From 729ba2cc21d47e0d1fdac5842953f96a5db7a27b Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 15 Feb 2016 15:28:30 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14590 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 38 +++++++-------- doc/Section_commands.txt | 4 +- doc/Section_python.html | 31 ++++++------ doc/Section_python.txt | 22 +++------ doc/_sources/Section_commands.txt | 78 +++++++++++++++---------------- doc/_sources/Section_python.txt | 30 +++++------- doc/_sources/fix.txt | 3 +- doc/_sources/fix_wall_region.txt | 10 ++-- doc/fix.html | 3 +- doc/fix.txt | 1 + doc/fix_wall_region.html | 9 ++-- doc/fix_wall_region.txt | 10 ++-- doc/searchindex.js | 2 +- 13 files changed, 119 insertions(+), 122 deletions(-) diff --git a/doc/Section_commands.html b/doc/Section_commands.html index dd0dc11e0e..79a8922f6f 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -607,12 +607,12 @@ This is indicated by additional letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

+-+- @@ -696,61 +696,61 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

- + - + + - - + + - - + + - - + + - - + + - - + + -
qeq/point qeq/shielded qeq/slaterreax/bondsrattle
recenter
reax/bondsrecenter restrain rigid (o) rigid/nph (o) rigid/npt (o) rigid/nve (o) rigid/nvt (o)rigid/small (o)
rigid/small/nph
rigid/small (o)rigid/small/nph rigid/small/npt rigid/small/nve rigid/small/nvt setforce (ck) shake (c) springspring/rg
spring/self
spring/rgspring/self srd store/force store/state temp/berendsen (c) temp/csld temp/csvrtemp/rescale (c)
tfmc
temp/rescale (c)tfmc thermal/conductivity tmd ttm tune/kspace vector viscosityviscous (c)
wall/colloid
viscous (c)wall/colloid wall/gran wall/harmonic wall/lj1043 wall/lj126 wall/lj93 wall/pistonwall/reflect (k)
wall/region
wall/reflect (k)wall/region wall/srd           
@@ -776,7 +776,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

drude drude/transform/direct drude/transform/reverse -eos/cv +eos/cv eos/table gle @@ -1448,8 +1448,8 @@ letters in parenthesis: c = USER-CUDA, g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.

+- @@ -1464,8 +1464,8 @@ KOKKOS, o = USER-OMP, t = OPT.

- - + + diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index bb54a5cbcb..4ad7f2eada 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -552,6 +552,7 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "qeq/point"_fix_qeq.html, "qeq/shielded"_fix_qeq.html, "qeq/slater"_fix_qeq.html, +"rattle"_fix_shake.html, "reax/bonds"_fix_reax_bonds.html, "recenter"_fix_recenter.html, "restrain"_fix_restrain.html, @@ -609,7 +610,7 @@ package"_Section_start.html#start_3. "drude"_fix_drude.html, "drude/transform/direct"_fix_drude_transform.html, "drude/transform/reverse"_fix_drude_transform.html, -"eos/cv"_fix_eos_vs.html, +"eos/cv"_fix_eos_cv.html, "eos/table"_fix_eos_table.html, "gle"_fix_gle.html, "imd"_fix_imd.html, @@ -1095,4 +1096,5 @@ KOKKOS, o = USER-OMP, t = OPT. "pppm/cg (o)"_kspace_style.html, "pppm/disp"_kspace_style.html, "pppm/disp/tip4p"_kspace_style.html, +"pppm/stagger"_kspace_style.html, "pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c) diff --git a/doc/Section_python.html b/doc/Section_python.html index ecebef2065..5678e5492d 100644 --- a/doc/Section_python.html +++ b/doc/Section_python.html @@ -281,8 +281,10 @@ examples of Python code you can write for both pure Python operations and callbacks to LAMMPS.

To run pure Python code from LAMMPS, you only need to build LAMMPS with the PYTHON package installed:

-

make yes-python -make machine

+
make yes-python
+make machine
+
+

Note that this will link LAMMPS with the Python library on your system, which typically requires several auxiliary system libraries to also be linked. The list of these libraries and the paths to find @@ -303,7 +305,7 @@ file and the shared library.

Section_start 5. A shared library is one that is dynamically loadable, which is what Python requires to wrap LAMMPS. On Linux this is a library file that ends in ”.so”, not ”.a”.

-

>From the src directory, type

+

From the src directory, type

make foo mode=shlib
@@ -313,10 +315,14 @@ well as a soft link liblammps.so, which is what the Python wrapper will load by default. Note that if you are building multiple machine versions of the shared library, the soft link is always set to the most recently built version.

-

If this fails, see Section_start 5 for -more details, especially if your LAMMPS build uses auxiliary libraries -like MPI or FFTW which may not be built as shared libraries on your -system.

+
+

Note

+

If you are building LAMMPS with an MPI or FFT library or other +auxiliary libraries (used by various packages), then all of these +extra libraries must also be shared libraries. If the LAMMPS +shared-library build fails with an error complaining about this, see +Section_start 5 for more details.

+
@@ -715,17 +721,6 @@ lmp = lammps(name="g++",cmdargs=list) # add LAMMPS command-line arg
-
-

Note

-

Currently, the creation of a LAMMPS object from within lammps.py -does not take an MPI communicator as an argument. There should be a -way to do this, so that the LAMMPS instance runs on a subset of -processors if desired, but I don’t know how to do it from Pypar. So -for now, it runs with MPI_COMM_WORLD, which is all the processors. If -someone figures out how to do this with one or more of the Python -wrappers for MPI, like Pypar, please let us know and we will amend -these doc pages.

-

The lines

from lammps import lammps
 lmp = lammps()
diff --git a/doc/Section_python.txt b/doc/Section_python.txt
index 3b3c28a817..4ed05e47d4 100644
--- a/doc/Section_python.txt
+++ b/doc/Section_python.txt
@@ -158,7 +158,7 @@ To run pure Python code from LAMMPS, you only need to build LAMMPS
 with the PYTHON package installed:
 
 make yes-python
-make machine
+make machine :pre
 
 Note that this will link LAMMPS with the Python library on your
 system, which typically requires several auxiliary system libraries to
@@ -183,7 +183,7 @@ Instructions on how to build LAMMPS as a shared library are given in
 that is dynamically loadable, which is what Python requires to wrap
 LAMMPS.  On Linux this is a library file that ends in ".so", not ".a".
 
->From the src directory, type
+From the src directory, type
 
 make foo mode=shlib :pre
 
@@ -194,10 +194,11 @@ load by default.  Note that if you are building multiple machine
 versions of the shared library, the soft link is always set to the
 most recently built version.
 
-If this fails, see "Section_start 5"_Section_start.html#start_5 for
-more details, especially if your LAMMPS build uses auxiliary libraries
-like MPI or FFTW which may not be built as shared libraries on your
-system.
+NOTE: If you are building LAMMPS with an MPI or FFT library or other
+auxiliary libraries (used by various packages), then all of these
+extra libraries must also be shared libraries.  If the LAMMPS
+shared-library build fails with an error complaining about this, see
+"Section_start 5"_Section_start.html#start_5 for more details.
 
 :line
 
@@ -610,15 +611,6 @@ lmp.scatter_atoms(name,type,count,data)   # scatter atom attribute of all atoms
 
 :line
 
-NOTE: Currently, the creation of a LAMMPS object from within lammps.py
-does not take an MPI communicator as an argument.  There should be a
-way to do this, so that the LAMMPS instance runs on a subset of
-processors if desired, but I don't know how to do it from Pypar.  So
-for now, it runs with MPI_COMM_WORLD, which is all the processors.  If
-someone figures out how to do this with one or more of the Python
-wrappers for MPI, like Pypar, please let us know and we will amend
-these doc pages.
-
 The lines
 
 from lammps import lammps
diff --git a/doc/_sources/Section_commands.txt b/doc/_sources/Section_commands.txt
index 7025e5797a..4618b33588 100644
--- a/doc/_sources/Section_commands.txt
+++ b/doc/_sources/Section_commands.txt
@@ -455,37 +455,37 @@ with the :doc:`appropriate accelerated package `.
 This is indicated by additional letters in parenthesis: c = USER-CUDA,
 g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`adapt `                 | :doc:`addforce (c) `                     | :doc:`append/atoms `   | :doc:`atom/swap `       | :doc:`aveforce (c) `             | :doc:`ave/atom `           | :doc:`ave/chunk `                     | :doc:`ave/correlate `   |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`ave/histo `         | :doc:`ave/histo/weight `                | :doc:`ave/spatial `     | :doc:`ave/time `         | :doc:`balance `                   | :doc:`bond/break `       | :doc:`bond/create `                 | :doc:`bond/swap `           |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`box/relax `         | :doc:`deform (k) `                         | :doc:`deposit `             | :doc:`drag `                 | :doc:`dt/reset `                 | :doc:`efield `               | :doc:`enforce2d (c) `                 | :doc:`evaporate `           |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`external `           | :doc:`freeze (c) `                         | :doc:`gcmc `                   | :doc:`gld `                   | :doc:`gravity (co) `              | :doc:`heat `                   | :doc:`indent `                           | :doc:`langevin (k) `         |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`lineforce `         | :doc:`momentum `                         | :doc:`move `                   | :doc:`msst `                 | :doc:`neb `                           | :doc:`nph (ko) `                 | :doc:`nphug (o) `                         | :doc:`nph/asphere (o) `   |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`nph/sphere (o) `   | :doc:`npt (ckio) `                             | :doc:`npt/asphere (o) ` | :doc:`npt/sphere (o) ` | :doc:`nve (ckio) `                    | :doc:`nve/asphere (i) ` | :doc:`nve/asphere/noforce ` | :doc:`nve/body `             |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`nve/limit `         | :doc:`nve/line `                         | :doc:`nve/noforce `     | :doc:`nve/sphere (o) ` | :doc:`nve/tri `                   | :doc:`nvt (cko) `                | :doc:`nvt/asphere (o) `             | :doc:`nvt/sllod (o) `       |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`nvt/sphere (o) `   | :doc:`oneway `                             | :doc:`orient/fcc `       | :doc:`planeforce `     | :doc:`poems `                       | :doc:`pour `                   | :doc:`press/berendsen `         | :doc:`print `                   |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`property/atom ` | :doc:`qeq/comb (o) `                     | :doc:`qeq/dynamic `             | :doc:`qeq/fire `              | :doc:`qeq/point `                     | :doc:`qeq/shielded `            | :doc:`qeq/slater `                          | :doc:`reax/bonds `         |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`recenter `           | :doc:`restrain `                         | :doc:`rigid (o) `             | :doc:`rigid/nph (o) `       | :doc:`rigid/npt (o) `               | :doc:`rigid/nve (o) `         | :doc:`rigid/nvt (o) `                     | :doc:`rigid/small (o) `         |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`rigid/small/nph `       | :doc:`rigid/small/npt `                     | :doc:`rigid/small/nve `       | :doc:`rigid/small/nvt `     | :doc:`setforce (ck) `            | :doc:`shake (c) `             | :doc:`spring `                           | :doc:`spring/rg `           |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`spring/self `     | :doc:`srd `                                   | :doc:`store/force `     | :doc:`store/state `   | :doc:`temp/berendsen (c) ` | :doc:`temp/csld `         | :doc:`temp/csvr `                     | :doc:`temp/rescale (c) ` |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`tfmc `                   | :doc:`thermal/conductivity ` | :doc:`tmd `                     | :doc:`ttm `                   | :doc:`tune/kspace `           | :doc:`vector `               | :doc:`viscosity `                     | :doc:`viscous (c) `           |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`wall/colloid `           | :doc:`wall/gran `                       | :doc:`wall/harmonic `          | :doc:`wall/lj1043 `          | :doc:`wall/lj126 `                   | :doc:`wall/lj93 `              | :doc:`wall/piston `                 | :doc:`wall/reflect (k) ` |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
-| :doc:`wall/region `     | :doc:`wall/srd `                         |                                          |                                        |                                                |                                          |                                                      |                                            |
-+------------------------------------------+--------------------------------------------------------+------------------------------------------+----------------------------------------+------------------------------------------------+------------------------------------------+------------------------------------------------------+--------------------------------------------+
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`adapt `                   | :doc:`addforce (c) `      | :doc:`append/atoms `                 | :doc:`atom/swap `       | :doc:`aveforce (c) `   | :doc:`ave/atom `                 | :doc:`ave/chunk `                     | :doc:`ave/correlate ` |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`ave/histo `           | :doc:`ave/histo/weight ` | :doc:`ave/spatial `                   | :doc:`ave/time `         | :doc:`balance `         | :doc:`bond/break `             | :doc:`bond/create `                 | :doc:`bond/swap `         |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`box/relax `           | :doc:`deform (k) `          | :doc:`deposit `                           | :doc:`drag `                 | :doc:`dt/reset `       | :doc:`efield `                     | :doc:`enforce2d (c) `                 | :doc:`evaporate `         |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`external `             | :doc:`freeze (c) `          | :doc:`gcmc `                                 | :doc:`gld `                   | :doc:`gravity (co) `    | :doc:`heat `                         | :doc:`indent `                           | :doc:`langevin (k) `       |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`lineforce `           | :doc:`momentum `          | :doc:`move `                                 | :doc:`msst `                 | :doc:`neb `                 | :doc:`nph (ko) `                       | :doc:`nphug (o) `                         | :doc:`nph/asphere (o) ` |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`nph/sphere (o) `     | :doc:`npt (ckio) `              | :doc:`npt/asphere (o) `               | :doc:`npt/sphere (o) ` | :doc:`nve (ckio) `          | :doc:`nve/asphere (i) `       | :doc:`nve/asphere/noforce ` | :doc:`nve/body `           |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`nve/limit `           | :doc:`nve/line `          | :doc:`nve/noforce `                   | :doc:`nve/sphere (o) ` | :doc:`nve/tri `         | :doc:`nvt (cko) `                      | :doc:`nvt/asphere (o) `             | :doc:`nvt/sllod (o) `     |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`nvt/sphere (o) `     | :doc:`oneway `              | :doc:`orient/fcc `                     | :doc:`planeforce `     | :doc:`poems `             | :doc:`pour `                         | :doc:`press/berendsen `         | :doc:`print `                 |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`property/atom `   | :doc:`qeq/comb (o) `      | :doc:`qeq/dynamic `                           | :doc:`qeq/fire `              | :doc:`qeq/point `           | :doc:`qeq/shielded `                  | :doc:`qeq/slater `                          | :doc:`rattle `                |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`reax/bonds `         | :doc:`recenter `          | :doc:`restrain `                         | :doc:`rigid (o) `           | :doc:`rigid/nph (o) `     | :doc:`rigid/npt (o) `               | :doc:`rigid/nve (o) `                     | :doc:`rigid/nvt (o) `         |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`rigid/small (o) `         | :doc:`rigid/small/nph `      | :doc:`rigid/small/npt `                     | :doc:`rigid/small/nve `     | :doc:`rigid/small/nvt `   | :doc:`setforce (ck) `            | :doc:`shake (c) `                         | :doc:`spring `               |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`spring/rg `           | :doc:`spring/self `    | :doc:`srd `                                   | :doc:`store/force `   | :doc:`store/state ` | :doc:`temp/berendsen (c) ` | :doc:`temp/csld `                     | :doc:`temp/csvr `         |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`temp/rescale (c) ` | :doc:`tfmc `                  | :doc:`thermal/conductivity ` | :doc:`tmd `                   | :doc:`ttm `                 | :doc:`tune/kspace `           | :doc:`vector `                           | :doc:`viscosity `         |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`viscous (c) `           | :doc:`wall/colloid `          | :doc:`wall/gran `                       | :doc:`wall/harmonic `        | :doc:`wall/lj1043 `        | :doc:`wall/lj126 `                   | :doc:`wall/lj93 `                          | :doc:`wall/piston `     |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
+| :doc:`wall/reflect (k) ` | :doc:`wall/region `    | :doc:`wall/srd `                         |                                        |                                      |                                                |                                                      |                                          |
++--------------------------------------------+-----------------------------------------+--------------------------------------------------------+----------------------------------------+--------------------------------------+------------------------------------------------+------------------------------------------------------+------------------------------------------+
 
 These are additional fix styles in USER packages, which can be used if
 :ref:`LAMMPS is built with the appropriate package `.
@@ -493,7 +493,7 @@ These are additional fix styles in USER packages, which can be used if
 +--------------------------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------------------------------------+----------------------------------------------------+------------------------------------------------------+------------------------------------------------------+
 | :doc:`adapt/fep `                                         | :doc:`addtorque `                    | :doc:`atc `                                                             | :doc:`ave/correlate/long ` | :doc:`ave/spatial/sphere `   | :doc:`colvars `                         |
 +--------------------------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------------------------------------+----------------------------------------------------+------------------------------------------------------+------------------------------------------------------+
-| :doc:`drude `                                                 | :doc:`drude/transform/direct ` | :doc:`drude/transform/reverse `                             | :doc:`eos/cv `                         | :doc:`eos/table `                     | :doc:`gle `                                 |
+| :doc:`drude `                                                 | :doc:`drude/transform/direct ` | :doc:`drude/transform/reverse `                             | :doc:`eos/cv `                         | :doc:`eos/table `                     | :doc:`gle `                                 |
 +--------------------------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------------------------------------+----------------------------------------------------+------------------------------------------------------+------------------------------------------------------+
 | :doc:`imd `                                                     | :doc:`ipi `                                | :doc:`langevin/drude `                                       | :doc:`langevin/eff `             | :doc:`lb/fluid `                       | :doc:`lb/momentum `                 |
 +--------------------------------------------------------------------------+-----------------------------------------------------+----------------------------------------------------------------------------------+----------------------------------------------------+------------------------------------------------------+------------------------------------------------------+
@@ -800,13 +800,13 @@ LAMMPS is built with the :doc:`appropriate accelerated package `      | :doc:`ewald/disp `  | :doc:`msm (o) `   | :doc:`msm/cg (o) `      |
-+--------------------------------------+-----------------------------------+---------------------------------+---------------------------------------+
-| :doc:`pppm (cgo) `     | :doc:`pppm/cg (o) ` | :doc:`pppm/disp ` | :doc:`pppm/disp/tip4p ` |
-+--------------------------------------+-----------------------------------+---------------------------------+---------------------------------------+
-| :doc:`pppm/tip4p (o) ` |                                   |                                 |                                       |
-+--------------------------------------+-----------------------------------+---------------------------------+---------------------------------------+
++------------------------------------+--------------------------------------+---------------------------------+---------------------------------------+
+| :doc:`ewald (o) `    | :doc:`ewald/disp `     | :doc:`msm (o) `   | :doc:`msm/cg (o) `      |
++------------------------------------+--------------------------------------+---------------------------------+---------------------------------------+
+| :doc:`pppm (cgo) `   | :doc:`pppm/cg (o) `    | :doc:`pppm/disp ` | :doc:`pppm/disp/tip4p ` |
++------------------------------------+--------------------------------------+---------------------------------+---------------------------------------+
+| :doc:`pppm/stagger ` | :doc:`pppm/tip4p (o) ` |                                 |                                       |
++------------------------------------+--------------------------------------+---------------------------------+---------------------------------------+
 
 
 .. _lws: http://lammps.sandia.gov
diff --git a/doc/_sources/Section_python.txt b/doc/_sources/Section_python.txt
index 966370ebcd..e8d36e0187 100644
--- a/doc/_sources/Section_python.txt
+++ b/doc/_sources/Section_python.txt
@@ -158,8 +158,10 @@ and callbacks to LAMMPS.
 To run pure Python code from LAMMPS, you only need to build LAMMPS
 with the PYTHON package installed:
 
-make yes-python
-make machine
+.. parsed-literal::
+
+   make yes-python
+   make machine
 
 Note that this will link LAMMPS with the Python library on your
 system, which typically requires several auxiliary system libraries to
@@ -189,7 +191,7 @@ Instructions on how to build LAMMPS as a shared library are given in
 that is dynamically loadable, which is what Python requires to wrap
 LAMMPS.  On Linux this is a library file that ends in ".so", not ".a".
 
