
vector of ints or doubles, allocated and initialized something like
this:
Note that the data returned by the gather methods,
e.g. gather_atoms("x"), is different from the data structure returned
by extract_atom("x") in four ways. (1) Gather_atoms() returns a
vector which you index as x\[i\]; extract_atom() returns an array
which you index as x\[i\]\[j\]. (2) Gather_atoms() orders the atoms
by atom ID while extract_atom() does not. (3) Gather_atoms() returns
a list of all atoms in the simulation; extract_atoms() returns just
the atoms local to each processor. (4) Finally, the gather_atoms()
data structure is a copy of the atom coords stored internally in
LAMMPS, whereas extract_atom() returns an array that effectively
points directly to the internal data. This means you can change
values inside LAMMPS from Python by assigning a new values to the
extract_atom() array. To do this with the gather_atoms() vector, you
need to change values in the vector, then invoke the scatter_atoms()
method.
For the scatter methods, the array of coordinates passed to must be a
ctypes vector of ints or doubles, allocated and initialized something
like this:
from ctypes import *
natoms = lmp.get_natoms()
@ -765,7 +766,7 @@ x\[n3-1\] = z coord of atom with ID natoms
lmp.scatter_atoms("x",1,3,x) :pre
Alternatively, you can just change values in the vector returned by
gather_atoms("x",1,3), since it is a ctypes vector of doubles.
the gather methods, since they are also ctypes vectors.
:line

