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Merge pull request #2335 from rbberger/doc_updates

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Update documentation pages headings and update style check tool to detect missing index entries.
This commit is contained in:
Axel Kohlmeyer
2020-09-02 15:46:10 -04:00
committed by GitHub
parent 80519cd109 8def5844c8
commit 2cd0e9edc4
191 changed files with 916 additions and 866 deletions
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12
doc/src/angle_charmm.rst
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.. index:: angle_style charmm .. index:: angle_style charmm
.. index:: angle_style charmm/intel
.. index:: angle_style charmm/kk
.. index:: angle_style charmm/omp
angle_style charmm command angle_style charmm command
========================== ==========================
angle_style charmm/intel command Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp*
================================
angle_style charmm/kk command
=============================
angle_style charmm/omp command
==============================
Syntax Syntax
"""""" """"""

9
doc/src/angle_class2.rst
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@ -1,13 +1,12 @@
.. index:: angle_style class2 .. index:: angle_style class2
.. index:: angle_style class2/kk
.. index:: angle_style class2/omp
.. index:: angle_style class2/p6
angle_style class2 command angle_style class2 command
========================== ==========================
angle_style class2/kk command Accelerator Variants: *class2/kk*, *class2/omp*
=============================
angle_style class2/omp command
==============================
angle_style class2/p6 command angle_style class2/p6 command
============================= =============================

8
doc/src/angle_cosine.rst
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@ -1,13 +1,11 @@
.. index:: angle_style cosine .. index:: angle_style cosine
.. index:: angle_style cosine/omp
.. index:: angle_style cosine/kk
angle_style cosine command angle_style cosine command
========================== ==========================
angle_style cosine/omp command Accelerator Variants: *cosine/omp*, *cosine/kk*
==============================
angle_style cosine/kk command
=============================
Syntax Syntax
"""""" """"""

4
doc/src/angle_cosine_delta.rst
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@ -1,10 +1,10 @@
.. index:: angle_style cosine/delta .. index:: angle_style cosine/delta
.. index:: angle_style cosine/delta/omp
angle_style cosine/delta command angle_style cosine/delta command
================================ ================================
angle_style cosine/delta/omp command Accelerator Variants: *cosine/delta/omp*
====================================
Syntax Syntax
"""""" """"""

4
doc/src/angle_cosine_periodic.rst
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@ -1,10 +1,10 @@
.. index:: angle_style cosine/periodic .. index:: angle_style cosine/periodic
.. index:: angle_style cosine/periodic/omp
angle_style cosine/periodic command angle_style cosine/periodic command
=================================== ===================================
angle_style cosine/periodic/omp command Accelerator Variants: *cosine/periodic/omp*
=======================================
Syntax Syntax
"""""" """"""

6
doc/src/angle_cosine_shift.rst
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@ -1,10 +1,10 @@
.. index:: angle_style cosine/shift .. index:: angle_style cosine/shift
.. index:: angle_style cosine/shift/omp
angle_style cosine/shift command angle_style cosine/shift command
================================= ================================
angle_style cosine/shift/omp command Accelerator Variants: *cosine/shift/omp*
====================================
Syntax Syntax
"""""" """"""

4
doc/src/angle_cosine_shift_exp.rst
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@ -1,10 +1,10 @@
.. index:: angle_style cosine/shift/exp .. index:: angle_style cosine/shift/exp
.. index:: angle_style cosine/shift/exp/omp
angle_style cosine/shift/exp command angle_style cosine/shift/exp command
==================================== ====================================
angle_style cosine/shift/exp/omp command Accelerator Variants: *cosine/shift/exp/omp*
========================================
Syntax Syntax
"""""" """"""

4
doc/src/angle_cosine_squared.rst
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@ -1,10 +1,10 @@
.. index:: angle_style cosine/squared .. index:: angle_style cosine/squared
.. index:: angle_style cosine/squared/omp
angle_style cosine/squared command angle_style cosine/squared command
================================== ==================================
angle_style cosine/squared/omp command Accelerator Variants: *cosine/squared/omp*
======================================
Syntax Syntax
"""""" """"""