->From the src directory, type
+From the src directory, type
 
 .. parsed-literal::
 
@@ -202,10 +204,13 @@ load by default.  Note that if you are building multiple machine
 versions of the shared library, the soft link is always set to the
 most recently built version.
 
-If this fails, see :ref:`Section_start 5 ` for
-more details, especially if your LAMMPS build uses auxiliary libraries
-like MPI or FFTW which may not be built as shared libraries on your
-system.
+.. note::
+
+   If you are building LAMMPS with an MPI or FFT library or other
+   auxiliary libraries (used by various packages), then all of these
+   extra libraries must also be shared libraries.  If the LAMMPS
+   shared-library build fails with an error complaining about this, see
+   :ref:`Section_start 5 ` for more details.
 
 
 ----------
@@ -723,17 +728,6 @@ version = lmp.version()  # return the numerical version id, e.g. LAMMPS 2 Sep 20
 ----------
 
 
-.. note::
-
-   Currently, the creation of a LAMMPS object from within lammps.py
-   does not take an MPI communicator as an argument.  There should be a
-   way to do this, so that the LAMMPS instance runs on a subset of
-   processors if desired, but I don't know how to do it from Pypar.  So
-   for now, it runs with MPI_COMM_WORLD, which is all the processors.  If
-   someone figures out how to do this with one or more of the Python
-   wrappers for MPI, like Pypar, please let us know and we will amend
-   these doc pages.
-
 The lines
 
 .. parsed-literal::
diff --git a/doc/_sources/fix.txt b/doc/_sources/fix.txt
index abcf0208ea..f48fc44992 100644
--- a/doc/_sources/fix.txt
+++ b/doc/_sources/fix.txt
@@ -231,7 +231,8 @@ of :ref:`this page `.
 * :doc:`press/berendsen ` - pressure control by      Berendsen barostat
 * :doc:`print ` - print text and variables during a simulation
 * :doc:`property/atom ` - add customized per-atom values
-* :doc:`qeq/comb ` - charge equilibration for COMB potential :doc:`qeq/dynamic ` - charge equilibration via dynamic method :doc:`qeq/fire ` - charge equilibration via FIRE minimizer :doc:`qeq/point ` - charge equilibration via point method :doc:`qeq/shielded ` - charge equilibration via shielded method :doc:`qeq/slater ` - charge equilibration via Slater method :doc:`reax/bonds ` - write out ReaxFF bond information :doc:`recenter ` - constrain the center-of-mass position   of a group of atoms
+* :doc:`qeq/comb ` - charge equilibration for COMB potential :doc:`qeq/dynamic ` - charge equilibration via dynamic method :doc:`qeq/fire ` - charge equilibration via FIRE minimizer :doc:`qeq/point ` - charge equilibration via point method :doc:`qeq/shielded ` - charge equilibration via shielded method :doc:`qeq/slater ` - charge equilibration via Slater method :doc:`rattle ` - RATTLE constraints on bonds and/or angles
+* :doc:`reax/bonds ` - write out ReaxFF bond information :doc:`recenter ` - constrain the center-of-mass position   of a group of atoms
 * :doc:`restrain ` - constrain a bond, angle, dihedral
 * :doc:`rigid ` - constrain one or more clusters of atoms to      move as a rigid body with NVE integration
 * :doc:`rigid/nph ` - constrain one or more clusters of atoms to      move as a rigid body with NPH integration
diff --git a/doc/_sources/fix_wall_region.txt b/doc/_sources/fix_wall_region.txt
index 12d418b06b..1125858428 100644
--- a/doc/_sources/fix_wall_region.txt
+++ b/doc/_sources/fix_wall_region.txt
@@ -43,9 +43,13 @@ from 1, 2, or 3 faces of the block.
 Regions are defined using the :doc:`region ` command.  Note that
 the region volume can be interior or exterior to the bounding surface,
 which will determine in which direction the surface interacts with
-particles, i.e. the direction of the surface normal.  Regions can
-either be primitive shapes (block, sphere, cylinder, etc) or
-combinations of primitive shapes specified via the *union* or
+particles, i.e. the direction of the surface normal.  The surface of
+the region only exerts forces on particles "inside" the region; if a
+particle is "outside" the region it will generate an error, because it
+has moved through the wall.
+
+Regions can either be primitive shapes (block, sphere, cylinder, etc)
+or combinations of primitive shapes specified via the *union* or
 *intersect* region styles.  These latter styles can be used to
 construct particle containers with complex shapes.  Regions can also
 change over time via the :doc:`region ` command keywords (move)
diff --git a/doc/fix.html b/doc/fix.html
index ebddae8661..485cf8a69e 100644
--- a/doc/fix.html
+++ b/doc/fix.html
@@ -337,7 +337,8 @@ of this p
 
  • press/berendsen - pressure control by      Berendsen barostat
    • 
 
  • print - print text and variables during a simulation
    • 
 
  • property/atom - add customized per-atom values
    • 
-
  • qeq/comb - charge equilibration for COMB potential qeq/dynamic - charge equilibration via dynamic method qeq/fire - charge equilibration via FIRE minimizer qeq/point - charge equilibration via point method qeq/shielded - charge equilibration via shielded method qeq/slater - charge equilibration via Slater method reax/bonds - write out ReaxFF bond information recenter - constrain the center-of-mass position   of a group of atoms
    • 
+
  • qeq/comb - charge equilibration for COMB potential qeq/dynamic - charge equilibration via dynamic method qeq/fire - charge equilibration via FIRE minimizer qeq/point - charge equilibration via point method qeq/shielded - charge equilibration via shielded method qeq/slater - charge equilibration via Slater method rattle - RATTLE constraints on bonds and/or angles
    • 
+
  • reax/bonds - write out ReaxFF bond information recenter - constrain the center-of-mass position   of a group of atoms
    • 
 
  • restrain - constrain a bond, angle, dihedral
    • 
 
  • rigid - constrain one or more clusters of atoms to      move as a rigid body with NVE integration
    • 
 
  • rigid/nph - constrain one or more clusters of atoms to      move as a rigid body with NPH integration
    • 
diff --git a/doc/fix.txt b/doc/fix.txt
index d4018751f9..a1aa45b5f5 100644
--- a/doc/fix.txt
+++ b/doc/fix.txt
@@ -234,6 +234,7 @@ of "this page"_Section_commands.html#cmd_5.
 "qeq/point"_fix_qeq.html - charge equilibration via point method \
 "qeq/shielded"_fix_qeq.html - charge equilibration via shielded method \
 "qeq/slater"_fix_qeq.html - charge equilibration via Slater method \
+"rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
 "reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information \
 "recenter"_fix_recenter.html - constrain the center-of-mass position \
   of a group of atoms
diff --git a/doc/fix_wall_region.html b/doc/fix_wall_region.html
index 03a310e5df..7e551255fc 100644
--- a/doc/fix_wall_region.html
+++ b/doc/fix_wall_region.html
@@ -163,9 +163,12 @@ from 1, 2, or 3 faces of the block.
    
 
    Regions are defined using the region command.  Note that
 the region volume can be interior or exterior to the bounding surface,
 which will determine in which direction the surface interacts with
-particles, i.e. the direction of the surface normal.  Regions can
-either be primitive shapes (block, sphere, cylinder, etc) or
-combinations of primitive shapes specified via the union or
+particles, i.e. the direction of the surface normal.  The surface of
+the region only exerts forces on particles “inside” the region; if a
+particle is “outside” the region it will generate an error, because it
+has moved through the wall.
    