106
doc/src/Section_start.txt
View File

@ -6,7 +6,7 @@
:line
2. Getting Started :h3
2. Getting Started :h2
This section describes how to build and run LAMMPS, for both new and
experienced users.
@ -22,7 +22,7 @@ experienced users.
:line
2.1 What's in the LAMMPS distribution :h4,link(start_1)
2.1 What's in the LAMMPS distribution :h3,link(start_1)
When you download a LAMMPS tarball you will need to unzip and untar
the downloaded file with the following commands, after placing the
@ -64,7 +64,7 @@ launch a LAMMPS Windows executable on a Windows box.
:line
2.2 Making LAMMPS :h4,link(start_2)
2.2 Making LAMMPS :h3,link(start_2)
This section has the following sub-sections:
@ -77,9 +77,9 @@ This section has the following sub-sections:
:line
Read this first :h5,link(start_2_1)
Read this first :h4,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.
@ -148,9 +148,9 @@ include it in the LAMMPS distribution.
:line
Steps to build a LAMMPS executable :h5,link(start_2_2)
Steps to build a LAMMPS executable :h4,link(start_2_2)
Step 0 :h6
Step 0 :h5
The src directory contains the C++ source and header files for LAMMPS.
It also contains a top-level Makefile and a MAKE sub-directory with
@ -198,7 +198,7 @@ Note that by default only a few of LAMMPS optional packages are
installed. To build LAMMPS with optional packages, see "this
section"_#start_3 below.
Step 1 :h6
Step 1 :h5
If Step 0 did not work, you will need to create a low-level Makefile
for your machine, like Makefile.foo. You should make a copy of an
@ -209,13 +209,13 @@ the first line, the "compiler/linker settings" section, and the
file in src/MAKE/MINE and it will not be altered by any future LAMMPS
updates.
Step 2 :h6
Step 2 :h5
Change the first line of Makefile.foo to list the word "foo" after the
"#", and whatever other options it will set. This is the line you
will see if you just type "make".
Step 3 :h6
Step 3 :h5
The "compiler/linker settings" section lists compiler and linker
settings for your C++ compiler, including optimization flags. You can
@ -244,7 +244,7 @@ first time on a new platform, a long list of *.d files will be printed
out rapidly. This is not an error; it is the Makefile doing its
normal creation of dependencies.
Step 4 :h6
Step 4 :h5
The "system-specific settings" section has several parts. Note that
if you change any -D setting in this section, you should do a full
@ -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
@ -351,7 +345,7 @@ platforms. The -DPACK_ARRAY setting is the default. See the
"kspace_style"_kspace_style.html command for info about PPPM. See
Step 6 below for info about building LAMMPS with an FFT library.
Step 5 :h6
Step 5 :h5
The 3 MPI variables are used to specify an MPI library to build LAMMPS
with. Note that you do not need to set these if you use the MPI
@ -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.
@ -407,7 +401,7 @@ Note that the ANSI-standard function clock() rolls over after an hour
or so, and is therefore insufficient for timing long LAMMPS
simulations.
Step 6 :h6
Step 6 :h5
The 3 FFT variables allow you to specify an FFT library which LAMMPS
uses (for performing 1d FFTs) when running the particle-particle
@ -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
@ -483,12 +477,12 @@ 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.
Step 7 :h6
Step 7 :h5
The 3 JPG variables allow you to specify a JPEG and/or PNG library
which LAMMPS uses when writing out JPEG or PNG files via the "dump
@ -511,13 +505,13 @@ find it.
As before, if these header and library files are in the usual place on
your machine, you may not need to set these variables.
Step 8 :h6
Step 8 :h5
Note that by default only a few of LAMMPS optional packages are
installed. To build LAMMPS with optional packages, see "this
section"_#start_3 below, before proceeding to Step 9.
Step 9 :h6
Step 9 :h5
That's it. Once you have a correct Makefile.foo, and you have
pre-built any other needed libraries (e.g. MPI, FFT, etc) all you need
@ -536,7 +530,7 @@ You should get the executable lmp_foo when the build is complete.
:line
Errors that can occur when making LAMMPS :h5 :link(start_2_3)
Errors that can occur when making LAMMPS :h4 :link(start_2_3)
If an error occurs when building LAMMPS, the compiler or linker will
state very explicitly what the problem is. The error message should
@ -573,21 +567,21 @@ above in Step 4.
:line
Additional build tips :h5,link(start_2_4)
Additional build tips :h4,link(start_2_4)
Building LAMMPS for multiple platforms. :h6
Building LAMMPS for multiple platforms. :h5
You can make LAMMPS for multiple platforms from the same src
directory. Each target creates its own object sub-directory called
Obj_target where it stores the system-specific *.o files.
Cleaning up. :h6
Cleaning up. :h5
Typing "make clean-all" or "make clean-machine" will delete *.o object
files created when LAMMPS is built, for either all builds or for a
particular machine.
Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h5
As explained above, any of these 3 settings can be specified on the
LMP_INC line in your low-level src/MAKE/Makefile.foo.
@ -637,14 +631,14 @@ neighbor lists and would run very slowly in terms of CPU secs/timestep.
:line
Building for a Mac :h5,link(start_2_5)
Building for a Mac :h4,link(start_2_5)