2
doc/src/angle_cross.rst
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@ -1,7 +1,7 @@
.. index:: angle_style cross .. index:: angle_style cross
angle_style cross command angle_style cross command
========================== =========================
Syntax Syntax
"""""" """"""

4
doc/src/angle_dipole.rst
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@ -1,10 +1,10 @@
.. index:: angle_style dipole .. index:: angle_style dipole
.. index:: angle_style dipole/omp
angle_style dipole command angle_style dipole command
========================== ==========================
angle_style dipole/omp command Accelerator Variants: *dipole/omp*
==============================
Syntax Syntax
"""""" """"""

4
doc/src/angle_fourier.rst
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@ -1,10 +1,10 @@
.. index:: angle_style fourier .. index:: angle_style fourier
.. index:: angle_style fourier/omp
angle_style fourier command angle_style fourier command
=========================== ===========================
angle_style fourier/omp command Accelerator Variants: *fourier/omp*
===============================
Syntax Syntax
"""""" """"""

4
doc/src/angle_fourier_simple.rst
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@ -1,10 +1,10 @@
.. index:: angle_style fourier/simple .. index:: angle_style fourier/simple
.. index:: angle_style fourier/simple/omp
angle_style fourier/simple command angle_style fourier/simple command
================================== ==================================
angle_style fourier/simple/omp command Accelerator Variants: *fourier/simple/omp*
======================================
Syntax Syntax
"""""" """"""

12
doc/src/angle_harmonic.rst
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@ -1,16 +1,12 @@
.. index:: angle_style harmonic .. index:: angle_style harmonic
.. index:: angle_style harmonic/intel
.. index:: angle_style harmonic/kk
.. index:: angle_style harmonic/omp
angle_style harmonic command angle_style harmonic command
============================ ============================
angle_style harmonic/intel command Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp*
==================================
angle_style harmonic/kk command
===============================
angle_style harmonic/omp command
================================
Syntax Syntax
"""""" """"""

4
doc/src/angle_quartic.rst
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@ -1,10 +1,10 @@
.. index:: angle_style quartic .. index:: angle_style quartic
.. index:: angle_style quartic/omp
angle_style quartic command angle_style quartic command
=========================== ===========================
angle_style quartic/omp command Accelerator Variants: *quartic/omp*
===============================
Syntax Syntax
"""""" """"""

4
doc/src/angle_sdk.rst
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@ -1,10 +1,10 @@
.. index:: angle_style sdk .. index:: angle_style sdk
.. index:: angle_style sdk/omp
angle_style sdk command angle_style sdk command
======================= =======================
angle_style sdk/omp command Accelerator Variants: *sdk/omp*
===========================
Syntax Syntax
"""""" """"""

4
doc/src/angle_table.rst
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@ -1,10 +1,10 @@
.. index:: angle_style table .. index:: angle_style table
.. index:: angle_style table/omp
angle_style table command angle_style table command
========================= =========================
angle_style table/omp command Accelerator Variants: *table/omp*
=============================
Syntax Syntax
"""""" """"""

8
doc/src/bond_class2.rst
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@ -1,13 +1,11 @@
.. index:: bond_style class2 .. index:: bond_style class2
.. index:: bond_style class2/omp
.. index:: bond_style class2/kk
bond_style class2 command bond_style class2 command
========================= =========================
bond_style class2/omp command Accelerator Variants: *class2/omp*, *class2/kk*
=============================
bond_style class2/kk command
============================
Syntax Syntax
"""""" """"""

12
doc/src/bond_fene.rst
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@ -1,16 +1,12 @@
.. index:: bond_style fene .. index:: bond_style fene
.. index:: bond_style fene/intel
.. index:: bond_style fene/kk
.. index:: bond_style fene/omp
bond_style fene command bond_style fene command
======================= =======================
bond_style fene/intel command Accelerator Variants: *fene/intel*, *fene/kk*, *fene/omp*
=============================
bond_style fene/kk command
==========================
bond_style fene/omp command
===========================
Syntax Syntax
"""""" """"""

4
doc/src/bond_fene_expand.rst
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@ -1,10 +1,10 @@
.. index:: bond_style fene/expand .. index:: bond_style fene/expand
.. index:: bond_style fene/expand/omp
bond_style fene/expand command bond_style fene/expand command
============================== ==============================
bond_style fene/expand/omp command Accelerator Variants: *fene/expand/omp*
==================================
Syntax Syntax
"""""" """"""