+
    Regions can either be primitive shapes (block, sphere, cylinder, etc)
+or combinations of primitive shapes specified via the union or
 intersect region styles.  These latter styles can be used to
 construct particle containers with complex shapes.  Regions can also
 change over time via the region command keywords (move)
diff --git a/doc/fix_wall_region.txt b/doc/fix_wall_region.txt
index 2d8bec3007..b5d1c089d4 100644
--- a/doc/fix_wall_region.txt
+++ b/doc/fix_wall_region.txt
@@ -41,9 +41,13 @@ from 1, 2, or 3 faces of the block.
 Regions are defined using the "region"_region.html command.  Note that
 the region volume can be interior or exterior to the bounding surface,
 which will determine in which direction the surface interacts with
-particles, i.e. the direction of the surface normal.  Regions can
-either be primitive shapes (block, sphere, cylinder, etc) or
-combinations of primitive shapes specified via the {union} or
+particles, i.e. the direction of the surface normal.  The surface of
+the region only exerts forces on particles "inside" the region; if a
+particle is "outside" the region it will generate an error, because it
+has moved through the wall.
+
+Regions can either be primitive shapes (block, sphere, cylinder, etc)
+or combinations of primitive shapes specified via the {union} or
 {intersect} region styles.  These latter styles can be used to
 construct particle containers with complex shapes.  Regions can also
 change over time via the "region"_region.html command keywords (move)
diff --git a/doc/searchindex.js b/doc/searchindex.js
index 86b36d7b53..1a26081c6b 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
@@ -1 +1 @@
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er:3,affect:[1,6,10,14,15,16,17,40,60,61,71,90,121,145,154,168,174,195,196,201,208,209,211,212,213,214,217,218,219,220,222,223,233,239,241,243,249,256,260,261,262,263,265,266,267,273,278,279,280,282,303,304,317,331,341,354,360,366,367,368,370,371,372,375,402,423,424,431,473,474,476,478,479,481,484,486],affin:[16,17,18,222,375,391],afil:237,aforement:18,afresh:[291,484,502],afshar:396,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,148,149,150,151,152,153,154,157,158,159,160,162,163,170,171,173,174,177,178,183,192,193,194,195,196,197,199,200,201,205,206,208,209,216,217,218,219,220,222,226,235,246,247,248,249,250,255,256,257,259,265,266,267,273,278,279,280,282,285,289,293,301,303,306,315,320,322,323,324,326,327,328,329,330,334,336,338,342,345,346,352,359,365,366,368,369,371,373,374,375,376,377,382,389,391,400,401,402,403,409,410,411,422,423,424,426,427,428,429,433,437,439,440,447,448,457,458,460,461,462,465,471,473,475,476,477,478,479,481,482,484,486,488,490,493,494,497,501,502,503,504,505,506],afterrun:484,afterward:3,afterword:41,ag1:169,ag2:169,again:[6,11,12,16,17,62,144,150,156,164,193,196,222,239,289,345,359,370,423,424,471,473,474,476,478,483,490,492,502,504],against:[11,12,13,64,223,370,439,440],aggreg:[6,12,65,68,69,79,95,112,119,239,255,301,303,317,471,503],aggress:[239,490],agilio:[9,13],agre:[3,8,190,368,377,411,440],agreement:[5,7],ahd:408,ahead:338,aidan:[0,5,7,9,13,363],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:195,akohlmei:[7,9,13,197,240],aktulga:[7,9,296,440],al2o3:447,al2o3_001:[122,304],al3:169,ala:[246,447],alain:9,alat:[284,426],alb:[437,460,462],albeit:302,albert:9,alchem:[89,164],alcohol:334,alcu:[376,382],alcu_eam:437,alderton:395,alejandr:[259,260],alessandro:13,algebra:429,algorithm:[0,1,6,7,8,9,41,61,196,205,216,219,222,246,248,249,273,286,294,303,306,307,326,327,331,334,339,366,367,368,372,375,398,402,424,429,444,446,471,473,490],alia:[12,16],alias:[1,361],aliceblu:196,align:[6,12,29,41,71,172,190,212,216,241,363,476,479,497],alkali:402,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,158,163,164,165,166,167,168,169,170,171,172,173,174,176,178,183,189,190,193,194,195,196,197,199,200,201,202,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,252,254,255,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,298,299,300,301,302,303,304,305,306,307,308,309,310,311,315,316,318,319,320,321,322,323,326,327,328,329,330,331,332,333,334,336,337,338,339,340,341,342,343,344,345,346,350,355,358,359,360,361,362,363,365,368,369,370,371,372,374,375,376,377,378,380,381,382,383,385,386,387,388,389,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,473,474,475,476,477,478,479,480,481,483,484,485,486,487,488,489,490,491,493,494,495,497,501,502,503,504,505,506],allen:[29,89,395,405],allentildeslei:89,allign:3,allindex:343,alloc:[3,5,6,8,9,11,12,60,233,333,369,371,375,435,440,476,484],allocat:3,alloi:[],allosw:71,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,94,110,112,146,148,149,150,163,168,169,170,172,178,189,190,193,195,196,197,199,200,202,204,205,206,208,209,210,211,212,213,214,216,218,219,220,221,222,223,227,228,233,235,236,237,238,240,243,246,249,250,254,256,259,260,284,288,289,290,291,292,293,297,303,304,306,308,310,311,315,319,326,327,328,329,331,332,333,334,335,336,342,344,346,355,360,361,363,368,369,370,371,374,375,378,382,383,384,385,386,387,392,400,402,406,407,408,409,414,418,423,424,429,431,437,440,441,444,446,447,456,466,468,471,474,476,478,479,480,481,482,483,486,488,489,490,493,494,502,503],almost:[2,3,12,60,241,293,331,361,372,375,456],alo:392,alon:[6,7,219,299,439,440,474],alond:13,along:[6,8,9,12,29,40,71,89,122,168,169,170,192,193,195,208,219,241,246,247,251,256,258,293,303,306,308,312,316,317,326,330,331,337,340,342,363,366,367,368,370,392,395,406,409,412,414,418,426,439,440,459,476,479,486,487,502],alonso:[427,428],alpha:[6,12,51,200,246,285,293,294,298,368,376,379,383,392,396,398,400,401,403,408,413,414,426,432,436,461,463,494,497],alpha_:[],alpha_c:422,alpha_i:448,alpha_ialpha_j:[],alpha_lj:422,alphabet:[2,3,22,37,44,55,63,178,189,199,346,355,369,389,457,476],alphanumer:[3,63,199,292,300,344,369,502],alreadi:[3,7,8,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dia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,177,178,189,345,346,355,388,457],compat:[3,5,7,8,9,11,12,13,17,18,41,71,121,123,181,193,197,201,207,208,209,211,212,213,214,216,285,297,323,326,333,336,339,360,375,410,429,431,459,473,474,502],compens:[6,217,218,301,371,402],compet:330,competit:361,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,168,193,194,195,197,240,330,361,375,429,476,477,481,502],compl:17,complain:[12,17],complement:426,complementari:[7,392,414],complet:[3,6,9,11,12,15,41,59,71,196,212,216,221,249,286,289,292,319,330,332,344,359,370,375,403,444,446,464,471,476,481,484,488,490,493,497,502],complex:[6,8,11,12,13,25,40,42,62,94,110,144,146,158,170,171,246,315,340,358,370,402,429,459,474,476,479,502],compli:[326,330],complic:[6,7,9,12,13,206,235,474],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,90,91,92,93,94,96,97,100,107,108,109,110,111,112,113,114,116,117,121,131,134,135,136,137,140,141,142,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,165,166,167,192,193,195,196,202,203,207,208,209,210,211,212,213,214,215,219,220,222,223,228,233,238,242,243,246,249,251,255,256,258,259,260,264,265,266,267,278,279,280,282,283,285,286,287,290,301,303,305,306,308,312,313,316,319,322,323,324,326,333,334,339,340,341,360,363,367,368,369,370,375,381,396,402,406,423,424,444,446,447,448,476,477,486,494,502,503],componenet:6,composit:[6,206,246,400],compound:[391,402,403,465],compres:[71,118,208],compress:[],compris:[40,340,441,464],compton:[122,169],comptu:3,compuat:361,comput:[],computation:[3,6,217,218,331,382],computational:497,compute_arrai:8,compute_fep:[201,422],compute_group_group:235,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[122,304],compute_scalar:8,compute_temp:8,compute_ti:201,compute_vector:8,compute_xrd:169,concaten:[2,3,505],concav:340,concentr:[71,400],concept:[6,150,160,208,485],conceptu:[3,6,71,158,220,222,370,392,409,426,481],concern:[6,73,89,194,236],concetr:71,concis:[11,330],conclud:12,concret:8,concurr:[9,16,361,502],conden:[331,460,462],condens:[6,152,331,377,394,400,414,465],condit:[],conducit:6,conduct:[],cone:479,confer:429,confid:[3,490],config:[12,193,473],configfil:221,configur:[1,2,6,12,15,17,38,59,126,172,190,192,193,195,199,220,221,222,223,227,235,242,243,273,286,294,330,358,368,370,377,382,401,426,429,458,460,462,465,471,476,478,479,490],confin:[476,490],conflict:[3,12,40,431,474],conform:[3,6,13,59,219,220,258,302,308,330,354,370,402,488],confus:[3,465],conjuct:396,conjug:[7,8,243,367,402,439,440],conjunct:[6,7,71,88,89,118,153,158,164,170,174,196,200,201,243,246,250,273,289,290,294,295,296,298,303,307,319,327,334,339,360,361,370,383,385,389,392,396,402,408,414,431,434,442,463,476,479,483,497,506],connect:[3,6,89,155,173,219,240,288,303,306,316,370,393,406,456,462,473,474,480,497],conput:3,consecut:[3,11,12,39,71,170,196,200,201,223,240,241,392,414,418,471,477,479],consequ:[1,6,206,331,413,490],conserv:[],consid:[6,9,70,71,78,89,119,152,155,156,173,193,196,200,201,207,209,212,216,218,219,223,247,260,285,303,326,327,330,331,334,361,389,402,409,440,441,447,456,471,472,474,477,478,479,481,484,486,494,497,502],consider:[6,8,243,244,322,323,324,375,485],consist:[3,6,8,9,11,12,40,42,65,69,79,95,107,112,115,116,119,150,153,155,170,182,192,197,202,203,208,222,223,226,228,233,236,243,244,245,256,259,261,262,263,264,265,266,267,268,269,271,272,273,274,276,277,278,279,280,281,282,290,293,298,300,302,303,322,323,324,325,335,360,361,363,369,370,375,377,382,384,390,392,402,405,409,412,423,424,426,429,431,441,444,446,447,459,466,474,476,477,478,479,480,481,488,497,502],consistent_fe_initi:205,consit:303,constant:[],constitu:[3,6,249,303,336,340,390,441],constitut:[444,446],constrain:[3,6,8,147,148,149,150,151,153,156,157,158,159,160,162,163,199,208,223,235,236,241,249,253,288,289,301,303,306,317,327,334,368,369,402,481,488,497],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,94,110,122,144,169,220,259,285,302,340,371,375,395,429,431,456,458,459,479,480,495,502],constructor:[8,11],consult:440,consum:[1,298,435,502],consumpt:358,contact:[],contact_stiff:[443,445],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,89,93,120,122,144,150,158,168,169,170,172,176,178,189,190,193,195,196,197,199,200,201,205,207,208,209,211,212,213,214,216,221,223,228,231,237,241,242,243,246,257,273,284,285,288,289,291,293,296,300,303,304,309,319,326,330,331,340,341,344,359,361,369,370,373,374,376,377,378,382,391,392,395,400,401,402,409,410,426,429,433,437,438,439,440,448,458,459,460,461,462,463,465,471,472,473,474,476,477,478,479,481,483,485,488,490,491,493,494,497,502,504,506],content:[12,18,440,492,494],context:[3,6,8,12,17,120,121,196,217,218,223,288,300,335,367,468,476,483,492,501,502,503],contibut:70,contigu:473,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,106,107,166,196,199,200,201,206,208,209,210,211,212,213,214,216,219,220,221,222,223,235,236,237,239,240,241,243,244,245,251,256,257,259,261,262,263,264,265,266,267,278,279,280,281,282,287,289,292,293,303,304,308,318,319,321,328,329,331,337,340,344,359,374,375,382,396,399,416,419,439,440,441,444,446,461,471,474,476,478,479,484,490,491,493,494,502,504],continuum:[6,7,9,205,331,444,446],contour_integr:205,contract:[59,220,222,259,290,303],contradictori:3,contrain:306,contraint:273,contrari:[237,244],contrast:[1,6,42,55,64,152,155,222,342,444,446,468,505],contrib:331,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,86,89,90,91,92,93,96,105,107,109,111,112,113,114,116,118,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,201,206,207,208,209,211,212,213,214,220,235,243,246,249,250,254,260,280,281,288,289,297,300,303,304,306,333,360,368,370,378,396,399,400,402,409,423,424,429,431,439,440,447,488,494,497],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,89,93,126,144,179,193,195,199,205,206,216,220,221,222,239,240,243,244,259,261,262,263,264,265,266,267,290,295,303,310,311,322,323,324,331,335,358,360,372,402,405,429,439,440,443,445,458,462,471,473,485,491,492],control_typ:205,controlfil:440,convect:93,conveni:[6,12,29,193,197,214,304,363,448,502],convent:[3,8,9,29,181,188,189,196,302,316,343,400,402,502],converg:[3,6,41,90,193,195,197,202,216,219,220,228,233,264,293,295,298,302,306,366,367,368,370,391,392,414,447,471,483,490],convers:[3,8,144,195,196,206,209,290,360,392,393,394,402,414,418,422,434,474,490,501],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,93,170,177,193,195,196,214,257,289,342,345,347,351,354,363,370,376,400,429,460,462,469,474,476,477,478,483,493,497,501,502,504,506],convex:[42,340,381],convinc:[7,12],cook:9,cooki:7,cool:[7,160,239,301],cooordin:193,cooper:[5,7],coord123:118,coord1:[3,118,208,212,213],coord2:[3,118,208,212,213],coord3:[3,118,208,212,213],coord:[],coordb:447,coordbb:447,coordiat:368,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,89,91,92,96,106,107,109,117,118,120,138,144,153,159,165,167,168,170,174,192,193,194,195,196,197,199,202,207,208,211,212,213,216,217,218,219,220,221,222,223,226,228,229,233,235,238,239,240,241,242,243,244,256,258,259,261,262,263,265,266,267,280,283,284,285,288,289,290,300,301,303,305,306,308,313,316,317,318,319,321,329,330,331,338,339,341,342,363,368,369,370,375,376,377,380,381,401,447,471,476,477,478,479,481,484,486,490,497,502,503],coordn:[118,208],coorind:[],copi:[0,3,4,8,11,12,15,17,40,123,195,331,370,389,439,474],copper:469,coproccesor:16,coprocessor:[1,4,7,9,16,17,375,489],coproprocessor:17,copy_arrai:8,copyright:[7,8,288],coral:196,core:[],core_shel:152,coreshel:[6,9,385,392,394],cornel:[6,176,488],corner123i:117,corner123x:117,corner123z:117,corner1i:117,corner1x:117,corner1z:117,corner2i:117,corner2x:117,corner2z:117,corner3i:117,corner3x:117,corner3z:117,corner:[3,6,40,117,195,340,341,363,464,476],cornflowerblu:196,cornsilk:196,corp:9,corpor:16,corr:391,correct:[3,6,9,11,12,16,17,59,89,90,105,106,114,120,152,157,164,195,222,235,237,243,259,260,280,288,290,293,330,336,340,360,370,376,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,464,465,467,468,469,476,491,494,497],correction_max_iter:205,correctli:[3,8,9,11,17,71,81,105,106,107,147,148,149,151,153,155,156,157,158,159,162,163,166,193,196,202,223,228,233,244,253,259,260,296,303,306,316,318,337,340,370,371,375,394,424,429,473,474,476,486,501,503],correl:[],correpond:231,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,89,99,100,113,116,117,118,119,122,123,131,134,135,136,137,138,140,141,142,144,147,148,157,164,168,169,176,177,178,179,180,181,182,184,185,187,188,190,192,193,195,196,200,201,202,208,210,211,212,213,215,218,220,222,229,233,234,238,243,246,247,255,256,257,259,261,262,263,264,265,266,267,268,269,273,276,278,279,280,282,285,286,290,295,303,305,306,322,324,326,335,336,337,339,340,341,343,345,346,347,348,350,351,354,356,361,365,367,369,370,376,377,379,383,384,385,386,387,388,389,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,412,414,415,416,417,418,419,420,421,422,423,426,427,429,431,432,433,434,436,437,439,440,441,442,447,448,449,458,459,460,461,462,465,467,468,469,471,473,474,476,477,479,489,490,491,493,494,497,502],correspondingli:[423,424,485],cosin:[],cosineshift:27,cosmo:[237,242],cossq:[],cost:[1,6,10,11,12,17,39,41,71,113,122,145,169,195,196,208,212,213,216,217,218,232,259,295,331,360,361,373,392,414,418,429,431,458,473,485],costheta0:[458,460,462,465],costheta:437,costli:[11,90,237,371],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,89,92,96,107,109,113,116,118,150,160,165,167,183,193,195,196,200,201,208,209,212,216,222,233,242,292,293,294,298,301,303,305,319,320,326,330,331,332,336,340,342,344,352,357,359,366,368,371,375,378,404,408,409,412,439,440,472,473,474,476,478,480,483,484,491,492,497,502,503],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,90,111,112,120,145,171,175,294,296,332,360,361,368,375,383,385,386,387,388,391,392,393,394,395,402,406,407,409,414,418,422,425,431,434,439,440,442,447,457,462,463,465,468,481,488,494,497,501],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,93,118,120,121,158,168,174,202,203,206,208,211,212,213,215,216,223,228,232,235,241,259,273,289,306,322,323,340,361,368,369,370,372,375,404,408,431,494,502],counter:[337,471,482,484,490],counteract:235,counterbal:239,counterbalanc:29,counterpart:[193,303,471],counterproduct:18,coupl:[],courant:309,cours:[3,8,130,132,164,193,200,201,236,302,316,330,336,338,339,341,342,361,423,449,473,476,489,497,502,504],courtesi:363,cov:447,coval:[6,29,402,426,447,497],covari:237,cover:[6,71,190,196,205,246,402,464],coverag:[71,212],cpc:242,cpp:[1,3,6,8,9,11,12,13,89,193,200,201,233,306],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,196,210,226,244,332,358,361,375,389,457,471,489,490,493,494,495,502],cpuremain:494,cr2:169,cr3:169,crack:[4,371],crada:[5,7],crai:[5,7,13,18,193],crash:[3,12,371,497],craympi:375,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:205,create_faceset:205,create_group:194,create_nodeset:205,createatom:[],creation:[],crimson:196,critchlei:288,criteria:[3,120,171,195,196,217,218,219,254,368,436,464,478,481,502],criterion:[12,41,125,170,173,206,216,219,235,273,295,309,337,342,368,370,391,402,406,447,481,490,491],criterioni:490,critic:[6,48,49,257,326,331,368],crmax:71,crmin:71,cross:[3,12,22,71,91,148,168,178,193,195,207,212,218,222,256,258,280,303,312,316,318,327,334,346,363,370,387,396,399,400,407,408,409,414,416,418,437,442,444,446,460,462,469,476,480,486,504],crossov