OS X is a derivative of BSD Unix, so it should just work. See the
src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.
:line
Building for Windows :h5,link(start_2_6)
Building for Windows :h4,link(start_2_6)
If you want to build a Windows version of LAMMPS, you can build it
yourself, but it may require some effort. LAMMPS expects a Unix-like
@ -684,7 +678,7 @@ examples, but no source code.
:line
2.3 Making LAMMPS with optional packages :h4,link(start_3)
2.3 Making LAMMPS with optional packages :h3,link(start_3)
This section has the following sub-sections:
@ -694,7 +688,7 @@ This section has the following sub-sections:
:line
Package basics: :h5,link(start_3_1)
Package basics: :h4,link(start_3_1)
The source code for LAMMPS is structured as a set of core files which
are always included, plus optional packages. Packages are groups of
@ -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
@ -725,7 +719,7 @@ known to your executable, and immediately exit.
:line
Including/excluding packages :h5,link(start_3_2)
Including/excluding packages :h4,link(start_3_2)
To use (or not use) a package you must install it (or un-install it)
before building LAMMPS. From the src directory, this is as simple as:
@ -809,6 +803,10 @@ currently installed. For those that are installed, it will list any
files that are different in the src directory and package
sub-directory.
Typing "make package-installed" or "make pi" will list which packages are
currently installed, without listing the status of packages that are not
installed.
Typing "make package-update" or "make pu" will overwrite src files
with files from the package sub-directories if the package is
installed. It should be used after a patch has been applied, since
@ -825,7 +823,7 @@ options.
:line
Packages that require extra libraries :h5,link(start_3_3)
Packages that require extra libraries :h4,link(start_3_3)
A few of the standard and user packages require extra libraries. See
"Section 4"_Section_packages.html for two tables of packages which
@ -859,7 +857,7 @@ 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
@ -927,7 +925,7 @@ Makefile.opt :ul
:line
2.4 Building LAMMPS as a library :h4,link(start_4)
2.4 Building LAMMPS as a library :h3,link(start_4)
LAMMPS can be built as either a static or shared library, which can
then be called from another application or a scripting language. See
@ -935,7 +933,7 @@ then be called from another application or a scripting language. See
LAMMPS to other codes. See "this section"_Section_python.html for
more info on wrapping and running LAMMPS from Python.
Static library :h5
Static library :h4
To build LAMMPS as a static library (*.a file on Linux), type
@ -949,7 +947,7 @@ will create the file liblammps_foo.a which another application can
link to. It will also create a soft link liblammps.a, which will
point to the most recently built static library.
Shared library :h5
Shared library :h4
To build LAMMPS as a shared library (*.so file on Linux), which can be
dynamically loaded, e.g. from Python, type
@ -963,7 +961,7 @@ 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.
@ -1006,7 +1004,7 @@ You may need to use "sudo make install" in place of the last line if
you do not have write privileges for /usr/local/lib. The end result
should be the file /usr/local/lib/libmpich.so.
[Additional requirement for using a shared library:] :h5
[Additional requirement for using a shared library:] :h4
The operating system finds shared libraries to load at run-time using
the environment variable LD_LIBRARY_PATH. So you may wish to copy the
@ -1021,7 +1019,7 @@ For the csh or tcsh shells, you would add something like this to your
setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
Calling the LAMMPS library :h5
Calling the LAMMPS library :h4
Either flavor of library (static or shared) allows one or more LAMMPS
objects to be instantiated from the calling program.
@ -1049,7 +1047,7 @@ interface and how to extend it for your needs.
:line
2.5 Running LAMMPS :h4,link(start_5)
2.5 Running LAMMPS :h3,link(start_5)
By default, LAMMPS runs by reading commands from standard input. Thus
if you run the LAMMPS executable by itself, e.g.
@ -1195,7 +1193,7 @@ more processors or setup a smaller problem.
:line
2.6 Command-line options :h4,link(start_6)
2.6 Command-line options :h3,link(start_6)
At run time, LAMMPS recognizes several optional command-line switches
which may be used in any order. Either the full word or a one-or-two
@ -1329,8 +1327,8 @@ 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 +1392,7 @@ 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.
@ -1625,7 +1623,7 @@ negative numeric value. It is OK if the first value1 starts with a
:line
2.7 LAMMPS screen output :h4,link(start_7)
2.7 LAMMPS screen output :h3,link(start_7)
As LAMMPS reads an input script, it prints information to both the
screen and a log file about significant actions it takes to setup a
@ -1673,7 +1671,7 @@ 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.
@ -1781,7 +1779,7 @@ communication, roughly 75% in the example above.
:line
2.8 Tips for users of previous LAMMPS versions :h4,link(start_8)
2.8 Tips for users of previous LAMMPS versions :h3,link(start_8)
The current C++ began with a complete rewrite of LAMMPS 2001, which
was written in F90. Features of earlier versions of LAMMPS are listed