4
doc/src/bond_gromos.rst
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@ -1,10 +1,10 @@
.. index:: bond_style gromos .. index:: bond_style gromos
.. index:: bond_style gromos/omp
bond_style gromos command bond_style gromos command
========================= =========================
bond_style gromos/omp command Accelerator Variants: *gromos/omp*
=============================
Syntax Syntax
"""""" """"""

12
doc/src/bond_harmonic.rst
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.. index:: bond_style harmonic .. index:: bond_style harmonic
.. index:: bond_style harmonic/intel
.. index:: bond_style harmonic/kk
.. index:: bond_style harmonic/omp
bond_style harmonic command bond_style harmonic command
=========================== ===========================
bond_style harmonic/intel command Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp*
=================================
bond_style harmonic/kk command
==============================
bond_style harmonic/omp command
===============================
Syntax Syntax
"""""" """"""

4
doc/src/bond_harmonic_shift.rst
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@ -1,10 +1,10 @@
.. index:: bond_style harmonic/shift .. index:: bond_style harmonic/shift
.. index:: bond_style harmonic/shift/omp
bond_style harmonic/shift command bond_style harmonic/shift command
================================= =================================
bond_style harmonic/shift/omp command Accelerator Variants: *harmonic/shift/omp*
=====================================
Syntax Syntax
"""""" """"""

4
doc/src/bond_harmonic_shift_cut.rst
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@ -1,10 +1,10 @@
.. index:: bond_style harmonic/shift/cut .. index:: bond_style harmonic/shift/cut
.. index:: bond_style harmonic/shift/cut/omp
bond_style harmonic/shift/cut command bond_style harmonic/shift/cut command
===================================== =====================================
bond_style harmonic/shift/cut/omp command Accelerator Variants: *harmonic/shift/cut/omp*
=========================================
Syntax Syntax
"""""" """"""

4
doc/src/bond_morse.rst
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@ -1,10 +1,10 @@
.. index:: bond_style morse .. index:: bond_style morse
.. index:: bond_style morse/omp
bond_style morse command bond_style morse command
======================== ========================
bond_style morse/omp command Accelerator Variants: *morse/omp*
============================
Syntax Syntax
"""""" """"""

4
doc/src/bond_nonlinear.rst
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@ -1,10 +1,10 @@
.. index:: bond_style nonlinear .. index:: bond_style nonlinear
.. index:: bond_style nonlinear/omp
bond_style nonlinear command bond_style nonlinear command
============================ ============================
bond_style nonlinear/omp command Accelerator Variants: *nonlinear/omp*
================================
Syntax Syntax
"""""" """"""

2
doc/src/bond_oxdna.rst
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@ -1,4 +1,6 @@
.. index:: bond_style oxdna/fene .. index:: bond_style oxdna/fene
.. index:: bond_style oxdna2/fene
.. index:: bond_style oxrna2/fene
bond_style oxdna/fene command bond_style oxdna/fene command
============================= =============================

4
doc/src/bond_quartic.rst
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@ -1,10 +1,10 @@
.. index:: bond_style quartic .. index:: bond_style quartic
.. index:: bond_style quartic/omp
bond_style quartic command bond_style quartic command
========================== ==========================
bond_style quartic/omp command Accelerator Variants: *quartic/omp*
==============================
Syntax Syntax
"""""" """"""

2
doc/src/bond_special.rst
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.. index:: bond_style special .. index:: bond_style special
bond_style special command bond_style special command
================================= ==========================
Syntax Syntax
"""""" """"""

4
doc/src/bond_table.rst
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@ -1,10 +1,10 @@
.. index:: bond_style table .. index:: bond_style table
.. index:: bond_style table/omp
bond_style table command bond_style table command
======================== ========================
bond_style table/omp command Accelerator Variants: *table/omp*
============================
Syntax Syntax
"""""" """"""

2
doc/src/compute_cluster_atom.rst
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@ -1,4 +1,6 @@
.. index:: compute cluster/atom .. index:: compute cluster/atom
.. index:: compute fragment/atom
.. index:: compute aggregate/atom
compute cluster/atom command compute cluster/atom command
============================ ============================