:1,crossterm:476,crozier:[0,7,13],crucial:293,crystal:[4,6,13,73,110,284,285,329,363,371,480,494,497],crystallin:[6,106,285,363,461,497],crystallis:326,crystallogr:[122,169],crystallograph:[363,494],crystallographi:[122,169,363],cs1:169,cs_chunk:6,cs_im:[40,476],cs_re:[40,476],csanyi:[144,438,448],cscl:426,csequ:6,csh:[11,12,389],cshrc:[11,12],csic:[401,458,460,462,465],csinfo:6,csisi:[401,458,460,462,465],csld:[],cst:400,cstherm:6,cstyle:473,csvr:[],ctcm:[376,400],ctemp_cor:226,cterm:308,ctr:9,ctype:11,cu1:169,cu2:169,cu3au:426,cube:[6,41,168,173,216,226,340,363,497],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:382,cummul:[3,6,214,217,218,219,221,232,237,243,245,319,322,323,324,325,327,334,408,494],cumul:[6,206,208,211,212,213,227,235,243,257,259,264,273,303,304,370],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,89,105,106,112,120,121,134,145,150,158,160,166,168,171,174,192,193,194,195,196,197,200,201,205,208,212,213,214,216,217,218,219,220,221,222,223,227,228,233,235,237,240,241,243,249,256,259,260,265,266,267,273,278,279,280,282,288,289,294,295,297,300,301,302,303,306,307,308,309,310,311,312,313,315,317,318,319,322,323,324,330,331,334,335,336,337,338,339,341,342,344,358,359,360,361,364,365,367,368,369,370,375,381,382,389,391,395,400,402,403,406,409,410,413,423,424,426,427,428,431,437,439,440,443,444,445,446,449,460,462,463,466,471,472,473,474,476,477,478,479,480,482,483,484,486,488,490,491,493,494,502,503,504,505,506],curv:[6,170,235,285],curvatur:[405,441,469],custom:[],cut0:474,cut1:485,cut2:485,cut:[],cuthi:[284,296],cutinn:[384,423,424],cutlo:[284,296],cutmax:437,cutoff1:[388,395,414,418,422,425,434,442],cutoff2:[383,385,386,388,394,395,414,418,422,425,434,442],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,89,94,110,112,119,120,144,168,171,173,174,218,219,224,231,284,293,294,296,298,300,303,307,319,332,336,340,342,358,360,361,368,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,447,448,449,450,451,452,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,474,478,481,485,497,502],cutoff_glob:381,cutoff_inn:381,cutoffa:401,cutoffc:401,cuu3:400,cval:169,cvd:326,cvel:308,cvff:[],cwiggl:[3,256,336,339,341,502],cyan:[2,195,196],cycl:[3,235,257,259,260,264],cyclic:[3,190],cygwin:12,cylind:[3,4,71,195,208,241,289,337,340,479],cylindr:[6,241,316,337],cypress:375,cyrot:382,cyrstal:285,d3q15:246,d3q19:246,d_double_doubl:15,d_e:331,d_flag2:292,d_flag:292,d_name:[117,193,292,321,486],d_single_doubl:15,d_single_singl:15,d_sx:292,d_sy:292,d_sz:292,daan:329,dai:12,daili:12,daivi:280,damag:[],dammak:298,damp:[3,6,199,204,243,244,245,250,259,260,264,290,293,294,298,303,322,323,335,337,338,367,368,370,383,385,387,392,395,402,406,414,422,434,442,457,463,490,497],damp_com:244,damp_drud:244,dampen:[303,497],dampflag:[337,406],dan:17,danger:[3,12,235,342,396,494],dangl:173,daniel:9,darden:[361,395],darkblu:196,darkcyan:196,darken:195,darkgoldenrod:196,darkgrai:196,darkgreen:196,darkkhaki:196,darkmagenta:196,darkolivegreen:196,darkorang:196,darkorchid:196,darkr:196,darksalmon:196,darkseagreen:196,darkslateblu:196,darkslategrai:196,darkturquois:196,darkviolet:196,dasgupta:294,dash:[406,493],dat:[6,93,190,205,472],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,304],dataset:304,datatyp:3,date:[0,6,12,13,192,439,440,502],datom1:119,datom2:119,datom3:119,datom4:119,datum:[3,6,42,65,68,69,79,95,112,119,193,209],davenport:425,davi:336,david:[9,19,360,361,460,462],daw:[400,437],dbg:14,dcd:[3,6,7,193,194,195,196,197,286,477,481],ddim:192,deactiv:422,dealt:242,debug:[6,7,11,12,13,14,17,122,126,169,170,286,291,358,360,375,410,431,466,474,475,483,486,493,502],deby:[],decai:[94,392,469],decid:[3,6,12,16,71,256,292,303,332,491],decipher:363,declar:194,declin:319,decod:195,decompos:[89,448],decomposit:[3,5,7,18,62,205,286,307],decoupl:[6,497],decreas:[3,193,202,203,210,219,222,228,233,235,243,330,360],decrement:308,deepli:357,deeppink:196,deepskyblu:196,def:[12,13,474],defaul:61,defect:[6,70,168,429],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,176,177,178,179,180,181,182,184,185,187,188,189,190,191,192,193,194,195,196,199,200,201,202,203,204,205,206,207,208,209,211,212,213,214,215,216,217,218,219,220,222,223,226,227,228,230,233,234,235,238,241,242,243,244,245,246,254,256,258,259,260,261,262,263,264,265,266,267,269,270,271,274,276,277,278,279,280,281,282,284,285,286,288,289,290,292,294,296,301,303,304,305,306,309,313,317,319,321,322,323,324,325,327,328,329,331,333,334,336,337,338,339,340,341,342,344,345,346,347,348,349,350,351,354,355,356,358,360,361,363,365,367,368,369,370,371,372,373,374,375,377,378,379,380,381,383,384,385,386,387,388,389,390,392,393,395,396,397,398,399,401,402,404,405,406,407,408,409,410,412,414,415,416,417,418,419,420,421,422,423,424,425,429,430,431,432,433,434,436,437,439,440,441,442,443,444,445,446,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,485,486,487,488,490,491,493,494,497,498,499,500,501,502,503],definit:[2,3,6,8,12,13,78,80,120,144,196,208,209,210,211,212,213,214,222,230,241,264,304,321,333,336,339,341,343,355,358,369,378,382,390,397,398,402,412,437,444,446,448,464,474,476,478,485,487,501,502],defint:494,deform:[],deg2theta:169,deg:497,degener:[3,288],degrad:[8,18,285,361,485],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,94,95,97,99,100,102,104,105,110,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,169,170,176,177,180,181,188,190,192,195,208,219,226,235,237,238,243,244,249,259,260,264,265,266,267,278,279,280,282,286,288,302,303,306,322,323,324,329,345,347,351,354,356,368,395,400,408,486,494,497,503],degress:[150,208],del:490,delai:[3,6,12,371,399,494],deleg:409,delet:[2,3,7,8,12,54,57,60,63,168,173,174,199,208,209,211,212,213,214,217,219,232,235,259,304,322,323,342,344,359,369,371,374,431,456,476,477,478,479,487,488,493,498,500,502,503],delete_atom:[],delete_bond:[],delete_el:205,deli:192,delimit:[474,502],deloc:[260,402,447],delr:426,delt_lo:490,delta:[],delta_1:382,delta_3:382,delta_7:382,delta_conf:3,delta_ij:[426,437],delta_mu:3,delta_pi:382,delta_r:437,delta_sigma:382,delta_ua:381,delx:192,delz:192,dem:381,demand:298,demo:11,demon:283,demonstr:[293,426],den:289,dendrim:408,denniston:[9,246,248,249,250,285],denomin:[7,175],denot:[122,226,244,285,296,298,392,407,409,440,444,446],dens:[71,219,402],densiti:[3,6,7,9,18,40,41,59,103,120,130,144,156,168,170,200,201,205,208,212,213,216,222,233,246,249,252,253,285,289,290,294,331,336,363,365,369,376,382,400,426,427,428,437,441,447,451,453,454,455,476,485,486,494,501],density_continu:446,density_summ:446,depart:[0,7],departur:[257,293],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,94,95,106,112,113,116,117,118,119,123,144,147,153,157,158,164,170,171,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,195,196,199,200,201,202,203,206,208,210,211,212,214,215,216,218,220,222,228,229,234,237,238,239,241,243,244,246,248,249,256,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,284,295,298,300,303,305,306,307,313,319,322,323,324,326,328,330,331,333,335,336,339,340,341,342,344,345,346,347,348,350,351,354,356,361,363,368,369,371,372,373,375,376,377,379,380,382,383,384,385,386,387,388,389,390,391,392,393,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,426,427,429,430,432,433,434,436,437,439,440,441,442,447,448,449,457,458,459,460,461,462,463,465,467,468,469,471,473,476,478,479,482,486,488,490,493,494,496,502,503],dependend:6,depflag:12,dephas:[471,490],depos:223,deposit:[],deprec:[294,439],depth:[51,148,195,331,405,441],dequidt:9,der:[89,111,390,391,422,439,440,468,497],deriv:[6,7,8,9,38,56,63,89,144,164,190,209,220,222,235,243,256,259,261,262,263,264,265,266,267,284,290,294,298,328,329,331,336,337,340,367,369,377,382,390,395,402,403,407,416,420,421,426,429,439,440,457,459,468,497],derjagin:468,derlet:284,descend:196,descent:[7,367],descib:[40,195,294],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,90,114,117,120,122,134,144,145,148,149,150,154,155,158,161,163,164,168,169,170,172,173,182,187,190,193,194,199,200,201,208,209,210,211,212,213,214,216,219,220,221,222,223,225,226,231,236,237,240,241,242,243,244,245,246,248,249,250,254,258,259,260,264,272,281,284,286,291,292,293,294,295,296,303,308,316,319,320,321,322,323,324,325,326,327,328,329,334,336,337,339,344,360,361,363,366,367,368,369,370,374,377,378,380,381,383,384,385,387,388,389,390,391,392,395,400,402,403,405,406,407,409,412,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,436,437,438,439,440,441,442,447,448,449,456,457,458,459,460,461,462,463,465,467,468,469,471,473,474,476,477,478,479,480,486,489,490,493,502,503,504],descript:[],descriptor:[144,193,410],deserno:361,design:[0,3,6,7,8,9,11,13,14,15,17,122,152,155,169,205,219,225,226,259,260,284,285,304,326,331,378,379,380,381,384,387,392,394,402,422,423,424,427,428,437,440,459],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,90,93,116,121,145,152,170,183,192,208,214,220,222,233,235,236,243,244,245,249,259,280,288,289,290,291,294,298,303,306,319,322,323,324,325,330,337,352,357,360,361,363,366,368,369,370,396,400,408,423,424,458,460,462,472,473,474,476,480,485,490,491,493,494,502,503,504],desk:7,desktop:[4,6,7,10,12,195],despit:497,destabil:382,destre:354,destroi:[11,39,217,218],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,92,93,96,105,107,109,111,113,115,116,118,121,123,144,145,147,148,149,150,153,163,164,165,167,170,171,174,175,178,189,192,193,195,196,199,200,201,205,208,209,210,211,212,214,216,218,219,220,221,222,223,233,235,236,237,238,240,241,243,245,246,250,256,257,258,259,260,261,262,263,264,265,266,267,271,273,278,279,280,281,282,285,288,289,290,292,293,295,296,297,303,306,307,319,322,323,324,325,326,327,329,330,331,332,333,334,335,342,344,346,355,360,361,364,368,369,371,372,375,376,377,378,380,381,382,384,386,387,388,389,390,391,392,395,396,402,403,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,425,426,430,431,436,439,440,441,447,448,449,457,464,467,468,474,476,477,478,479,481,482,485,486,488,491,494,495,502,503,506],detect:[2,3,12,42,61,63,88,94,234,289,330,370,391,408,413,471,473,476,487,490,502],determ:375,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,89,105,111,113,116,122,123,131,145,158,159,168,169,170,192,193,195,196,197,198,202,203,204,207,208,209,210,211,212,213,214,215,216,220,222,223,226,228,235,238,239,241,243,244,249,254,256,257,259,265,266,267,278,279,280,282,284,286,289,290,293,300,301,302,303,304,305,309,311,313,319,322,323,324,326,332,333,336,337,338,339,340,341,342,355,360,361,363,369,371,372,375,377,378,386,391,395,399,400,404,406,409,410,418,426,429,431,440,441,447,456,459,463,468,473,476,477,479,481,483,486,490,492,493,495,501,502,503],determinist:307,detil:112,devan:[9,442],devanathan:462,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,240,264,288,293,294,297,377,382,402,428,429,447,465,478],devemi:9,deviat:[257,264,284,404],deviator:9,devic:[1,3,12,15,17,240,375],device_typ:375,devin:[295,391],devis:428,dfactor:195,dff:497,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,361],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,297,429],dhi:[59,192,222,289],dhug:[257,293],dhugoniot:[257,293],dia:426,diagnost:[],diagon:[3,6,85,144,145,146,220,259,290,303,334,444,446],diagonalstyl:448,diagram:[41,122,169,189,216,286],diallo:408,diam:[195,196,289,369],diamet:[3,6,40,42,117,170,193,195,196,200,201,243,289,303,319,321,335,337,369,381,390,405,406,416,441,464,468,476,477,486],diamond:[363,402,426],diamter:[40,289],dick:6,dicsuss:256,dictat:[206,257],did:[3,12,368,396,399,400,406,431,460,462,484],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,166,333,360],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,89,94,97,99,100,124,144,147,148,149,150,151,153,156,157,158,159,160,162,163,164,170,171,173,178,189,190,192,193,195,196,199,201,204,206,208,211,216,217,218,219,220,221,222,226,231,234,235,236,237,238,239,240,243,244,246,256,259,260,261,262,263,265,266,267,269,271,274,276,277,278,279,282,284,286,288,290,293,294,295,298,301,303,30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9,341,354,360,361,390,395,396,398,402,403,406,411,423,424,426,431,441,444,446,451,452,454,455,469,497],equi:260,equidist:258,equil:[3,294,364,483,506],equilater:486,equilibr:[3,4,5,6,7,9,59,93,170,199,206,209,219,220,235,257,259,260,280,281,293,294,295,296,327,328,329,334,391,392,439,440,472,486],equilibria:334,equilibribum:[217,218],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,153,154,177,179,220,222,235,236,237,244,246,259,264,280,293,294,298,302,306,308,316,319,326,327,329,334,345,347,351,354,391,426,433,447,497],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:205,equival:[6,12,13,29,59,61,128,129,137,142,168,172,196,211,214,220,222,235,243,259,280,290,302,303,339,396,402,447,460,462,476,479,484,485,494,497],equlibrium:6,equliibr:[294,296],er3:169,eradiu:[40,117,402,476],eras:[305,328],erat:[222,424],erc:392,erfc:[392,414,431],erforc:117,erg:501,erhart:[206,400,460,462],ermscal:378,ernst:9,eror:3,eros:426,erose_form:426,erot:[],errata:[460,462],erratum:336,erron:3,error:[],erta:406,ervel:[117,476],escap:[223,497],especi:[8,11,16,158,170,199,206,216,235,293,298,301,302,375,473],espresso:[9,297],essenti:[8,11,12,27,90,132,151,152,153,156,157,158,159,160,162,179,209,264,285,335,361,377,392,414,462,481,494],essex:29,establish:[89,239],estim:[1,3,6,10,12,38,41,56,93,145,205,216,227,257,319,326,360,361,366,431,440,459,490,494],esu:501,esub:426,eta:[6,246,259,293,294,296,335,401,403,405,437,461,465,501],eta_dot:259,eta_ij:437,eta_ji:403,etag:[40,476],etail:494,etap:259,etap_dot:259,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,91,92,93,97,113,114,117,119,145,147,150,151,152,153,154,156,157,158,159,160,162,164,170,172,173,174,183,193,195,196,199,200,205,206,207,208,211,212,213,214,217,218,222,223,233,235,236,243,259,289,300,304,331,332,340,344,359,360,368,369,370,371,373,400,401,409,422,424,429,435,439,440,458,460,462,465,471,474,476,477,478,483,485,486,490,491,492,493,494,495,497,501,502,504,506],ethernet:18,etol:[368,370,471,490],etot0:293,etot:[6,97,99,100,114,145,156,196,226,244,257,293,493,494],eu2:169,eu3:169,euler:[368,370],eulerian:205,euqat:450,europhi:246,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,89,90,93,111,121,144,146,150,160,168,170,192,193,195,196,200,201,202,203,205,207,208,209,210,211,212,213,214,215,222,228,236,238,239,241,242,243,244,285,291,294,305,309,313,322,323,324,333,336,339,341,342,344,360,361,366,368,375,429,431,437,443,445,447,459,471,472,474,478,479,481,483,484,485,486,490,492,494,502,503],evalut:[344,474],evan:[158,280],evanseck:[6,20,176,387,488],evapor:[],evaul:[8,368],evdwl:[111,439,440,494],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,123,168,171,172,186,190,193,196,199,200,201,206,207,208,211,212,213,214,216,217,218,220,222,223,226,241,244,257,259,260,285,289,298,300,303,304,315,319,327,331,334,336,340,342,353,360,366,368,370,375,380,402,403,406,409,412,431,441,465,466,476,477,479,481,482,483,485,486,488,491,493,494,495,497,506],evenli:[3,41,145,190,216,246,412,466],event:[],eventu:[3,6,12,15,172,294,490],ever:[54,56,242,319],evera:[390,405,441,457],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,93,117,123,132,158,173,193,194,195,196,197,199,200,201,202,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,227,232,233,235,237,239,240,241,246,247,255,259,260,264,283,284,285,289,290,291,292,293,294,295,296,298,300,301,303,304,306,308,319,321,322,323,324,325,326,327,330,331,332,333,334,342,344,359,361,370,371,372,375,396,399,409,422,439,440,447,453,470,471,472,476,478,480,481,483,484,485,490,491,492,494,502,506],everyth:[8,111],everywher:[120,416],eviri:402,evolut:[237,246,286,471],evolv:[246,286,332],ewald:[2,3,5,6,7,8,12,90,114,122,145,332,360,361,368,383,385,386,392,395,402,414,418,434,442,457,459],ewald_disp:395,ewalddisp:3,exact:[22,41,44,71,126,164,173,178,216,219,236,237,243,244,245,289,298,299,319,331,346,360,389,478,483,490,502,504,506],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,93,120,148,154,161,170,190,200,201,211,216,222,227,231,236,243,244,245,260,272,273,281,285,293,319,324,325,338,375,389,396,400,406,409,423,431,459,478,479,486,490,502],exager:497,examin:[6,8,9,17,219,285],examp:[474,502],exampl:[],exce:[3,6,16,17,18,41,58,71,172,207,208,211,212,213,214,216,220,222,227,232,259,285,300,304,310,311,319,368,375,476,502],exceed:[3,41,59,216,222,259,319,484],excel:402,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,91,92,112,113,116,121,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,170,174,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,196,199,202,208,209,211,215,216,220,222,229,234,235,238,241,243,245,259,260,261,262,263,264,265,266,267,268,269,272,273,276,278,279,280,281,282,286,295,296,303,305,306,316,319,322,324,325,331,335,339,342,344,345,346,347,348,350,351,354,355,356,360,361,363,365,369,370,371,373,374,375,376,377,379,383,384,385,386,387,388,389,390,391,392,394,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,427,432,433,434,436,439,440,441,442,449,457,458,459,460,461,462,465,467,468,469,471,473,474,476,478,479,481,484,485,486,487,488,490,494,497,501,502,503,505],excess:[210,402],exchang:[2,3,6,8,9,61,62,199,205,206,235,243,295,303,327,331,334,360,375,402,491],exchange:360,excit:[9,402],exclud:[3,6,9,12,16,17,63,71,116,144,150,157,158,174,193,208,212,217,218,247,255