84
doc/src/Section_tools.txt
View File

@ -8,7 +8,7 @@ Section"_Section_modify.html :c
:line
9. Additional tools :h3
9. Additional tools :h2
LAMMPS is designed to be a computational kernel for performing
molecular dynamics computations. Additional pre- and post-processing
@ -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
@ -74,7 +75,7 @@ own sub-directories with their own Makefiles and/or README files.
:line
amber2lmp tool :h4,link(amber)
amber2lmp tool :h3,link(amber)
The amber2lmp sub-directory contains two Python scripts for converting
files back-and-forth between the AMBER MD code and LAMMPS. See the
@ -89,7 +90,7 @@ necessary modifications yourself.
:line
binary2txt tool :h4,link(binary)
binary2txt tool :h3,link(binary)
The file binary2txt.cpp converts one or more binary LAMMPS dump file
into ASCII text files. The syntax for running the tool is
@ -102,7 +103,7 @@ since binary files are not compatible across all platforms.
:line
ch2lmp tool :h4,link(charmm)
ch2lmp tool :h3,link(charmm)
The ch2lmp sub-directory contains tools for converting files
back-and-forth between the CHARMM MD code and LAMMPS.
@ -110,17 +111,24 @@ 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)
chain tool :h3,link(chain)
The file chain.f creates a LAMMPS data file containing bead-spring
polymer chains and/or monomer solvent atoms. It uses a text file
@ -137,7 +145,7 @@ system for the "chain benchmark"_Section_perf.html.
:line
colvars tools :h4,link(colvars)
colvars tools :h3,link(colvars)
The colvars directory contains a collection of tools for postprocessing
data produced by the colvars collective variable library.
@ -159,7 +167,7 @@ gmail.com) at ICTP, Italy.
:line
createatoms tool :h4,link(createatoms)
createatoms tool :h3,link(createatoms)
The tools/createatoms directory contains a Fortran program called
createAtoms.f which can generate a variety of interesting crystal
@ -172,7 +180,19 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
:line
drude tool :h4,link(drude)
doxygen tool :h3,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 :h3,link(drude)
The tools/drude directory contains a Python script called
polarizer.py which can add Drude oscillators to a LAMMPS
@ -185,7 +205,7 @@ at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
:line
eam database tool :h4,link(eamdb)
eam database tool :h3,link(eamdb)
The tools/eam_database directory contains a Fortran program that will
generate EAM alloy setfl potential files for any combination of 16
@ -201,7 +221,7 @@ X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
:line
eam generate tool :h4,link(eamgn)
eam generate tool :h3,link(eamgn)
The tools/eam_generate directory contains several one-file C programs
that convert an analytic formula into a tabulated "embedded atom
@ -214,7 +234,7 @@ The source files and potentials were provided by Gerolf Ziegenhain
:line
eff tool :h4,link(eff)
eff tool :h3,link(eff)
The tools/eff directory contains various scripts for generating
structures and post-processing output for simulations using the
@ -225,7 +245,7 @@ These tools were provided by Andres Jaramillo-Botero at CalTech
:line
emacs tool :h4,link(emacs)
emacs tool :h3,link(emacs)
The tools/emacs directory contains a Lips add-on file for Emacs that
enables a lammps-mode for editing of input scripts when using Emacs,
@ -236,7 +256,7 @@ These tools were provided by Aidan Thompson at Sandia
:line
fep tool :h4,link(fep)
fep tool :h3,link(fep)
The tools/fep directory contains Python scripts useful for
post-processing results from performing free-energy perturbation
@ -249,7 +269,7 @@ See README file in the tools/fep directory.
:line
i-pi tool :h4,link(ipi)
i-pi tool :h3,link(ipi)
The tools/i-pi directory contains a version of the i-PI package, with
all the LAMMPS-unrelated files removed. It is provided so that it can
@ -266,7 +286,7 @@ calculations with LAMMPS.
:line
ipp tool :h4,link(ipp)
ipp tool :h3,link(ipp)
The tools/ipp directory contains a Perl script ipp which can be used