4
doc/src/compute_coord_atom.rst
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@ -1,10 +1,10 @@
.. index:: compute coord/atom .. index:: compute coord/atom
.. index:: compute coord/atom/kk
compute coord/atom command compute coord/atom command
========================== ==========================
compute coord/atom/kk command Accelerator Variants: *coord/atom/kk*
===================================
Syntax Syntax
"""""" """"""

2
doc/src/compute_mesont.rst
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.. index:: compute mesont .. index:: compute mesont
compute mesont command compute mesont command
========================== ======================
Syntax Syntax
"""""" """"""

4
doc/src/compute_orientorder_atom.rst
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@ -1,10 +1,10 @@
.. index:: compute orientorder/atom .. index:: compute orientorder/atom
.. index:: compute orientorder/atom/kk
compute orientorder/atom command compute orientorder/atom command
================================ ================================
compute orientorder/atom/kk command Accelerator Variants: *orientorder/atom/kk*
===================================
Syntax Syntax
"""""" """"""

1
doc/src/compute_reduce.rst
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@ -1,4 +1,5 @@
.. index:: compute reduce .. index:: compute reduce
.. index:: compute reduce/region
compute reduce command compute reduce command
====================== ======================

2
doc/src/compute_smd_ulsph_effm.rst
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@ -1,7 +1,7 @@
.. index:: compute smd/ulsph/effm .. index:: compute smd/ulsph/effm
compute smd/ulsph/effm command compute smd/ulsph/effm command
================================ ==============================
Syntax Syntax
"""""" """"""

3
doc/src/compute_sna_atom.rst
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@ -1,4 +1,7 @@
.. index:: compute sna/atom .. index:: compute sna/atom
.. index:: compute snad/atom
.. index:: compute snav/atom
.. index:: compute snap
compute sna/atom command compute sna/atom command
======================== ========================

2
doc/src/compute_sph_e_atom.rst
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@ -1,7 +1,7 @@
.. index:: compute sph/e/atom .. index:: compute sph/e/atom
compute sph/e/atom command compute sph/e/atom command
=========================== ==========================
Syntax Syntax
"""""" """"""

2
doc/src/compute_sph_rho_atom.rst
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.. index:: compute sph/rho/atom .. index:: compute sph/rho/atom
compute sph/rho/atom command compute sph/rho/atom command
============================= ============================
Syntax Syntax
"""""" """"""

2
doc/src/compute_sph_t_atom.rst
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.. index:: compute sph/t/atom .. index:: compute sph/t/atom
compute sph/t/atom command compute sph/t/atom command
=========================== ==========================
Syntax Syntax
"""""" """"""

1
doc/src/compute_stress_atom.rst
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.. index:: compute stress/atom .. index:: compute stress/atom
.. index:: compute centroid/stress/atom
compute stress/atom command compute stress/atom command
=========================== ===========================

1
doc/src/compute_stress_mop.rst
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.. index:: compute stress/mop .. index:: compute stress/mop
.. index:: compute stress/mop/profile
compute stress/mop command compute stress/mop command
========================== ==========================

4
doc/src/compute_tally.rst
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@ -1,4 +1,8 @@
.. index:: compute force/tally .. index:: compute force/tally
.. index:: compute heat/flux/tally
.. index:: compute pe/tally
.. index:: compute pe/mol/tally
.. index:: compute stress/tally
compute force/tally command compute force/tally command
=========================== ===========================

4
doc/src/compute_temp.rst
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@ -1,10 +1,10 @@
.. index:: compute temp .. index:: compute temp
.. index:: compute temp/kk
compute temp command compute temp command
==================== ====================
compute temp/kk command Accelerator Variants: *temp/kk*
=======================
Syntax Syntax
"""""" """"""

13
doc/src/dihedral_charmm.rst
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.. index:: dihedral_style charmm .. index:: dihedral_style charmm
.. index:: dihedral_style charmm/intel
.. index:: dihedral_style charmm/kk
.. index:: dihedral_style charmm/omp
.. index:: dihedral_style charmmfsw
dihedral_style charmm command dihedral_style charmm command
============================= =============================
dihedral_style charmm/intel command Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp*
===================================
dihedral_style charmm/kk command
================================
dihedral_style charmm/omp command
=================================
dihedral_style charmmfsw command dihedral_style charmmfsw command
================================ ================================