,288,301,303,326,337,342,368,369,371,384,406,409,412,423,424,431,456,488],exclus:[1,3,9,12,16,89,375,391,429,431,485,495],excurs:[259,471],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,171,195,240,297,344,359,362,374,472,474,484,487,490,502],exempl:447,exemplari:236,exemplifi:402,exert:[6,241,244,298,338,339,340,361],exhaust:[205,374,502],exhibit:[94,259,367,402,485],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,126,170,171,189,194,195,196,199,204,215,218,220,223,235,288,289,291,342,345,347,348,349,351,355,364,369,375,397,398,409,439,456,466,472,474,476,477,478,487,488,489,502,503,504],exit:[2,3,11,12,41,57,193,216,231,359,374,474,475,484,493,502],exlanatori:3,exp:[],expand:[],expans:[12,144,193,487,502],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,105,151,162,168,190,216,228,235,237,256,284,290,292,293,298,303,342,361,371,389,426,429,431,471,474,476,478,481,485,490,502],expens:[6,10,71,196,284,288,303,331,342,360,361,371,375,474],experi:[6,13,15,17,215,223,240,249,258,290,302,303,366,370,396,431,485,490],experienc:[6,12,248,249],experiment:[235,360,375,490],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,88,95,150,158,190,193,195,196,199,208,209,214,216,218,220,222,259,284,292,303,316,342,344,359,360,363,369,370,374,380,400,412,447,449,464,474,477,478,481,483,486,497,502,506],explan:[3,6,59,117,144,193,208,258,284,409,470,473,474,476,485],explanatori:[3,8,121,193,207,208,211,212,213,303,369,473,502],explantori:[3,299],explic:430,explicit:[6,9,11,22,44,77,89,117,120,164,178,200,201,222,310,311,346,365,377,378,382,387,389,400,402,413,423,463,470,473,477,480],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,113,116,147,157,160,168,170,176,177,179,180,181,182,184,185,187,188,190,193,196,202,212,215,222,229,234,236,238,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,292,293,295,303,305,306,322,324,325,331,335,339,345,347,348,350,351,354,356,369,375,376,377,379,383,384,385,386,387,388,389,390,391,392,393,395,396,399,400,401,403,404,405,406,407,408,409,413,414,415,416,417,418,419,420,421,422,423,427,429,431,432,433,434,436,441,442,449,450,451,452,453,454,455,457,458,459,460,461,462,463,465,467,468,469,476,478,479,485,486,488,489,495,497],explictli:[16,489],exploit:[9,15,17,286],explor:[122,169],expon:[3,294,296,400,405,408,422,430,442],exponenti:[89,437,458,465,469,490,502],expos:11,exposit:[205,396,399],express:[6,144,156,170,200,201,220,256,284,294,331,337,344,382,400,402,416,426,447,448,457,502],expressiont:382,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,84,85,86,89,90,93,97,100,101,111,113,121,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,199,202,203,206,214,215,221,224,228,233,234,235,237,238,239,241,243,245,257,259,264,273,284,285,301,302,303,305,308,313,316,318,322,323,324,325,326,328,329,331,333,336,340,341,405,426,429,440,441,448,493,494],extent:[1,3,41,42,45,57,71,168,172,193,204,212,216,241,338,341,360,363,377,443,445,459,473,476,479],exterior:[3,6,168,340],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,105,113,114,116,122,145,147,148,149,151,153,156,157,158,159,160,162,163,169,170,171,172,176,196,211,216,218,259,291,292,293,303,319,368,369,372,373,395,406,409,412,426,431,473,474,476,479,488,497,502],extract:[3,6,11,13,36,63,89,111,119,121,123,200,201,296,370,392,403,426,448,474,481,493],extract_atom:11,extract_comput:[11,474],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,195,210,220,222,259,329,402,461,497],extrema:422,extrins:205,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[166,333],f_a:[460,461,462],f_ave:121,f_c:461,f_f:462,f_fix_id:293,f_harm:329,f_i:[29,437],f_id:[6,71,121,123,193,199,207,208,209,210,211,212,213,214,254,321,333,494,502],f_ij:437,f_indent:214,f_int:328,f_j:29,f_jj:93,f_k:437,f_langevin:331,f_max:[293,298],f_msst:257,f_r:[244,460,461,462],f_sigma:382,f_solid:329,f_ss:6,f_temp:[],face:[3,6,57,59,71,158,168,172,204,212,213,336,338,339,340,341,363,405,426,441,476,479],face_threshold:168,facet:168,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,237,289,319,329,406,447,488],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,89,93,105,112,119,120,122,144,164,169,172,176,187,192,193,195,196,200,201,209,216,220,222,223,235,240,243,245,246,257,259,260,264,286,290,294,302,306,309,311,319,323,327,334,335,336,340,351,361,363,369,375,377,378,382,383,385,387,392,393,394,396,397,398,402,406,409,413,414,426,429,431,433,434,440,442,449,458,463,473,476,479,480,485,488,490,491,494,497,501,502],factori:[3,474],factoriz:360,fail:[3,11,12,59,174,220,223,360,368,370,394,440,474],failur:[125,444,475,502],fairli:[11,431,485,490],faken:73,falcon:240,fall:[3,6,196,211,289,474,502],fals:[88,342,344,447,502],fame:8,famili:[465,473],familiar:[0,11],fan:437,far:[3,6,12,17,57,59,61,88,193,196,197,216,217,218,220,223,259,284,302,303,319,336,347,351,366,370,371,464,474,476,481,494],farago:243,farrel:[460,462],farther:193,fashion:[6,8,41,71,170,196,199,200,201,206,212,216,218,223,235,237,241,256,257,259,261,262,263,264,265,266,267,275,278,279,280,281,282,292,293,295,303,308,312,318,321,329,331,335,336,337,339,341,370,409,423,479,488,502,505],fasolino:411,fast:[6,7,9,12,13,17,39,193,270,293,332,360,361,384,423,424,429,457,459,478,483,485,494,503,506],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,108,113,116,147,157,176,177,179,180,181,182,184,185,187,188,190,193,196,202,215,216,222,229,234,238,242,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,290,294,295,303,305,306,319,322,324,326,328,331,335,339,345,347,348,350,351,354,356,360,361,372,373,375,376,377,379,382,383,384,385,386,387,388,389,390,391,392,395,396,400,401,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,427,432,433,434,436,441,442,449,457,458,459,460,461,462,465,467,468,469,471,479,485,489,497],fastest:[1,6,14,17,158,212,331,332,375,473],fatal:[3,493],fault:[70,440],faulti:12,fava:405,favor:219,favorit:7,fbmc:326,fcc:[],fcm:[275,502],fdirect:226,fdotr:410,fdt:[],fdti:89,fe2:169,fe3:169,fe_md_boundari:205,featu:8,featur:[],fecr:400,feedback:[7,240],feel:[7,240,241,249,284,340,342,370,431],felling:428,felt:340,femtosecond:501,fene:[],fennel:[392,414],fep:[],ferguson:[6,176,488],fermi:[1,12,15,156,375,462],fermion:[9,402],fernando:425,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,63,197,207,208,209,211,212,213,214,244,259,289,292,294,306,333,360,368,369,370,377,447,473,476,481,485,487,495,502,504],fewer:[1,3,11,15,16,61,249,485],fewest:3,fextern:233,feynman:286,fff:474,ffield:[391,403,439,440,447],ffmpeg:[3,12,195],ffplai:195,fft:[1,3,7,12,14,15,90,113,114,145,285,360,361,485],fft_inc:[12,361],fft_lib:12,fft_path:12,fftbench:[360,495],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:456,fictiti:[6,202,203,228,233,237,286,302,392,414,418,456],field1:[477,481],field2:477,field:[],fifth:[316,433],figur:[1,3,8,11,12,293,473,474],fij:395,file0:284,file1:[11,13,284,330,344,369,481,483,487],file2:[11,13,330,344,369,481,483,487],file:[],file_from:194,filen:369,filenam:[3,12,13,38,41,56,190,193,195,196,197,205,208,209,210,211,212,213,214,216,221,231,284,288,291,294,295,296,299,300,303,304,330,331,357,358,359,369,370,376,377,382,392,400,401,403,411,426,427,428,433,437,438,439,440,447,448,458,459,460,461,462,465,472,473,474,477,478,483,487,494,502,504,505,506],filennam:483,filep:[3,193,196,478,483,506],filepo:300,fill:[7,9,170,195,289,331,363,371,382,429,440,479],filter:[196,205],final_integr:8,final_integrate_respa:8,finchham:[6,152,394],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,89,121,173,190,197,206,219,220,231,232,235,258,284,289,290,298,302,366,368,370,371,392,409,414,418,426,447,457,459,497,502],find_custom:8,fine:[16,17,174,202,228,329,371,375,502],finer:[144,170,502],finest:360,finger:[170,192,256,479],finish:[6,11,41,216,344,357,359,360,372,374,375,464,481,502,503],finit:[],finni:[7,400,457],finvers:226,fiorin:[9,221],fire:[],firebrick:196,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,90,93,106,107,108,110,116,120,121,131,134,137,138,142,145,155,158,164,166,168,169,171,172,173,177,190,193,194,195,196,197,199,200,208,209,211,212,213,214,216,219,222,231,235,236,241,246,256,257,258,259,284,286,291,292,293,295,300,303,306,308,316,317,319,320,321,328,329,330,331,333,337,342,344,345,352,363,368,369,370,371,374,375,376,377,380,382,383,385,387,389,391,392,400,402,403,406,407,409,410,411,412,413,414,418,423,424,426,428,429,431,433,437,439,440,447,448,456,458,459,460,461,462,465,469,471,472,473,474,476,477,478,481,483,485,488,489,490,493,494,497,502,503,504,506],fischer:[6,9,19,20,176,387,488],fit:[3,6,9,12,38,56,190,231,302,319,377,382,411,426,431,452,459,461,484,502],five:[73,156,293,369,382,427,476,490],fix:[],fix_adapt:[164,201,422],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,206,289],fix_eo:9,fix_evapor:206,fix_flux:205,fix_gcmc:[206,369],fix_gl:237,fix_gld:237,fix_grav:289,fix_id:[3,220,257,259,261,262,263,264,265,266,267,290,293],fix_modifi:[],fix_mov:[192,337],fix_nh:8,fix_npt:237,fix_nvt:[206,235],fix_poem:[3,6],fix_pour:[3,223],fix_qbmsst:9,fix_qeq:[3,391],fix_rattl:306,fix_reax_bond:439,fix_rigid:[249,380],fix_saed_vtk:304,fix_setforc:8,fix_shak:306,fix_shardlow:9,fix_srd:3,fix_styl:264,fix_temp_rescal:325,fixedpoint:[220,259],fixextern:233,fixid:205,fji:395,flag1:[225,373],flag2:[225,373],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,88,91,92,96,106,107,109,122,165,169,173,193,19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117,118,119,121,123,321],input:[],input_doubl:3,inquir:309,insensit:12,insert:[3,5,7,8,12,59,170,199,223,235,241,289,360,448,456,474,480,497],insid:[2,3,6,8,11,71,133,139,170,193,196,207,212,213,223,224,232,235,241,246,249,289,303,319,336,338,339,340,341,342,358,363,416,474,475,476,478,479,486,490,502],insight:[6,13],instabl:[246,395,446],instal:[],instanc:[6,11,200,221,237,338,404,409,431,437,474,497],instantan:[6,63,219,220,236,237,259,264,285,290,293,298,300,303,326,482,494],instanti:[6,11,12,205,409,473],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,61,63,70,71,92,106,121,148,152,174,190,193,201,208,211,212,213,214,216,220,221,235,243,246,249,250,285,291,301,303,321,339,358,360,361,364,371,375,385,386,400,413,415,422,426,429,471,479,483,490,492,497,502],institut:[9,240,288],instruct:[],insuffici:[3,6,12],insult:259,insur:[3,6,11,12,17,39,40,61,73,105,107,170,171,190,193,195,196,202,217,218,223,228,229,232,233,235,238,243,255,291,292,301,303,319,331,336,340,341,342,344,359,369,371,375,390,405,409,435,441,459,473,474,476,477,481,484,485,493,494,502,503],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,110,117,119,121,123,144,168,170,173,174,176,180,181,185,190,192,193,195,196,206,208,212,213,217,218,219,223,225,233,235,236,237,240,243,244,245,246,285,288,289,292,293,298,303,319,321,323,326,330,331,350,360,363,384,396,398,399,412,426,439,440,444,446,448,471,473,474,475,476,484,485,486,490,493,502,503],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,210,236,438,476],intens:[1,3,6,9,63,66,74,75,88,91,92,93,96,106,107,108,109,116,118,120,121,122,123,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,167,169,199,208,209,211,212,213,214,216,217,218,219,227,232,239,249,257,259,264,300,303,304,319,327,331,333,334,493,494],intepol:502,inter:[14,18,42,61,62,150,173,174,193,219,243,245,258,295,303,360,370,382,486,497,502,504,506],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,40,42,44,50,54,55,57,61,63,65,69,72,77,79,89,90,94,95,110,111,112,114,116,119,120,126,127,128,129,131,132,133,134,135,136,137,139,140,141,142,144,145,146,148,149,163,164,168,171,172,173,174,175,176,178,182,183,189,193,199,200,201,217,218,219,234,235,240,241,243,245,249,273,284,286,288,289,294,296,302,303,310,311,319,320,326,331,335,336,337,340,341,346,347,348,349,351,355,360,361,368,369,370,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,440,441,442,444,446,447,448,449,456,457,458,460,461,462,463,464,465,466,467,468,469,471,474,476,478,480,481,485,486,488,493,494,497,504],interatom:[3,4,7,170,193,258,328,329,376,382,400,402,410,426,429,447,461,502],intercept:122,interchang:6,interconnect:18,interconvert:402,intereract:39,interesect:340,interest:[1,5,7,8,9,11,13,71,169,286,326,329,361,401,424,439,440,474,502],interf:375,interfac:[],interfer:[12,259,377],interg:[6,497],intergr:[485,489],interi:424,interior:[3,6,41,340,479],interlac:426,interleav:[6,170,484],intermedi:[6,12,59,195,258,284,354,370,474,475,484,488],intermix:471,intermolecular:377,intern:[],internal_element_set:205,internal_quadratur:205,internet:242,interpenetr:426,interpentr:[451,452,454],interpol:[6,15,38,56,103,190,195,196,205,231,246,284,360,361,370,382,431,440,453,459,460],interpret:[2,6,11,195,211,406,449,471,474,490,502],interrupt:293,intersect:[3,6,122,196,340,342,479],intersert:340,interspers:368,interstiti:[168,429],intertia:[3,96],interv:[3,6,93,194,209,243,259,293,298,299,311,447,453,471,490,502],intestieti:122,intial:[6,375,377],intiial:[41,481],intiti:[3,318],intra:303,intra_energi:235,intramolecular:[29,235],introduc:[6,9,94,110,195,259,293,298,303,354,360,376,392,402,414,418,422,458,490,502],introduct:[],intsal:[],intuit:363,inv:[122,169,304],invalid:[3,12,71,91,173,273,370,423,424,478],invari:[110,137,142,144],invent:306,invers:[],invert:[1,6,174,285],invis:340,invoc:[168,219,375,444,446,474],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,89,90,91,92,96,106,107,109,113,114,115,116,121,147,157,164,165,168,170,171,173,174,176,177,179,180,181,182,184,185,187,188,190,193,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,227,228,229,232,233,234,235,236,238,239,240,241,243,244,245,246,247,248,249,250,251,252,253,255,256,258,259,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,294,295,296,297,298,299,300,301,303,304,305,306,308,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,345,347,348,350,351,354,356,359,360,361,362,363,368,370,375,376,377,379,383,384,385,386,387,388,390,391,392,395,396,400,401,403,404,4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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style body/rounded/polygon command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":217,"default":[37,39,40,55,57,58,59,61,62,71,89,90,94,105,106,108,110,111,122,126,127,144,150,158,159,163,169,170,173,175,189,191,192,193,195,196,197,198,200,201,202,204,205,206,208,212,213,214,217,218,220,221,222,223,227,232,235,236,241,243,244,245,246,247,249,254,257,259,260,264,280,281,285,286,289,290,291,292,293,295,298,300,301,303,304,319,321,326,327,328,329,332,334,336,338,342,355,358,360,361,363,364,366,367,369,371,372,373,375,378,382,384,402,423,424,429,431,439,440,456,457,471,472,473,476,477,479,481,483,484,485,488,490,492,493,494,495,496,501,503,504,505],"function":502,"long":[210,383,385,386,387,388,392,394,395,414,418,422,434,442],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[200,201],addforc:202,addit:[12,13],addtorqu:203,adiabat:6,adjust_dt:309,adp:376,airebo:377,alloi:400,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:204,arrai:6,aspher:[6,84,148,261,265,269,270,278],atc:[9,205],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,83,87,94,98,99,102,103,104,110,114,115,117,144,145,168,204,206,207,292,502],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:215,awpmd:[9,378],balanc:[41,216],barostat:6,basal:67,beck:379,berendsen:[290,322],between:6,binary2txt:13,bodi:[6,8,42,68,149,262,266,271,279,380,381],bond:[8,13,69,217,218,219,299],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:382,born:[383,394],boundari:[7,57],box:[6,58,220],brownian:384,buck:[385,386,394,425],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,176,387,422],chunk:[6,66,71,75,92,96,107,109,118,150,165,167,208],citat:7,class2:[21,43,177,345,388],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[336,390,468],colvar:[9,13,221],com:[74,75,151],comb3:391,comb:[295,391],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,502],compute_modifi:105,condit:7,conduct:[6,327],conserv:397,constant:6,constraint:7,contact:[76,124],contact_radiu:[],coord:77,core:6,correl:[209,210],cosin:[23,24,25,26,27,28,179],cossq:347,coul:[383,385,386,387,388,392,393,394,407,414,418,422,434,442],coupl:6,creat:218,create_atom:170,create_bond:171,create_box:172,createatom:13,creation:7,csld:323,csvr:323,cubic:416,cuda:[9,14,113,116,147,157,202,215,229,234,238,259,268,305,306,322,324,335,383,385,387,388,400,406,407,414,415,417,420,432,458,460],custom:8,cut:[49,378,385,388,392,395,402,404,414,415,422,430,434],cvff:348,damag:[78,125],data2xmovi:13,data:6,databas:13,deby:[392,414],dec:[],defgrad:131,deform:[153,154,222],delete_atom:173,delete_bond:174,delta:24,deposit:223,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],diagnost:7,diel:393,dielectr:175,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:178,dihedral_styl:[2,176,177,179,180,181,182,183,184,185,186,187,188,189,190],dilat:80,dimens:191,dipol:[6,29,395],direct:226,discuss:6,disp:6,displac:[81,88],displace_atom:192,distanc:349,distribut:[7,12],document:0,dpd:[9,82,83,396,397,398],drag:224,dreid:[6,408],drude:[6,9,155,225,226,244],dsf:[392,414],dsmc:399,dump:[6,8,193,194,195,197],dump_modifi:196,dynam:294,eam:[13,400],echo:198,edip:401,eff:[9,13,99,100,154,156,161,245,260,272,281,325,402],efield:228,eim:403,elast:6,emac:13,energi:[127,398],enforce2d:229,ensembl:7,erot:[84,85,86,87],error:[3,126],evapor:232,event:88