to facilitate the creation of a complicated file (say, a lammps input
@ -280,7 +300,7 @@ tools/createatoms tool's input file.
:line
kate tool :h4,link(kate)
kate tool :h3,link(kate)
The file in the tools/kate directory is an add-on to the Kate editor
in the KDE suite that allow syntax highlighting of LAMMPS input
@ -291,7 +311,7 @@ The file was provided by Alessandro Luigi Sellerio
:line
lmp2arc tool :h4,link(arc)
lmp2arc tool :h3,link(arc)
The lmp2arc sub-directory contains a tool for converting LAMMPS output
files to the format for Accelrys' Insight MD code (formerly
@ -307,7 +327,7 @@ Greathouse at Sandia (jagreat at sandia.gov).
:line
lmp2cfg tool :h4,link(cfg)
lmp2cfg tool :h3,link(cfg)
The lmp2cfg sub-directory contains a tool for converting LAMMPS output
files into a series of *.cfg files which can be read into the
@ -318,7 +338,7 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
:line
matlab tool :h4,link(matlab)
matlab tool :h3,link(matlab)
The matlab sub-directory contains several "MATLAB"_matlabhome scripts for
post-processing LAMMPS output. The scripts include readers for log
@ -336,7 +356,7 @@ These scripts were written by Arun Subramaniyan at Purdue Univ
:line
micelle2d tool :h4,link(micelle)
micelle2d tool :h3,link(micelle)
The file micelle2d.f creates a LAMMPS data file containing short lipid
chains in a monomer solution. It uses a text file containing lipid
@ -353,7 +373,7 @@ definition file. This tool was used to create the system for the
:line
moltemplate tool :h4,link(moltemplate)
moltemplate tool :h3,link(moltemplate)
The moltemplate sub-directory contains a Python-based tool for
building molecular systems based on a text-file description, and
@ -367,7 +387,7 @@ supports it. It has its own WWW page at
:line
msi2lmp tool :h4,link(msi)
msi2lmp tool :h3,link(msi)
The msi2lmp sub-directory contains a tool for creating LAMMPS template
input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
@ -384,7 +404,7 @@ See the README file in the tools/msi2lmp folder for more information.
:line
phonon tool :h4,link(phonon)
phonon tool :h3,link(phonon)
The phonon sub-directory contains a post-processing tool useful for
analyzing the output of the "fix phonon"_fix_phonon.html command in
@ -399,7 +419,7 @@ University.
:line
polybond tool :h4,link(polybond)
polybond tool :h3,link(polybond)
The polybond sub-directory contains a Python-based tool useful for
performing "programmable polymer bonding". The Python file
@ -413,7 +433,7 @@ This tool was written by Zachary Kraus at Georgia Tech.
:line
pymol_asphere tool :h4,link(pymol)
pymol_asphere tool :h3,link(pymol)
The pymol_asphere sub-directory contains a tool for converting a
LAMMPS dump file that contains orientation info for ellipsoidal
@ -431,7 +451,7 @@ This tool was written by Mike Brown at Sandia.
:line
python tool :h4,link(pythontools)
python tool :h3,link(pythontools)
The python sub-directory contains several Python scripts
that perform common LAMMPS post-processing tasks, such as:
@ -447,7 +467,7 @@ README for more info on Pizza.py and how to use these scripts.
:line
reax tool :h4,link(reax_tool)
reax tool :h3,link(reax_tool)
The reax sub-directory contains stand-alond codes that can
post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
@ -458,7 +478,7 @@ These tools were written by Aidan Thompson at Sandia.
:line
smd tool :h4,link(smd)
smd tool :h3,link(smd)
The smd sub-directory contains a C++ file dump2vtk_tris.cpp and
Makefile which can be compiled and used to convert triangle output
@ -474,7 +494,7 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
:line
vim tool :h4,link(vim)
vim tool :h3,link(vim)
The files in the tools/vim directory are add-ons to the VIM editor
that allow easier editing of LAMMPS input scripts. See the README.txt
@ -485,7 +505,7 @@ ziegenhain.com)
:line
xmgrace tool :h4,link(xmgrace)
xmgrace tool :h3,link(xmgrace)
The files in the tools/xmgrace directory can be used to plot the
thermodynamic data in LAMMPS log files via the xmgrace plotting