8
doc/src/dihedral_class2.rst
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.. index:: dihedral_style class2 .. index:: dihedral_style class2
.. index:: dihedral_style class2/omp
.. index:: dihedral_style class2/kk
dihedral_style class2 command dihedral_style class2 command
============================= =============================
dihedral_style class2/omp command Accelerator Variants: *class2/omp*, *class2/kk*
=================================
dihedral_style class2/kk command
================================
Syntax Syntax
"""""" """"""

4
doc/src/dihedral_cosine_shift_exp.rst
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.. index:: dihedral_style cosine/shift/exp .. index:: dihedral_style cosine/shift/exp
.. index:: dihedral_style cosine/shift/exp/omp
dihedral_style cosine/shift/exp command dihedral_style cosine/shift/exp command
======================================= =======================================
dihedral_style cosine/shift/exp/omp command Accelerator Variants: *cosine/shift/exp/omp*
===========================================
Syntax Syntax
"""""" """"""

8
doc/src/dihedral_fourier.rst
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@ -1,13 +1,11 @@
.. index:: dihedral_style fourier .. index:: dihedral_style fourier
.. index:: dihedral_style fourier/intel
.. index:: dihedral_style fourier/omp
dihedral_style fourier command dihedral_style fourier command
============================== ==============================
dihedral_style fourier/intel command Accelerator Variants: *fourier/intel*, *fourier/omp*
====================================
dihedral_style fourier/omp command
==================================
Syntax Syntax
"""""" """"""

12
doc/src/dihedral_harmonic.rst
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@ -1,16 +1,12 @@
.. index:: dihedral_style harmonic .. index:: dihedral_style harmonic
.. index:: dihedral_style harmonic/intel
.. index:: dihedral_style harmonic/kk
.. index:: dihedral_style harmonic/omp
dihedral_style harmonic command dihedral_style harmonic command
=============================== ===============================
dihedral_style harmonic/intel command Accelerator Variants: *harmonic/intel*, *harmonic/kk*, *harmonic/omp*
=====================================
dihedral_style harmonic/kk command
==================================
dihedral_style harmonic/omp command
===================================
Syntax Syntax
"""""" """"""

4
doc/src/dihedral_helix.rst
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.. index:: dihedral_style helix .. index:: dihedral_style helix
.. index:: dihedral_style helix/omp
dihedral_style helix command dihedral_style helix command
============================ ============================
dihedral_style helix/omp command Accelerator Variants: *helix/omp*
================================
Syntax Syntax
"""""" """"""

4
doc/src/dihedral_multi_harmonic.rst
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@ -1,10 +1,10 @@
.. index:: dihedral_style multi/harmonic .. index:: dihedral_style multi/harmonic
.. index:: dihedral_style multi/harmonic/omp
dihedral_style multi/harmonic command dihedral_style multi/harmonic command
===================================== =====================================
dihedral_style multi/harmonic/omp command Accelerator Variants: *multi/harmonic/omp*
=========================================
Syntax Syntax
"""""" """"""

6
doc/src/dihedral_nharmonic.rst
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@ -1,10 +1,10 @@
.. index:: dihedral_style nharmonic .. index:: dihedral_style nharmonic
.. index:: dihedral_style nharmonic/omp
dihedral_style nharmonic command dihedral_style nharmonic command
================================= ================================
dihedral_style nharmonic/omp command Accelerator Variants: *nharmonic/omp*
=====================================
Syntax Syntax
"""""" """"""

12
doc/src/dihedral_opls.rst
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@ -1,16 +1,12 @@
.. index:: dihedral_style opls .. index:: dihedral_style opls
.. index:: dihedral_style opls/intel
.. index:: dihedral_style opls/kk
.. index:: dihedral_style opls/omp
dihedral_style opls command dihedral_style opls command
=========================== ===========================
dihedral_style opls/intel command Accelerator Variants: *opls/intel*, *opls/kk*, *opls/omp*
=================================
dihedral_style opls/kk command
==============================
dihedral_style opls/omp command
===============================
Syntax Syntax
"""""" """"""