,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],exp:[27,179],expand:[46,417],extend:[8,11],extern:233,fcc:284,fdt:398,featur:[7,8,502],feb:0,fene:[45,46],fep:[9,13,89,201],field:[6,7],file:6,finit:6,fire:294,fix:[2,6,8,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,3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er:3,affect:[1,6,10,14,15,16,17,40,60,61,71,90,121,145,154,168,174,195,196,201,208,209,211,212,213,214,217,218,219,220,222,223,233,239,241,243,249,256,260,261,262,263,265,266,267,273,278,279,280,282,303,304,317,331,341,354,360,366,367,368,370,371,372,375,402,423,424,431,473,474,476,478,479,481,484,486],affin:[16,17,18,222,375,391],afil:237,aforement:18,afresh:[291,484,502],afshar:396,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,148,149,150,151,152,153,154,157,158,159,160,162,163,170,171,173,174,177,178,183,192,193,194,195,196,197,199,200,201,205,206,208,209,216,217,218,219,220,222,226,235,246,247,248,249,250,255,256,257,259,265,266,267,273,278,279,280,282,285,289,293,301,303,306,315,320,322,323,324,326,327,328,329,330,334,336,338,342,345,346,352,359,365,366,368,369,371,373,374,375,376,377,382,389,391,400,401,402,403,409,410,411,422,423,424,426,427,428,429,433,437,439,440,447,448,457,458,460,461,462,465,471,473,475,476,477,478,479,481,482,484,486,488,490,493,494,497,501,502,503,504,505,506],afterrun:484,afterward:3,afterword:41,ag1:169,ag2:169,again:[6,11,12,16,17,62,144,150,156,164,193,196,222,239,289,345,359,370,423,424,471,473,474,476,478,483,490,492,502,504],against:[11,12,13,64,223,370,439,440],aggreg:[6,12,65,68,69,79,95,112,119,239,255,301,303,317,471,503],aggress:[239,490],agilio:[9,13],agre:[3,8,190,368,377,411,440],agreement:[5,7],ahd:408,ahead:338,aidan:[0,5,7,9,13,363],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:195,akohlmei:[7,9,13,197,240],aktulga:[7,9,296,440],al2o3:447,al2o3_001:[122,304],al3:169,ala:[246,447],alain:9,alat:[284,426],alb:[437,460,462],albeit:302,albert:9,alchem:[89,164],alcohol:334,alcu:[376,382],alcu_eam:437,alderton:395,alejandr:[259,260],alessandro:13,algebra:429,algorithm:[0,1,6,7,8,9,41,61,196,205,216,219,222,246,248,249,273,286,294,303,306,307,326,327,331,334,339,366,367,368,372,375,398,402,424,429,444,446,471,473,490],alia:[12,16],alias:[1,361],aliceblu:196,align:[6,12,29,41,71,172,190,212,216,241,363,476,479,497],alkali:402,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,158,163,164,165,166,167,168,169,170,171,172,173,174,176,178,183,189,190,193,194,195,196,197,199,200,201,202,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,225,226,227,228,229,230,231,232,233,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,252,254,255,257,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,276,277,278,279,280,281,282,283,284,285,286,288,289,290,291,292,293,294,295,296,298,299,300,301,302,303,304,305,306,307,308,309,310,311,315,316,318,319,320,321,322,323,326,327,328,329,330,331,332,333,334,336,337,338,339,340,341,342,343,344,345,346,350,355,358,359,360,361,362,363,365,368,369,370,371,372,374,375,376,377,378,380,381,382,383,385,386,387,388,389,391,392,395,396,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,422,423,424,425,426,427,428,429,430,431,432,433,434,436,437,438,439,440,441,442,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,468,469,470,471,473,474,475,476,477,478,479,480,481,483,484,485,486,487,488,489,490,491,493,494,495,497,501,502,503,504,505,506],allen:[29,89,395,405],allentildeslei:89,allign:3,allindex:343,alloc:[3,5,6,8,9,11,12,60,233,333,369,371,375,435,440,476,484],allocat:3,alloi:[],allosw:71,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,94,110,112,146,148,149,150,163,168,169,170,172,178,189,190,193,195,196,197,199,200,202,204,205,206,208,209,210,211,212,213,214,216,218,219,220,221,222,223,227,228,233,235,236,237,238,240,243,246,249,250,254,256,259,260,284,288,289,290,291,292,293,297,303,304,306,308,310,311,315,319,326,327,328,329,331,332,333,334,335,336,342,344,346,355,360,361,363,368,369,370,371,374,375,378,382,383,384,385,386,387,392,400,402,406,407,408,409,414,418,423,424,429,431,437,440,441,444,446,447,456,466,468,471,474,476,478,479,480,481,482,483,486,488,489,490,493,494,502,503],almost:[2,3,12,60,241,293,331,361,372,375,456],alo:392,alon:[6,7,219,299,439,440,474],alond:13,along:[6,8,9,12,29,40,71,89,122,168,169,170,192,193,195,208,219,241,246,247,251,256,258,293,303,306,308,312,316,317,326,330,331,337,340,342,363,366,367,368,370,392,395,406,409,412,414,418,426,439,440,459,476,479,486,487,502],alonso:[427,428],alpha:[6,12,51,200,246,285,293,294,298,368,376,379,383,392,396,398,400,401,403,408,413,414,426,432,436,461,463,494,497],alpha_:[],alpha_c:422,alpha_i:448,alpha_ialpha_j:[],alpha_lj:422,alphabet:[2,3,22,37,44,55,63,178,189,199,346,355,369,389,457,476],alphanumer:[3,63,199,292,300,344,369,502],alreadi:[3,7,8,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dia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,177,178,189,345,346,355,388,457],compat:[3,5,7,8,9,11,12,13,17,18,41,71,121,123,181,193,197,201,207,208,209,211,212,213,214,216,285,297,323,326,333,336,339,360,375,410,429,431,459,473,474,502],compens:[6,217,218,301,371,402],compet:330,competit:361,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,168,193,194,195,197,240,330,361,375,429,476,477,481,502],compl:17,complain:[11,12,17],complement:426,complementari:[7,392,414],complet:[3,6,9,11,12,15,41,59,71,196,212,216,221,249,286,289,292,319,330,332,344,359,370,375,403,444,446,464,471,476,481,484,488,490,493,497,502],complex:[6,8,11,12,13,25,40,42,62,94,110,144,146,158,170,171,246,315,340,358,370,402,429,459,474,476,479,502],compli:[326,330],complic:[6,7,9,12,13,206,235,474],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,90,91,92,93,94,96,97,100,107,108,109,110,111,112,113,114,116,117,121,131,134,135,136,137,140,141,142,144,145,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,165,166,167,192,193,195,196,202,203,207,208,209,210,211,212,213,214,215,219,220,222,223,228,233,238,242,243,246,249,251,255,256,258,259,260,264,265,266,267,278,279,280,282,283,285,286,287,290,301,303,305,306,308,312,313,316,319,322,323,324,326,333,334,339,340,341,360,363,367,368,369,370,375,381,396,402,406,423,424,444,446,447,448,476,477,486,494,502,503],componenet:6,composit:[6,206,246,400],compound:[391,402,403,465],compres:[71,118,208],compress:[],compris:[40,340,441,464],compton:[122,169],comptu:3,compuat:361,comput:[],computation:[3,6,217,218,331,382],computational:497,compute_arrai:8,compute_fep:[201,422],compute_group_group:235,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[122,304],compute_scalar:8,compute_temp:8,compute_ti:201,compute_vector:8,compute_xrd:169,concaten:[2,3,505],concav:340,concentr:[71,400],concept:[6,150,160,208,485],conceptu:[3,6,71,158,220,222,370,392,409,426,481],concern:[6,73,89,194,236],concetr:71,concis:[11,330],conclud:12,concret:8,concurr:[9,16,361,502],conden:[331,460,462],condens:[6,152,331,377,394,400,414,465],condit:[],conducit:6,conduct:[],cone:479,confer:429,confid:[3,490],config:[12,193,473],configfil:221,configur:[1,2,6,12,15,17,38,59,126,172,190,192,193,195,199,220,221,222,223,227,235,242,243,273,286,294,330,358,368,370,377,382,401,426,429,458,460,462,465,471,476,478,479,490],confin:[476,490],conflict:[3,12,40,431,474],conform:[3,6,13,59,219,220,258,302,308,330,354,370,402,488],confus:[3,465],conjuct:396,conjug:[7,8,243,367,402,439,440],conjunct:[6,7,71,88,89,118,153,158,164,170,174,196,200,201,243,246,250,273,289,290,294,295,296,298,303,307,319,327,334,339,360,361,370,383,385,389,392,396,402,408,414,431,434,442,463,476,479,483,497,506],connect:[3,6,89,155,173,219,240,288,303,306,316,370,393,406,456,462,473,474,480,497],conput:3,consecut:[3,11,12,39,71,170,196,200,201,223,240,241,392,414,418,471,477,479],consequ:[1,6,206,331,413,490],conserv:[],consid:[6,9,70,71,78,89,119,152,155,156,173,193,196,200,201,207,209,212,216,218,219,223,247,260,285,303,326,327,330,331,334,361,389,402,409,440,441,447,456,471,472,474,477,478,479,481,484,486,494,497,502],consider:[6,8,243,244,322,323,324,375,485],consist:[3,6,8,9,11,12,40,42,65,69,79,95,107,112,115,116,119,150,153,155,170,182,192,197,202,203,208,222,223,226,228,233,236,243,244,245,256,259,261,262,263,264,265,266,267,268,269,271,272,273,274,276,277,278,279,280,281,282,290,293,298,300,302,303,322,323,324,325,335,360,361,363,369,370,375,377,382,384,390,392,402,405,409,412,423,424,426,429,431,441,444,446,447,459,466,474,476,477,478,479,480,481,488,497,502],consistent_fe_initi:205,consit:303,constant:[],constitu:[3,6,249,303,336,340,390,441],constitut:[444,446],constrain:[3,6,8,147,148,149,150,151,153,156,157,158,159,160,162,163,199,208,223,235,236,241,249,253,288,289,301,303,306,317,327,334,368,369,402,481,488,497],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,94,110,122,144,169,220,259,285,302,340,371,375,395,429,431,456,458,459,479,480,495,502],constructor:[8,11],consult:440,consum:[1,298,435,502],consumpt:358,contact:[],contact_stiff:[443,445],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,89,93,120,122,144,150,158,168,169,170,172,176,178,189,190,193,195,196,197,199,200,201,205,207,208,209,211,212,213,214,216,221,223,228,231,237,241,242,243,246,257,273,284,285,288,289,291,293,296,300,303,304,309,319,326,330,331,340,341,344,359,361,369,370,373,374,376,377,378,382,391,392,395,400,401,402,409,410,426,429,433,437,438,439,440,448,458,459,460,461,462,463,465,471,472,473,474,476,477,478,479,481,483,485,488,490,491,493,494,497,502,504,506],content:[12,18,440,492,494],context:[3,6,8,12,17,120,121,196,217,218,223,288,300,335,367,468,476,483,492,501,502,503],contibut:70,contigu:473,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,106,107,166,196,199,200,201,206,208,209,210,211,212,213,214,216,219,220,221,222,223,235,236,237,239,240,241,243,244,245,251,256,257,259,261,262,263,264,265,266,267,278,279,280,281,282,287,289,292,293,303,304,308,318,319,321,328,329,331,337,340,344,359,374,375,382,396,399,416,419,439,440,441,444,446,461,471,474,476,478,479,484,490,491,493,494,502,504],continuum:[6,7,9,205,331,444,446],contour_integr:205,contract:[59,220,222,259,290,303],contradictori:3,contrain:306,contraint:273,contrari:[237,244],contrast:[1,6,42,55,64,152,155,222,342,444,446,468,505],contrib:331,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,86,89,90,91,92,93,96,105,107,109,111,112,113,114,116,118,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,201,206,207,208,209,211,212,213,214,220,235,243,246,249,250,254,260,280,281,288,289,297,300,303,304,306,333,360,368,370,378,396,399,400,402,409,423,424,429,431,439,440,447,488,494,497],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,89,93,126,144,179,193,195,199,205,206,216,220,221,222,239,240,243,244,259,261,262,263,264,265,266,267,290,295,303,310,311,322,323,324,331,335,358,360,372,402,405,429,439,440,443,445,458,462,471,473,485,491,492],control_typ:205,controlfil:440,convect:93,conveni:[6,12,29,193,197,214,304,363,448,502],convent:[3,8,9,29,181,188,189,196,302,316,343,400,402,502],converg:[3,6,41,90,193,195,197,202,216,219,220,228,233,264,293,295,298,302,306,366,367,368,370,391,392,414,447,471,483,490],convers:[3,8,144,195,196,206,209,290,360,392,393,394,402,414,418,422,434,474,490,501],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,93,170,177,193,195,196,214,257,289,342,345,347,351,354,363,370,376,400,429,460,462,469,474,476,477,478,483,493,497,501,502,504,506],convex:[42,340,381],convinc:[7,12],cook:9,cooki:7,cool:[7,160,239,301],cooordin:193,cooper:[5,7],coord123:118,coord1:[3,118,208,212,213],coord2:[3,118,208,212,213],coord3:[3,118,208,212,213],coord:[],coordb:447,coordbb:447,coordiat:368,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,89,91,92,96,106,107,109,117,118,120,138,144,153,159,165,167,168,170,174,192,193,194,195,196,197,199,202,207,208,211,212,213,216,217,218,219,220,221,222,223,226,228,229,233,235,238,239,240,241,242,243,244,256,258,259,261,262,263,265,266,267,280,283,284,285,288,289,290,300,301,303,305,306,308,313,316,317,318,319,321,329,330,331,338,339,341,342,363,368,369,370,375,376,377,380,381,401,447,471,476,477,478,479,481,484,486,490,497,502,503],coordn:[118,208],coorind:[],copi:[0,3,4,8,11,12,15,17,40,123,195,331,370,389,439,474],copper:469,coproccesor:16,coprocessor:[1,4,7,9,16,17,375,489],coproprocessor:17,copy_arrai:8,copyright:[7,8,288],coral:196,core:[],core_shel:152,coreshel:[6,9,385,392,394],cornel:[6,176,488],corner123i:117,corner123x:117,corner123z:117,corner1i:117,corner1x:117,corner1z:117,corner2i:117,corner2x:117,corner2z:117,corner3i:117,corner3x:117,corner3z:117,corner:[3,6,40,117,195,340,341,363,464,476],cornflowerblu:196,cornsilk:196,corp:9,corpor:16,corr:391,correct:[3,6,9,11,12,16,17,59,89,90,105,106,114,120,152,157,164,195,222,235,237,243,259,260,280,288,290,293,330,336,340,360,370,376,377,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,395,396,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,464,465,467,468,469,476,491,494,497],correction_max_iter:205,correctli:[3,8,9,11,17,71,81,105,106,107,147,148,149,151,153,155,156,157,158,159,162,163,166,193,196,202,223,228,233,244,253,259,260,296,303,306,316,318,337,340,370,371,375,394,424,429,473,474,476,486,501,503],correl:[],correpond:231,correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,89,99,100,113,116,117,118,119,122,123,131,134,135,136,137,138,140,141,142,144,147,148,157,164,168,169,176,177,178,179,180,181,182,184,185,187,188,190,192,193,195,196,200,201,202,208,210,211,212,213,215,218,220,222,229,233,234,238,243,246,247,255,256,257,259,261,262,263,264,265,266,267,268,269,273,276,278,279,280,282,285,286,290,295,303,305,306,322,324,326,335,336,337,339,340,341,343,345,346,347,348,350,351,354,356,361,365,367,369,370,376,377,379,383,384,385,386,387,388,389,390,391,392,395,396,400,401,402,403,404,405,406,407,408,409,412,414,415,416,417,418,419,420,421,422,423,426,427,429,431,432,433,434,436,437,439,440,441,442,447,448,449,458,459,460,461,462,465,467,468,469,471,473,474,476,477,479,489,490,491,493,494,497,502],correspondingli:[423,424,485],cosin:[],cosineshift:27,cosmo:[237,242],cossq:[],cost:[1,6,10,11,12,17,39,41,71,113,122,145,169,195,196,208,212,213,216,217,218,232,259,295,331,360,361,373,392,414,418,429,431,458,473,485],costheta0:[458,460,462,465],costheta:437,costli:[11,90,237,371],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,89,92,96,107,109,113,116,118,150,160,165,167,183,193,195,196,200,201,208,209,212,216,222,233,242,292,293,294,298,301,303,305,319,320,326,330,331,332,336,340,342,344,352,357,359,366,368,371,375,378,404,408,409,412,439,440,472,473,474,476,478,480,483,484,491,492,497,502,503],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,90,111,112,120,145,171,175,294,296,332,360,361,368,375,383,385,386,387,388,391,392,393,394,395,402,406,407,409,414,418,422,425,431,434,439,440,442,447,457,462,463,465,468,481,488,494,497,501],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,93,118,120,121,158,168,174,202,203,206,208,211,212,213,215,216,223,228,232,235,241,259,273,289,306,322,323,340,361,368,369,370,372,375,404,408,431,494,502],counter:[337,471,482,484,490],counteract:235,counterbal:239,counterbalanc:29,counterpart:[193,303,471],counterproduct:18,coupl:[],courant:309,cours:[3,8,130,132,164,193,200,201,236,302,316,330,336,338,339,341,342,361,423,449,473,476,489,497,502,504],courtesi:363,cov:447,coval:[6,29,402,426,447,497],covari:237,cover:[6,71,190,196,205,246,402,464],coverag:[71,212],cpc:242,cpp:[1,3,6,8,9,11,12,13,89,193,200,201,233,306],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,196,210,226,244,332,358,361,375,389,457,471,489,490,493,494,495,502],cpuremain:494,cr2:169,cr3:169,crack:[4,371],crada:[5,7],crai:[5,7,13,18,193],crash:[3,12,371,497],craympi:375,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:205,create_faceset:205,create_group:194,create_nodeset:205,createatom:[],creation:[],crimson:196,critchlei:288,criteria:[3,120,171,195,196,217,218,219,254,368,436,464,478,481,502],criterion:[12,41,125,170,173,206,216,219,235,273,295,309,337,342,368,370,391,402,406,447,481,490,491],criterioni:490,critic:[6,48,49,257,326,331,368],crmax:71,crmin:71,cross:[3,12,22,71,91,148,168,178,193,195,207,212,218,222,256,258,280,303,312,316,318,327,334,346,363,370,387,396,399,400,407,408,409,414,416,418,437,442,444,446,460,462,469,476,480,486,504],crossov:1,crossterm:476,crozier:[0,7,13],crucial:293,crystal:[4,6,13,73,110,284,285,329,363,371,480,494,497],crystallin:[6,106,285,363,461,497],crystallis:326,crystallogr:[122,169],crystallograph:[363,494],crystallographi:[122,169,363],cs1:169,cs_chunk:6,cs_im:[40,476],cs_re:[40,476],csanyi:[144,438,448],cscl:426,csequ:6,csh:[11,12,389],cshrc:[11,12],csic:[401,458,460,462,465],csinfo:6,csisi:[401,458,460,462,465],csld:[],cst:400,cstherm:6,cstyle:473,csvr:[],ctcm:[376,400],ctemp_cor:226,cterm:308,ctr:9,ctype:11,cu1:169,cu2:169,cu3au:426,cube:[6,41,168,173,216,226,340,363,497],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:382,cummul:[3,6,214,217,218,219,221,232,237,243,245,319,322,323,324,325,327,334,408,494],cumul:[6,206,208,211,212,213,227,235,243,257,259,264,273,303,304,370],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,89,105,106,112,120,121,134,145,150,158,160,166,168,171,174,192,193,194,195,196,197,200,201,205,208,212,213,214,216,217,218,219