46
doc/src/USER/atc/man_add_molecule.html
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@ -7,24 +7,22 @@
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</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;
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<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;

46
doc/src/USER/atc/man_add_species.html
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@ -7,24 +7,22 @@
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<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;
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<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;

46
doc/src/USER/atc/man_atom_element_map.html
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@ -7,42 +7,40 @@
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<center>
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<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;

46
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@ -7,24 +7,22 @@
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<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>
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<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>
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42
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<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>
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<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>
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<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">

48
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<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;

46
doc/src/USER/atc/man_consistent_fe_initialization.html
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<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>
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48
doc/src/USER/atc/man_contour_integral.html
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<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;

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<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>

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<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;

46
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<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>

46
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<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>
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<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>
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44
doc/src/USER/atc/man_electron_integration.html
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<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>

46
doc/src/USER/atc/man_equilibrium_start.html
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@ -7,40 +7,38 @@
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<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;

48
doc/src/USER/atc/man_extrinsic_exchange.html
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<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;

46
doc/src/USER/atc/man_fe_md_boundary.html
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<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>
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doc/src/USER/atc/man_fem_mesh.html
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<!-- 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>
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<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;
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doc/src/USER/atc/man_filter_scale.html
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<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>
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<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>
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<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>
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@ -7,44 +7,42 @@
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<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
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<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>
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<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
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<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>
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<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>
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<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
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<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>
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<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>
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<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>
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<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>

48
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<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>
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<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>
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<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;

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<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;

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<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>
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<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>
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<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>
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</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;
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46
doc/src/USER/atc/man_mask_direction.html
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<body>
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<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;
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46
doc/src/USER/atc/man_mass_matrix.html
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<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;

46
doc/src/USER/atc/man_material.html
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@ -7,39 +7,37 @@
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<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;

46
doc/src/USER/atc/man_mesh_add_to_nodeset.html
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<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;

46
doc/src/USER/atc/man_mesh_create.html
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@ -7,24 +7,22 @@
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<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>
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<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>
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46
doc/src/USER/atc/man_mesh_create_faceset_box.html
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<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>
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<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>
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doc/src/USER/atc/man_mesh_create_nodeset.html
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<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>
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doc/src/USER/atc/man_mesh_delete_elements.html
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<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;

46
doc/src/USER/atc/man_mesh_nodeset_to_elementset.html
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<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>
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46
doc/src/USER/atc/man_mesh_output.html
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<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>
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doc/src/USER/atc/man_mesh_quadrature.html
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<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>
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<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>
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<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>
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doc/src/USER/atc/man_momentum_time_integration.html
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<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;

48
doc/src/USER/atc/man_output.html
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@ -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;
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<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;

48
doc/src/USER/atc/man_output_elementset.html
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@ -7,44 +7,42 @@
<link href="doxygen.css" rel="stylesheet" type="text/css"/>
</head>
<body>
<center>
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<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;

48
doc/src/USER/atc/man_output_nodeset.html
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@ -7,24 +7,22 @@
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<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;

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doc/src/USER/atc/man_pair_interactions.html
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<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>
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doc/src/USER/atc/man_poisson_solver.html
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<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>
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<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;

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doc/src/USER/atc/man_remove_molecule.html
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<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>
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doc/src/USER/atc/man_remove_source.html
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<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">

46
doc/src/USER/atc/man_remove_species.html
View File

@ -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;
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<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;

46
doc/src/USER/atc/man_reset_atomic_reference_positions.html
View File

@ -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;
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<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;

70
doc/src/USER/atc/man_reset_time.html
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<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
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<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;

48
doc/src/USER/atc/man_sample_frequency.html
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<body>
<center>
<a href="http://lammps.sandia.gov">LAMMPS Website</a> &nbsp; &nbsp;
<a href="../../Manual.html">LAMMPS Manual</a> &nbsp; &nbsp;
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<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;

48
doc/src/USER/atc/man_set.html
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<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>
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<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>
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<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>
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