4
doc/src/dihedral_quadratic.rst
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@ -1,10 +1,10 @@
.. index:: dihedral_style quadratic .. index:: dihedral_style quadratic
.. index:: dihedral_style quadratic/omp
dihedral_style quadratic command dihedral_style quadratic command
================================ ================================
dihedral_style quadratic/omp command Accelerator Variants: *quadratic/omp*
====================================
Syntax Syntax
"""""" """"""

4
doc/src/dihedral_table.rst
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@ -1,10 +1,10 @@
.. index:: dihedral_style table .. index:: dihedral_style table
.. index:: dihedral_style table/omp
dihedral_style table command dihedral_style table command
============================ ============================
dihedral_style table/omp command Accelerator Variants: *table/omp*
================================
Syntax Syntax
"""""" """"""

2
doc/src/dihedral_zero.rst
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@ -1,7 +1,7 @@
.. index:: dihedral_style zero .. index:: dihedral_style zero
dihedral_style zero command dihedral_style zero command
============================ ===========================
Syntax Syntax
"""""" """"""

1
doc/src/fix_ave_histo.rst
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@ -1,4 +1,5 @@
.. index:: fix ave/histo .. index:: fix ave/histo
.. index:: fix ave/histo/weight
fix ave/histo command fix ave/histo command
===================== =====================

1
doc/src/fix_bond_create.rst
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@ -1,4 +1,5 @@
.. index:: fix bond/create .. index:: fix bond/create
.. index:: fix bond/create/angle
fix bond/create command fix bond/create command
======================= =======================

4
doc/src/fix_deform.rst
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@ -1,10 +1,10 @@
.. index:: fix deform .. index:: fix deform
.. index:: fix deform/kk
fix deform command fix deform command
================== ==================
fix deform/kk command Accelerator Variants: *deform/kk*
=====================
Syntax Syntax
"""""" """"""

4
doc/src/fix_dpd_energy.rst
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@ -1,10 +1,10 @@
.. index:: fix dpd/energy .. index:: fix dpd/energy
.. index:: fix dpd/energy/kk
fix dpd/energy command fix dpd/energy command
====================== ======================
fix dpd/energy/kk command Accelerator Variants: *dpd/energy/kk*
=========================
Syntax Syntax
"""""" """"""

1
doc/src/fix_dpd_source.rst
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@ -1,4 +1,5 @@
.. index:: fix edpd/source .. index:: fix edpd/source
.. index:: fix tdpd/source
fix edpd/source command fix edpd/source command
======================= =======================

1
doc/src/fix_drude_transform.rst
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@ -1,4 +1,5 @@
.. index:: fix drude/transform/direct .. index:: fix drude/transform/direct
.. index:: fix drude/transform/inverse
fix drude/transform/direct command fix drude/transform/direct command
================================== ==================================

4
doc/src/fix_enforce2d.rst
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@ -1,10 +1,10 @@
.. index:: fix enforce2d .. index:: fix enforce2d
.. index:: fix enforce2d/kk
fix enforce2d command fix enforce2d command
===================== =====================
fix enforce2d/kk command Accelerator Variants: *enforce2d/kk*
========================
Syntax Syntax
"""""" """"""

4
doc/src/fix_eos_table_rx.rst
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@ -1,10 +1,10 @@
.. index:: fix eos/table/rx .. index:: fix eos/table/rx
.. index:: fix eos/table/rx/kk
fix eos/table/rx command fix eos/table/rx command
======================== ========================
fix eos/table/rx/kk command Accelerator Variants: *eos/table/rx/kk*
===========================
Syntax Syntax
"""""" """"""

4
doc/src/fix_freeze.rst
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@ -1,10 +1,10 @@
.. index:: fix freeze .. index:: fix freeze
.. index:: fix freeze/kk
fix freeze command fix freeze command
================== ==================
fix freeze/kk command Accelerator Variants: *freeze/kk*
=====================
Syntax Syntax
"""""" """"""