,220,221,222,223,227,228,233,235,237,240,241,243,249,256,259,260,265,266,267,273,278,279,280,282,288,289,294,295,297,300,301,302,303,306,307,308,309,310,311,312,313,315,317,318,319,322,323,324,330,331,334,335,336,337,338,339,341,342,344,358,359,360,361,364,365,367,368,369,370,375,381,382,389,391,395,400,402,403,406,409,410,413,423,424,426,427,428,431,437,439,440,443,444,445,446,449,460,462,463,466,471,472,473,474,476,477,478,479,480,482,483,484,486,488,490,491,493,494,502,503,504,505,506],curv:[6,170,235,285],curvatur:[405,441,469],custom:[],cut0:474,cut1:485,cut2:485,cut:[],cuthi:[284,296],cutinn:[384,423,424],cutlo:[284,296],cutmax:437,cutoff1:[388,395,414,418,422,425,434,442],cutoff2:[383,385,386,388,394,395,414,418,422,425,434,442],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,89,94,110,112,119,120,144,168,171,173,174,218,219,224,231,284,293,294,296,298,300,303,307,319,332,336,340,342,358,360,361,368,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,388,390,392,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,439,440,441,442,447,448,449,450,451,452,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,474,478,481,485,497,502],cutoff_glob:381,cutoff_inn:381,cutoffa:401,cutoffc:401,cuu3:400,cval:169,cvd:326,cvel:308,cvff:[],cwiggl:[3,256,336,339,341,502],cyan:[2,195,196],cycl:[3,235,257,259,260,264],cyclic:[3,190],cygwin:12,cylind:[3,4,71,195,208,241,289,337,340,479],cylindr:[6,241,316,337],cypress:375,cyrot:382,cyrstal:285,d3q15:246,d3q19:246,d_double_doubl:15,d_e:331,d_flag2:292,d_flag:292,d_name:[117,193,292,321,486],d_single_doubl:15,d_single_singl:15,d_sx:292,d_sy:292,d_sz:292,daan:329,dai:12,daili:12,daivi:280,damag:[],dammak:298,damp:[3,6,199,204,243,244,245,250,259,260,264,290,293,294,298,303,322,323,335,337,338,367,368,370,383,385,387,392,395,402,406,414,422,434,442,457,463,490,497],damp_com:244,damp_drud:244,dampen:[303,497],dampflag:[337,406],dan:17,danger:[3,12,235,342,396,494],dangl:173,daniel:9,darden:[361,395],darkblu:196,darkcyan:196,darken:195,darkgoldenrod:196,darkgrai:196,darkgreen:196,darkkhaki:196,darkmagenta:196,darkolivegreen:196,darkorang:196,darkorchid:196,darkr:196,darksalmon:196,darkseagreen:196,darkslateblu:196,darkslategrai:196,darkturquois:196,darkviolet:196,dasgupta:294,dash:[406,493],dat:[6,93,190,205,472],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,304],dataset:304,datatyp:3,date:[0,6,12,13,192,439,440,502],datom1:119,datom2:119,datom3:119,datom4:119,datum:[3,6,42,65,68,69,79,95,112,119,193,209],davenport:425,davi:336,david:[9,19,360,361,460,462],daw:[400,437],dbg:14,dcd:[3,6,7,193,194,195,196,197,286,477,481],ddim:192,deactiv:422,dealt:242,debug:[6,7,11,12,13,14,17,122,126,169,170,286,291,358,360,375,410,431,466,474,475,483,486,493,502],deby:[],decai:[94,392,469],decid:[3,6,12,16,71,256,292,303,332,491],decipher:363,declar:194,declin:319,decod:195,decompos:[89,448],decomposit:[3,5,7,18,62,205,286,307],decoupl:[6,497],decreas:[3,193,202,203,210,219,222,228,233,235,243,330,360],decrement:308,deepli:357,deeppink:196,deepskyblu:196,def:[12,13,474],defaul:61,defect:[6,70,168,429],defgrad:[],defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,176,177,178,179,180,181,182,184,185,187,188,189,190,191,192,193,194,195,196,199,200,201,202,203,204,205,206,207,208,209,211,212,213,214,215,216,217,218,219,220,222,223,226,227,228,230,233,234,235,238,241,242,243,244,245,246,254,256,258,259,260,261,262,263,264,265,266,267,269,270,271,274,276,277,278,279,280,281,282,284,285,286,288,289,290,292,294,296,301,303,304,305,306,309,313,317,319,321,322,323,324,325,327,328,329,331,333,334,336,337,338,339,340,341,342,344,345,346,347,348,349,350,351,354,355,356,358,360,361,363,365,367,368,369,370,371,372,373,374,375,377,378,379,380,381,383,384,385,386,387,388,389,390,392,393,395,396,397,398,399,401,402,404,405,406,407,408,409,410,412,414,415,416,417,418,419,420,421,422,423,424,425,429,430,431,432,433,434,436,437,439,440,441,442,443,444,445,446,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,473,474,476,477,479,480,481,482,485,486,487,488,490,491,493,494,497,498,499,500,501,502,503],definit:[2,3,6,8,12,13,78,80,120,144,196,208,209,210,211,212,213,214,222,230,241,264,304,321,333,336,339,341,343,355,358,369,378,382,390,397,398,402,412,437,444,446,448,464,474,476,478,485,487,501,502],defint:494,deform:[],deg2theta:169,deg:497,degener:[3,288],degrad:[8,18,285,361,485],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,94,95,97,99,100,102,104,105,110,116,147,148,149,150,151,152,153,154,155,156,157,158,159,160,162,163,169,170,176,177,180,181,188,190,192,195,208,219,226,235,237,238,243,244,249,259,260,264,265,266,267,278,279,280,282,286,288,302,303,306,322,323,324,329,345,347,351,354,356,368,395,400,408,486,494,497,503],degress:[150,208],del:490,delai:[3,6,12,371,399,494],deleg:409,delet:[2,3,7,8,12,54,57,60,63,168,173,174,199,208,209,211,212,213,214,217,219,232,235,259,304,322,323,342,344,359,369,371,374,431,456,476,477,478,479,487,488,493,498,500,502,503],delete_atom:[],delete_bond:[],delete_el:205,deli:192,delimit:[474,502],deloc:[260,402,447],delr:426,delt_lo:490,delta:[],delta_1:382,delta_3:382,delta_7:382,delta_conf:3,delta_ij:[426,437],delta_mu:3,delta_pi:382,delta_r:437,delta_sigma:382,delta_ua:381,delx:192,delz:192,dem:381,demand:298,demo:11,demon:283,demonstr:[293,426],den:289,dendrim:408,denniston:[9,246,248,249,250,285],denomin:[7,175],denot:[122,226,244,285,296,298,392,407,409,440,444,446],dens:[71,219,402],densiti:[3,6,7,9,18,40,41,59,103,120,130,144,156,168,170,200,201,205,208,212,213,216,222,233,246,249,252,253,285,289,290,294,331,336,363,365,369,376,382,400,426,427,428,437,441,447,451,453,454,455,476,485,486,494,501],density_continu:446,density_summ:446,depart:[0,7],departur:[257,293],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,94,95,106,112,113,116,117,118,119,123,144,147,153,157,158,164,170,171,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,195,196,199,200,201,202,203,206,208,210,211,212,214,215,216,218,220,222,228,229,234,237,238,239,241,243,244,246,248,249,256,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,284,295,298,300,303,305,306,307,313,319,322,323,324,326,328,330,331,333,335,336,339,340,341,342,344,345,346,347,348,350,351,354,356,361,363,368,369,371,372,373,375,376,377,379,380,382,383,384,385,386,387,388,389,390,391,392,393,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,426,427,429,430,432,433,434,436,437,439,440,441,442,447,448,449,457,458,459,460,461,462,463,465,467,468,469,471,473,476,478,479,482,486,488,490,493,494,496,502,503],dependend:6,depflag:12,dephas:[471,490],depos:223,deposit:[],deprec:[294,439],depth:[51,148,195,331,405,441],dequidt:9,der:[89,111,390,391,422,439,440,468,497],deriv:[6,7,8,9,38,56,63,89,144,164,190,209,220,222,235,243,256,259,261,262,263,264,265,266,267,284,290,294,298,328,329,331,336,337,340,367,369,377,382,390,395,402,403,407,416,420,421,426,429,439,440,457,459,468,497],derjagin:468,derlet:284,descend:196,descent:[7,367],descib:[40,195,294],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,90,114,117,120,122,134,144,145,148,149,150,154,155,158,161,163,164,168,169,170,172,173,182,187,190,193,194,199,200,201,208,209,210,211,212,213,214,216,219,220,221,222,223,225,226,231,236,237,240,241,242,243,244,245,246,248,249,250,254,258,259,260,264,272,281,284,286,291,292,293,294,295,296,303,308,316,319,320,321,322,323,324,325,326,327,328,329,334,336,337,339,344,360,361,363,366,367,368,369,370,374,377,378,380,381,383,384,385,387,388,389,390,391,392,395,400,402,403,405,406,407,409,412,414,415,416,417,418,419,420,421,422,423,424,425,426,429,430,436,437,438,439,440,441,442,447,448,449,456,457,458,459,460,461,462,463,465,467,468,469,471,473,474,476,477,478,479,480,486,489,490,493,502,503,504],descript:[],descriptor:[144,193,410],deserno:361,design:[0,3,6,7,8,9,11,13,14,15,17,122,152,155,169,205,219,225,226,259,260,284,285,304,326,331,378,379,380,381,384,387,392,394,402,422,423,424,427,428,437,440,459],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,90,93,116,121,145,152,170,183,192,208,214,220,222,233,235,236,243,244,245,249,259,280,288,289,290,291,294,298,303,306,319,322,323,324,325,330,337,352,357,360,361,363,366,368,369,370,396,400,408,423,424,458,460,462,472,473,474,476,480,485,490,491,493,494,502,503,504],desk:7,desktop:[4,6,7,10,12,195],despit:497,destabil:382,destre:354,destroi:[11,39,217,218],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,92,93,96,105,107,109,111,113,115,116,118,121,123,144,145,147,148,149,150,153,163,164,165,167,170,171,174,175,178,189,192,193,195,196,199,200,201,205,208,209,210,211,212,214,216,218,219,220,221,222,223,233,235,236,237,238,240,241,243,245,246,250,256,257,258,259,260,261,262,263,264,265,266,267,271,273,278,279,280,281,282,285,288,289,290,292,293,295,296,297,303,306,307,319,322,323,324,325,326,327,329,330,331,332,333,334,335,342,344,346,355,360,361,364,368,369,371,372,375,376,377,378,380,381,382,384,386,387,388,389,390,391,392,395,396,402,403,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,425,426,430,431,436,439,440,441,447,448,449,457,464,467,468,474,476,477,478,479,481,482,485,486,488,491,494,495,502,503,506],detect:[2,3,12,42,61,63,88,94,234,289,330,370,391,408,413,471,473,476,487,490,502],determ:375,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,89,105,111,113,116,122,123,131,145,158,159,168,169,170,192,193,195,196,197,198,202,203,204,207,208,209,210,211,212,213,214,215,216,220,222,223,226,228,235,238,239,241,243,244,249,254,256,257,259,265,266,267,278,279,280,282,284,286,289,290,293,300,301,302,303,304,305,309,311,313,319,322,323,324,326,332,333,336,337,338,339,340,341,342,355,360,361,363,369,371,372,375,377,378,386,391,395,399,400,404,406,409,410,418,426,429,431,440,441,447,456,459,463,468,473,476,477,479,481,483,486,490,492,493,495,501,502,503],determinist:307,detil:112,devan:[9,442],devanathan:462,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,240,264,288,293,294,297,377,382,402,428,429,447,465,478],devemi:9,deviat:[257,264,284,404],deviator:9,devic:[1,3,12,15,17,240,375],device_typ:375,devin:[295,391],devis:428,dfactor:195,dff:497,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,361],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,297,429],dhi:[59,192,222,289],dhug:[257,293],dhugoniot:[257,293],dia:426,diagnost:[],diagon:[3,6,85,144,145,146,220,259,290,303,334,444,446],diagonalstyl:448,diagram:[41,122,169,189,216,286],diallo:408,diam:[195,196,289,369],diamet:[3,6,40,42,117,170,193,195,196,200,201,243,289,303,319,321,335,337,369,381,390,405,406,416,441,464,468,476,477,486],diamond:[363,402,426],diamter:[40,289],dick:6,dicsuss:256,dictat:[206,257],did:[3,12,368,396,399,400,406,431,460,462,484],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,166,333,360],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,89,94,97,99,100,124,144,147,148,149,150,151,153,156,157,158,159,160,162,163,164,170,171,173,178,189,190,192,193,195,196,199,201,204,206,208,211,216,217,218,219,220,221,222,226,231,234,235,236,237,238,239,240,243,244,246,256,259,260,261,262,263,265,266,267,269,271,274,276,277,278,279,282,284,286,288,290,293,294,295,298,301,303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9,341,354,360,361,390,395,396,398,402,403,406,411,423,424,426,431,441,444,446,451,452,454,455,469,497],equi:260,equidist:258,equil:[3,294,364,483,506],equilater:486,equilibr:[3,4,5,6,7,9,59,93,170,199,206,209,219,220,235,257,259,260,280,281,293,294,295,296,327,328,329,334,391,392,439,440,472,486],equilibria:334,equilibribum:[217,218],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,153,154,177,179,220,222,235,236,237,244,246,259,264,280,293,294,298,302,306,308,316,319,326,327,329,334,345,347,351,354,391,426,433,447,497],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:205,equival:[6,12,13,29,59,61,128,129,137,142,168,172,196,211,214,220,222,235,243,259,280,290,302,303,339,396,402,447,460,462,476,479,484,485,494,497],equlibrium:6,equliibr:[294,296],er3:169,eradiu:[40,117,402,476],eras:[305,328],erat:[222,424],erc:392,erfc:[392,414,431],erforc:117,erg:501,erhart:[206,400,460,462],ermscal:378,ernst:9,eror:3,eros:426,erose_form:426,erot:[],errata:[460,462],erratum:336,erron:3,error:[],erta:406,ervel:[117,476],escap:[223,497],especi:[8,16,158,170,199,206,216,235,293,298,301,302,375,473],espresso:[9,297],essenti:[8,11,12,27,90,132,151,152,153,156,157,158,159,160,162,179,209,264,285,335,361,377,392,414,462,481,494],essex:29,establish:[89,239],estim:[1,3,6,10,12,38,41,56,93,145,205,216,227,257,319,326,360,361,366,431,440,459,490,494],esu:501,esub:426,eta:[6,246,259,293,294,296,335,401,403,405,437,461,465,501],eta_dot:259,eta_ij:437,eta_ji:403,etag:[40,476],etail:494,etap:259,etap_dot:259,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,91,92,93,97,113,114,117,119,145,147,150,151,152,153,154,156,157,158,159,160,162,164,170,172,173,174,183,193,195,196,199,200,205,206,207,208,211,212,213,214,217,218,222,223,233,235,236,243,259,289,300,304,331,332,340,344,359,360,368,369,370,371,373,400,401,409,422,424,429,435,439,440,458,460,462,465,471,474,476,477,478,483,485,486,490,491,492,493,494,495,497,501,502,504,506],ethernet:18,etol:[368,370,471,490],etot0:293,etot:[6,97,99,100,114,145,156,196,226,244,257,293,493,494],eu2:169,eu3:169,euler:[368,370],eulerian:205,euqat:450,europhi:246,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,89,90,93,111,121,144,146,150,160,168,170,192,193,195,196,200,201,202,203,205,207,208,209,210,211,212,213,214,215,222,228,236,238,239,241,242,243,244,285,291,294,305,309,313,322,323,324,333,336,339,341,342,344,360,361,366,368,375,429,431,437,443,445,447,459,471,472,474,478,479,481,483,484,485,486,490,492,494,502,503],evalut:[344,474],evan:[158,280],evanseck:[6,20,176,387,488],evapor:[],evaul:[8,368],evdwl:[111,439,440,494],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,123,168,171,172,186,190,193,196,199,200,201,206,207,208,211,212,213,214,216,217,218,220,222,223,226,241,244,257,259,260,285,289,298,300,303,304,315,319,327,331,334,336,340,342,353,360,366,368,370,375,380,402,403,406,409,412,431,441,465,466,476,477,479,481,482,483,485,486,488,491,493,494,495,497,506],evenli:[3,41,145,190,216,246,412,466],event:[],eventu:[3,6,12,15,172,294,490],ever:[54,56,242,319],evera:[390,405,441,457],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,93,117,123,132,158,173,193,194,195,196,197,199,200,201,202,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,227,232,233,235,237,239,240,241,246,247,255,259,260,264,283,284,285,289,290,291,292,293,294,295,296,298,300,301,303,304,306,308,319,321,322,323,324,325,326,327,330,331,332,333,334,342,344,359,361,370,371,372,375,396,399,409,422,439,440,447,453,470,471,472,476,478,480,481,483,484,485,490,491,492,494,502,506],everyth:[8,111],everywher:[120,416],eviri:402,evolut:[237,246,286,471],evolv:[246,286,332],ewald:[2,3,5,6,7,8,12,90,114,122,145,332,360,361,368,383,385,386,392,395,402,414,418,434,442,457,459],ewald_disp:395,ewalddisp:3,exact:[22,41,44,71,126,164,173,178,216,219,236,237,243,244,245,289,298,299,319,331,346,360,389,478,483,490,502,504,506],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,93,120,148,154,161,170,190,200,201,211,216,222,227,231,236,243,244,245,260,272,273,281,285,293,319,324,325,338,375,389,396,400,406,409,423,431,459,478,479,486,490,502],exager:497,examin:[6,8,9,17,219,285],examp:[474,502],exampl:[],exce:[3,6,16,17,18,41,58,71,172,207,208,211,212,213,214,216,220,222,227,232,259,285,300,304,310,311,319,368,375,476,502],exceed:[3,41,59,216,222,259,319,484],excel:402,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,63,71,91,92,112,113,116,121,145,147,148,149,150,151,152,153,154,156,157,158,159,160,161,162,163,170,174,176,177,178,179,180,181,182,184,185,187,188,189,190,192,193,196,199,202,208,209,211,215,216,220,222,229,234,235,238,241,243,245,259,260,261,262,263,264,265,266,267,268,269,272,273,276,278,279,280,281,282,286,295,296,303,305,306,316,319,322,324,325,331,335,339,342,344,345,346,347,348,350,351,354,355,356,360,361,363,365,369,370,371,373,374,375,376,377,379,383,384,385,386,387,388,389,390,391,392,394,395,396,400,401,402,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,424,427,432,433,434,436,439,440,441,442,449,457,458,459,460,461,462,465,467,468,469,471,473,474,476,478,479,481,484,485,486,487,488,490,494,497,501,502,503,505],excess:[210,402],exchang:[2,3,6,8,9,61,62,199,205,206,235,243,295,303,327,331,334,360,375,402,491],exchange:360,excit:[9,402],exclud:[3,6,9,12,16,17,63,71,116,144,150,157,158,174,193,208,212,217,218,247,255,288,301,303,326,337,342,368,369,371,384,406,409,412,423,424,431,456,488],exclus:[1,3,9,12,16,89,375,391,429,431,485,495],excurs:[259,471],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,171,195,240,297,344,359,362,374,472,474,484,487,490,502],exempl:447,exemplari:236,exemplifi:402,exert:[6,241,244,298,338,339,340,361],exhaust:[205,374,502],exhibit:[94,259,367,402,485],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,126,170,171,189,194,195,196,199,204,215,218,220,223,235,288,289,291,342,345,347,348,349,351,355,364,369,375,397,398,409,439,456,466,472,474,476,477,478,487,488,489,502,503,504],exit:[2,3,11,12,41,57,193,216,231,359,374,474,475,484,493,502],exlanatori:3,exp:[],expand:[],expans:[12,144,193,487,502],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