8
doc/src/fix_gravity.rst
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@ -1,13 +1,11 @@
.. index:: fix gravity .. index:: fix gravity
.. index:: fix gravity/omp
.. index:: fix gravity/kk
fix gravity command fix gravity command
=================== ===================
fix gravity/omp command Accelerator Variants: *gravity/omp*, *gravity/kk*
=======================
fix gravity/kk command
======================
Syntax Syntax
"""""" """"""

4
doc/src/fix_langevin.rst
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@ -1,10 +1,10 @@
.. index:: fix langevin .. index:: fix langevin
.. index:: fix langevin/kk
fix langevin command fix langevin command
==================== ====================
fix langevin/kk command Accelerator Variants: *langevin/kk*
=======================
Syntax Syntax
"""""" """"""

5
doc/src/fix_momentum.rst
View File

@ -1,10 +1,11 @@
.. index:: fix momentum .. index:: fix momentum
.. index:: fix momentum/kk
.. index:: fix momentum/chunk
fix momentum command fix momentum command
==================== ====================
fix momentum/kk command Accelerator Variants: *momentum/kk*
=======================
fix momentum/chunk command fix momentum/chunk command
========================== ==========================

2
doc/src/fix_mvv_dpd.rst
View File

@ -1,4 +1,6 @@
.. index:: fix mvv/dpd .. index:: fix mvv/dpd
.. index:: fix mvv/edpd
.. index:: fix mvv/tdpd
fix mvv/dpd command fix mvv/dpd command
=================== ===================

34
doc/src/fix_nh.rst
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@ -1,37 +1,29 @@
.. index:: fix nvt .. index:: fix nvt
.. index:: fix nvt/intel
.. index:: fix nvt/kk
.. index:: fix nvt/omp
.. index:: fix npt
.. index:: fix npt/intel
.. index:: fix npt/kk
.. index:: fix npt/omp
.. index:: fix nph
.. index:: fix nph/kk
.. index:: fix nph/omp
fix nvt command fix nvt command
=============== ===============
fix nvt/intel command Accelerator Variants: *nvt/intel*, *nvt/kk*, *nvt/omp*
=====================
fix nvt/kk command
==================
fix nvt/omp command
===================
fix npt command fix npt command
=============== ===============
fix npt/intel command Accelerator Variants: *npt/intel*, *npt/kk*, *npt/omp*
=====================
fix npt/kk command
==================
fix npt/omp command
===================
fix nph command fix nph command
=============== ===============
fix nph/kk command Accelerator Variants: *nph/kk*, *nph/omp*
==================
fix nph/omp command
===================
Syntax Syntax
"""""" """"""

2
doc/src/fix_nh_eff.rst
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@ -1,4 +1,6 @@
.. index:: fix nvt/eff .. index:: fix nvt/eff
.. index:: fix npt/eff
.. index:: fix nph/eff
fix nvt/eff command fix nvt/eff command
=================== ===================

1
doc/src/fix_nh_uef.rst
View File

@ -1,4 +1,5 @@
.. index:: fix nvt/uef .. index:: fix nvt/uef
.. index:: fix npt/uef
fix nvt/uef command fix nvt/uef command
=================== ===================

4
doc/src/fix_nph_asphere.rst
View File

@ -1,10 +1,10 @@
.. index:: fix nph/asphere .. index:: fix nph/asphere
.. index:: fix nph/asphere/omp
fix nph/asphere command fix nph/asphere command
======================= =======================
fix nph/asphere/omp command Accelerator Variants: *nph/asphere/omp*
===========================
Syntax Syntax
"""""" """"""

4
doc/src/fix_nph_sphere.rst
View File

@ -1,10 +1,10 @@
.. index:: fix nph/sphere .. index:: fix nph/sphere
.. index:: fix nph/sphere/omp
fix nph/sphere command fix nph/sphere command
====================== ======================
fix nph/sphere/omp command Accelerator Variants: *nph/sphere/omp*
==========================
Syntax Syntax
"""""" """"""

4
doc/src/fix_nphug.rst
View File

@ -1,10 +1,10 @@
.. index:: fix nphug .. index:: fix nphug
.. index:: fix nphug/omp
fix nphug command fix nphug command
================= =================
fix nphug/omp command Accelerator Variants: *nphug/omp*
=====================
Syntax Syntax
"""""" """"""