,105,151,162,168,190,216,228,235,237,256,284,290,292,293,298,303,342,361,371,389,426,429,431,471,474,476,478,481,485,490,502],expens:[6,10,71,196,284,288,303,331,342,360,361,371,375,474],experi:[6,13,15,17,215,223,240,249,258,290,302,303,366,370,396,431,485,490],experienc:[6,12,248,249],experiment:[235,360,375,490],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,88,95,150,158,190,193,195,196,199,208,209,214,216,218,220,222,259,284,292,303,316,342,344,359,360,363,369,370,374,380,400,412,447,449,464,474,477,478,481,483,486,497,502,506],explan:[3,6,59,117,144,193,208,258,284,409,470,473,474,476,485],explanatori:[3,8,121,193,207,208,211,212,213,303,369,473,502],explantori:[3,299],explic:430,explicit:[6,9,11,22,44,77,89,117,120,164,178,200,201,222,310,311,346,365,377,378,382,387,389,400,402,413,423,463,470,473,477,480],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,113,116,147,157,160,168,170,176,177,179,180,181,182,184,185,187,188,190,193,196,202,212,215,222,229,234,236,238,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,292,293,295,303,305,306,322,324,325,331,335,339,345,347,348,350,351,354,356,369,375,376,377,379,383,384,385,386,387,388,389,390,391,392,393,395,396,399,400,401,403,404,405,406,407,408,409,413,414,415,416,417,418,419,420,421,422,423,427,429,431,432,433,434,436,441,442,449,450,451,452,453,454,455,457,458,459,460,461,462,463,465,467,468,469,476,478,479,485,486,488,489,495,497],explictli:[16,489],exploit:[9,15,17,286],explor:[122,169],expon:[3,294,296,400,405,408,422,430,442],exponenti:[89,437,458,465,469,490,502],expos:11,exposit:[205,396,399],express:[6,144,156,170,200,201,220,256,284,294,331,337,344,382,400,402,416,426,447,448,457,502],expressiont:382,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,84,85,86,89,90,93,97,100,101,111,113,121,123,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,199,202,203,206,214,215,221,224,228,233,234,235,237,238,239,241,243,245,257,259,264,273,284,285,301,302,303,305,308,313,316,318,322,323,324,325,326,328,329,331,333,336,340,341,405,426,429,440,441,448,493,494],extent:[1,3,41,42,45,57,71,168,172,193,204,212,216,241,338,341,360,363,377,443,445,459,473,476,479],exterior:[3,6,168,340],extern:[],extra:[3,6,8,11,12,16,17,40,41,46,61,71,105,113,114,116,122,145,147,148,149,151,153,156,157,158,159,160,162,163,169,170,171,172,176,196,211,216,218,259,291,292,293,303,319,368,369,372,373,395,406,409,412,426,431,473,474,476,479,488,497,502],extract:[3,6,11,13,36,63,89,111,119,121,123,200,201,296,370,392,403,426,448,474,481,493],extract_atom:11,extract_comput:[11,474],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,195,210,220,222,259,329,402,461,497],extrema:422,extrins:205,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[166,333],f_a:[460,461,462],f_ave:121,f_c:461,f_f:462,f_fix_id:293,f_harm:329,f_i:[29,437],f_id:[6,71,121,123,193,199,207,208,209,210,211,212,213,214,254,321,333,494,502],f_ij:437,f_indent:214,f_int:328,f_j:29,f_jj:93,f_k:437,f_langevin:331,f_max:[293,298],f_msst:257,f_r:[244,460,461,462],f_sigma:382,f_solid:329,f_ss:6,f_temp:[],face:[3,6,57,59,71,158,168,172,204,212,213,336,338,339,340,341,363,405,426,441,476,479],face_threshold:168,facet:168,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,237,289,319,329,406,447,488],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,89,93,105,112,119,120,122,144,164,169,172,176,187,192,193,195,196,200,201,209,216,220,222,223,235,240,243,245,246,257,259,260,264,286,290,294,302,306,309,311,319,323,327,334,335,336,340,351,361,363,369,375,377,378,382,383,385,387,392,393,394,396,397,398,402,406,409,413,414,426,429,431,433,434,440,442,449,458,463,473,476,479,480,485,488,490,491,494,497,501,502],factori:[3,474],factoriz:360,fail:[3,11,12,59,174,220,223,360,368,370,394,440,474],failur:[125,444,475,502],fairli:[11,431,485,490],faken:73,falcon:240,fall:[3,6,196,211,289,474,502],fals:[88,342,344,447,502],fame:8,famili:[465,473],familiar:[0,11],fan:437,far:[3,6,12,17,57,59,61,88,193,196,197,216,217,218,220,223,259,284,302,303,319,336,347,351,366,370,371,464,474,476,481,494],farago:243,farrel:[460,462],farther:193,fashion:[6,8,41,71,170,196,199,200,201,206,212,216,218,223,235,237,241,256,257,259,261,262,263,264,265,266,267,275,278,279,280,281,282,292,293,295,303,308,312,318,321,329,331,335,336,337,339,341,370,409,423,479,488,502,505],fasolino:411,fast:[6,7,9,12,13,17,39,193,270,293,332,360,361,384,423,424,429,457,459,478,483,485,494,503,506],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,108,113,116,147,157,176,177,179,180,181,182,184,185,187,188,190,193,196,202,215,216,222,229,234,238,242,243,259,261,262,263,264,265,266,267,268,269,276,278,279,280,282,290,294,295,303,305,306,319,322,324,326,328,331,335,339,345,347,348,350,351,354,356,360,361,372,373,375,376,377,379,382,383,384,385,386,387,388,389,390,391,392,395,396,400,401,403,404,405,406,407,408,409,414,415,416,417,418,419,420,421,422,423,427,432,433,434,436,441,442,449,457,458,459,460,461,462,465,467,468,469,471,479,485,489,497],fastest:[1,6,14,17,158,212,331,332,375,473],fatal:[3,493],fault:[70,440],faulti:12,fava:405,favor:219,favorit:7,fbmc:326,fcc:[],fcm:[275,502],fdirect:226,fdotr:410,fdt:[],fdti:89,fe2:169,fe3:169,fe_md_boundari:205,featu:8,featur:[],fecr:400,feedback:[7,240],feel:[7,240,241,249,284,340,342,370,431],felling:428,felt:340,femtosecond:501,fene:[],fennel:[392,414],fep:[],ferguson:[6,176,488],fermi:[1,12,15,156,375,462],fermion:[9,402],fernando:425,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,63,197,207,208,209,211,212,213,214,244,259,289,292,294,306,333,360,368,369,370,377,447,473,476,481,485,487,495,502,504],fewer:[1,3,11,15,16,61,249,485],fewest:3,fextern:233,feynman:286,fff:474,ffield:[391,403,439,440,447],ffmpeg:[3,12,195],ffplai:195,fft:[1,3,7,11,12,14,15,90,113,114,145,285,360,361,485],fft_inc:[12,361],fft_lib:12,fft_path:12,fftbench:[360,495],fftw2:12,fftw3:12,fftw:12,fhg:[7,9],ficiti:456,fictiti:[6,202,203,228,233,237,286,302,392,414,418,456],field1:[477,481],field2:477,field:[],fifth:[316,433],figur:[1,3,8,12,293,473,474],fij:395,file0:284,file1:[11,13,284,330,344,369,481,483,487],file2:[11,13,330,344,369,481,483,487],file:[],file_from:194,filen:369,filenam:[3,12,13,38,41,56,190,193,195,196,197,205,208,209,210,211,212,213,214,216,221,231,284,288,291,294,295,296,299,300,303,304,330,331,357,358,359,369,370,376,377,382,392,400,401,403,411,426,427,428,433,437,438,439,440,447,448,458,459,460,461,462,465,472,473,474,477,478,483,487,494,502,504,505,506],filennam:483,filep:[3,193,196,478,483,506],filepo:300,fill:[7,9,170,195,289,331,363,371,382,429,440,479],filter:[196,205],final_integr:8,final_integrate_respa:8,finchham:[6,152,394],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,89,121,173,190,197,206,219,220,231,232,235,258,284,289,290,298,302,366,368,370,371,392,409,414,418,426,447,457,459,497,502],find_custom:8,fine:[16,17,174,202,228,329,371,375,502],finer:[144,170,502],finest:360,finger:[170,192,256,479],finish:[6,11,41,216,344,357,359,360,372,374,375,464,481,502,503],finit:[],finni:[7,400,457],finvers:226,fiorin:[9,221],fire:[],firebrick:196,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,90,93,106,107,108,110,116,120,121,131,134,137,138,142,145,155,158,164,166,168,169,171,172,173,177,190,193,194,195,196,197,199,200,208,209,211,212,213,214,216,219,222,231,235,236,241,246,256,257,258,259,284,286,291,292,293,295,300,303,306,308,316,317,319,320,321,328,329,330,331,333,337,342,344,345,352,363,368,369,370,371,374,375,376,377,380,382,383,385,387,389,391,392,400,402,403,406,407,409,410,411,412,413,414,418,423,424,426,428,429,431,433,437,439,440,447,448,456,458,459,460,461,462,465,469,471,472,473,474,476,477,478,481,483,485,488,489,490,493,494,497,502,503,504,506],fischer:[6,9,19,20,176,387,488],fit:[3,6,9,12,38,56,190,231,302,319,377,382,411,426,431,452,459,461,484,502],five:[73,156,293,369,382,427,476,490],fix:[],fix_adapt:[164,201,422],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,206,289],fix_eo:9,fix_evapor:206,fix_flux:205,fix_gcmc:[206,369],fix_gl:237,fix_gld:237,fix_grav:289,fix_id:[3,220,257,259,261,262,263,264,265,266,267,290,293],fix_modifi:[],fix_mov:[192,337],fix_nh:8,fix_npt:237,fix_nvt:[206,235],fix_poem:[3,6],fix_pour:[3,223],fix_qbmsst:9,fix_qeq:[3,391],fix_rattl:306,fix_reax_bond:439,fix_rigid:[249,380],fix_saed_vtk:304,fix_setforc:8,fix_shak:306,fix_shardlow:9,fix_srd:3,fix_styl:264,fix_temp_rescal:325,fixedpoint:[220,259],fixextern:233,fixid:205,fji:395,flag1:[225,373],flag2:[225,373],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,88,91,92,96,106,107,109,122,165,169,173,193,195,196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18,119,121,123,321],input:[],input_doubl:3,inquir:309,insensit:12,insert:[3,5,7,8,12,59,170,199,223,235,241,289,360,448,456,474,480,497],insid:[2,3,6,8,11,71,133,139,170,193,196,207,212,213,223,224,232,235,241,246,249,289,303,319,336,338,339,340,341,342,358,363,416,474,475,476,478,479,486,490,502],insight:[6,13],instabl:[246,395,446],instal:[],instanc:[6,11,200,221,237,338,404,409,431,437,474,497],instantan:[6,63,219,220,236,237,259,264,285,290,293,298,300,303,326,482,494],instanti:[6,11,12,205,409,473],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,61,63,70,71,92,106,121,148,152,174,190,193,201,208,211,212,213,214,216,220,221,235,243,246,249,250,285,291,301,303,321,339,358,360,361,364,371,375,385,386,400,413,415,422,426,429,471,479,483,490,492,497,502],institut:[9,240,288],instruct:[],insuffici:[3,6,12],insult:259,insur:[3,6,11,12,17,39,40,61,73,105,107,170,171,190,193,195,196,202,217,218,223,228,229,232,233,235,238,243,255,291,292,301,303,319,331,336,340,341,342,344,359,369,371,375,390,405,409,435,441,459,473,474,476,477,481,484,485,493,494,502,503],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,110,117,119,121,123,144,168,170,173,174,176,180,181,185,190,192,193,195,196,206,208,212,213,217,218,219,223,225,233,235,236,237,240,243,244,245,246,285,288,289,292,293,298,303,319,321,323,326,330,331,350,360,363,384,396,398,399,412,426,439,440,444,446,448,471,473,474,475,476,484,485,486,490,493,502,503],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,210,236,438,476],intens:[1,3,6,9,63,66,74,75,88,91,92,93,96,106,107,108,109,116,118,120,121,122,123,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,165,166,167,169,199,208,209,211,212,213,214,216,217,218,219,227,232,239,249,257,259,264,300,303,304,319,327,331,333,334,493,494],intepol:502,inter:[14,18,42,61,62,150,173,174,193,219,243,245,258,295,303,360,370,382,486,497,502,504,506],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,40,42,44,50,54,55,57,61,63,65,69,72,77,79,89,90,94,95,110,111,112,114,116,119,120,126,127,128,129,131,132,133,134,135,136,137,139,140,141,142,144,145,146,148,149,163,164,168,171,172,173,174,175,176,178,182,183,189,193,199,200,201,217,218,219,234,235,240,241,243,245,249,273,284,286,288,289,294,296,302,303,310,311,319,320,326,331,335,336,337,340,341,346,347,348,349,351,355,360,361,368,369,370,371,372,373,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,434,436,437,440,441,442,444,446,447,448,449,456,457,458,460,461,462,463,464,465,466,467,468,469,471,474,476,478,480,481,485,486,488,493,494,497,504],interatom:[3,4,7,170,193,258,328,329,376,382,400,402,410,426,429,447,461,502],intercept:122,interchang:6,interconnect:18,interconvert:402,intereract:39,interesect:340,interest:[1,5,7,8,9,11,13,71,169,286,326,329,361,401,424,439,440,474,502],interf:375,interfac:[],interfer:[12,259,377],interg:[6,497],intergr:[485,489],interi:424,interior:[3,6,41,340,479],interlac:426,interleav:[6,170,484],intermedi:[6,12,59,195,258,284,354,370,474,475,484,488],intermix:471,intermolecular:377,intern:[],internal_element_set:205,internal_quadratur:205,internet:242,interpenetr:426,interpentr:[451,452,454],interpol:[6,15,38,56,103,190,195,196,205,231,246,284,360,361,370,382,431,440,453,459,460],interpret:[2,6,11,195,211,406,449,471,474,490,502],interrupt:293,intersect:[3,6,122,196,340,342,479],intersert:340,interspers:368,interstiti:[168,429],intertia:[3,96],interv:[3,6,93,194,209,243,259,293,298,299,311,447,453,471,490,502],intestieti:122,intial:[6,375,377],intiial:[41,481],intiti:[3,318],intra:303,intra_energi:235,intramolecular:[29,235],introduc:[6,9,94,110,195,259,293,298,303,354,360,376,392,402,414,418,422,458,490,502],introduct:[],intsal:[],intuit:363,inv:[122,169,304],invalid:[3,12,71,91,173,273,370,423,424,478],invari:[110,137,142,144],invent:306,invers:[],invert:[1,6,174,285],invis:340,invoc:[168,219,375,444,446,474],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,89,90,91,92,96,106,107,109,113,114,115,116,121,147,157,164,165,168,170,171,173,174,176,177,179,180,181,182,184,185,187,188,190,193,195,196,197,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,227,228,229,232,233,234,235,236,238,239,240,241,243,244,245,246,247,248,249,250,251,252,253,255,256,258,259,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,287,288,289,290,291,292,294,295,296,297,298,299,300,301,303,304,305,306,308,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,345,347,348,350,351,354,356,359,360,361,362,363,368,370,375,376,377,379,383,384,385,386,387,388,390,391,392,395,396,400,401,403,404,405,40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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style body/rounded/polygon command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/conservative command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":217,"default":[37,39,40,55,57,58,59,61,62,71,89,90,94,105,106,108,110,111,122,126,127,144,150,158,159,163,169,170,173,175,189,191,192,193,195,196,197,198,200,201,202,204,205,206,208,212,213,214,217,218,220,221,222,223,227,232,235,236,241,243,244,245,246,247,249,254,257,259,260,264,280,281,285,286,289,290,291,292,293,295,298,300,301,303,304,319,321,326,327,328,329,332,334,336,338,342,355,358,360,361,363,364,366,367,369,371,372,373,375,378,382,384,402,423,424,429,431,439,440,456,457,471,472,473,476,477,479,481,483,484,485,488,490,492,493,494,495,496,501,503,504,505],"function":502,"long":[210,383,385,386,387,388,392,394,395,414,418,422,434,442],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[200,201],addforc:202,addit:[12,13],addtorqu:203,adiabat:6,adjust_dt:309,adp:376,airebo:377,alloi:400,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:204,arrai:6,aspher:[6,84,148,261,265,269,270,278],atc:[9,205],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,83,87,94,98,99,102,103,104,110,114,115,117,144,145,168,204,206,207,292,502],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:215,awpmd:[9,378],balanc:[41,216],barostat:6,basal:67,beck:379,berendsen:[290,322],between:6,binary2txt:13,bodi:[6,8,42,68,149,262,266,271,279,380,381],bond:[8,13,69,217,218,219,299],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:382,born:[383,394],boundari:[7,57],box:[6,58,220],brownian:384,buck:[385,386,394,425],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,176,387,422],chunk:[6,66,71,75,92,96,107,109,118,150,165,167,208],citat:7,class2:[21,43,177,345,388],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[336,390,468],colvar:[9,13,221],com:[74,75,151],comb3:391,comb:[295,391],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,502],compute_modifi:105,condit:7,conduct:[6,327],conserv:397,constant:6,constraint:7,contact:[76,124],contact_radiu:[],coord:77,core:6,correl:[209,210],cosin:[23,24,25,26,27,28,179],cossq:347,coul:[383,385,386,387,388,392,393,394,407,414,418,422,434,442],coupl:6,creat:218,create_atom:170,create_bond:171,create_box:172,createatom:13,creation:7,csld:323,csvr:323,cubic:416,cuda:[9,14,113,116,147,157,202,215,229,234,238,259,268,305,306,322,324,335,383,385,387,388,400,406,407,414,415,417,420,432,458,460],custom:8,cut:[49,378,385,388,392,395,402,404,414,415,422,430,434],cvff:348,damag:[78,125],data2xmovi:13,data:6,databas:13,deby:[392,414],dec:[],defgrad:131,deform:[153,154,222],delete_atom:173,delete_bond:174,delta:24,deposit:223,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],diagnost:7,diel:393,dielectr:175,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:178,dihedral_styl:[2,176,177,179,180,181,182,183,184,185,186,187,188,189,190],dilat:80,dimens:191,dipol:[6,29,395],direct:226,discuss:6,disp:6,displac:[81,88],displace_atom:192,distanc:349,distribut:[7,12],document:0,dpd:[9,82,83,396,397,398],drag:224,dreid:[6,408],drude:[6,9,155,225,226,244],dsf:[392,414],dsmc:399,dump:[6,8,193,194,195,197],dump_modifi:196,dynam:294,eam:[13,400],echo:198,edip:401,eff:[9,13,99,100,154,156,161,245,260,272,281,325,402],efield:228,eim:403,elast:6,emac:13,energi:[127,398],enforce2d:229,ensembl:7,erot:[84,85,86,87],error:[3,126],evapor:232,event:88,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,315,316,317,318,319,320,321,322,323,324,325,326,327,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,489,490,491,492,493,494,495,496,498,499,500,501,502,503,504,505,506],exp:[27,179],expand:[46,417],extend:[8,11],extern:233,fcc:284,fdt:398,featur:[7,8,502],feb:0,fene:[45,46],fep:[9,13,89,201],field:[6,7],file:6,finit:6,fire:294,fix:[2,6,8,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,3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\ No newline at end of file
    pppm/disp pppm/disp/tip4p
    pppm/tip4p (o) 
    pppm/staggerpppm/tip4p (o)