4
doc/src/fix_npt_asphere.rst
View File

@ -1,10 +1,10 @@
.. index:: fix npt/asphere .. index:: fix npt/asphere
.. index:: fix npt/asphere/omp
fix npt/asphere command fix npt/asphere command
======================= =======================
fix npt/asphere/omp command Accelerator Variants: *npt/asphere/omp*
===========================
Syntax Syntax
"""""" """"""

4
doc/src/fix_npt_sphere.rst
View File

@ -1,10 +1,10 @@
.. index:: fix npt/sphere .. index:: fix npt/sphere
.. index:: fix npt/sphere/omp
fix npt/sphere command fix npt/sphere command
====================== ======================
fix npt/sphere/omp command Accelerator Variants: *npt/sphere/omp*
==========================
Syntax Syntax
"""""" """"""

2
doc/src/fix_numdiff.rst
View File

@ -1,7 +1,7 @@
.. index:: fix numdiff .. index:: fix numdiff
fix numdiff command fix numdiff command
==================== ===================
Syntax Syntax
"""""" """"""

12
doc/src/fix_nve.rst
View File

@ -1,16 +1,12 @@
.. index:: fix nve .. index:: fix nve
.. index:: fix nve/intel
.. index:: fix nve/kk
.. index:: fix nve/omp
fix nve command fix nve command
=============== ===============
fix nve/intel command Accelerator Variants: *nve/intel*, *nve/kk*, *nve/omp*
=====================
fix nve/kk command
==================
fix nve/omp command
===================
Syntax Syntax
"""""" """"""

4
doc/src/fix_nve_asphere.rst
View File

@ -1,10 +1,10 @@
.. index:: fix nve/asphere .. index:: fix nve/asphere
.. index:: fix nve/asphere/intel
fix nve/asphere command fix nve/asphere command
======================= =======================
fix nve/asphere/intel command Accelerator Variants: *nve/asphere/intel*
=============================
Syntax Syntax
"""""" """"""

8
doc/src/fix_nve_sphere.rst
View File

@ -1,13 +1,11 @@
.. index:: fix nve/sphere .. index:: fix nve/sphere
.. index:: fix nve/sphere/omp
.. index:: fix nve/sphere/kk
fix nve/sphere command fix nve/sphere command
====================== ======================
fix nve/sphere/omp command Accelerator Variants: *nve/sphere/omp*, *nve/sphere/kk*
==========================
fix nve/sphere/kk command
=========================
Syntax Syntax
"""""" """"""

4
doc/src/fix_nvt_asphere.rst
View File

@ -1,10 +1,10 @@
.. index:: fix nvt/asphere .. index:: fix nvt/asphere
.. index:: fix nvt/asphere/omp
fix nvt/asphere command fix nvt/asphere command
======================= =======================
fix nvt/asphere/omp command Accelerator Variants: *nvt/asphere/omp*
===========================
Syntax Syntax
"""""" """"""

8
doc/src/fix_nvt_sllod.rst
View File

@ -1,13 +1,11 @@
.. index:: fix nvt/sllod .. index:: fix nvt/sllod
.. index:: fix nvt/sllod/intel
.. index:: fix nvt/sllod/omp
fix nvt/sllod command fix nvt/sllod command
===================== =====================
fix nvt/sllod/intel command Accelerator Variants: *nvt/sllod/intel*, *nvt/sllod/omp*
===========================
fix nvt/sllod/omp command
=========================
Syntax Syntax
"""""" """"""

4
doc/src/fix_nvt_sphere.rst
View File

@ -1,10 +1,10 @@
.. index:: fix nvt/sphere .. index:: fix nvt/sphere
.. index:: fix nvt/sphere/omp
fix nvt/sphere command fix nvt/sphere command
====================== ======================
fix nvt/sphere/omp command Accelerator Variants: *nvt/sphere/omp*
==========================
Syntax Syntax
"""""" """"""

1
doc/src/fix_orient.rst
View File

@ -1,4 +1,5 @@
.. index:: fix orient/fcc .. index:: fix orient/fcc
.. index:: fix orient/bcc
fix orient/fcc command fix orient/fcc command
====================== ======================

4
doc/src/fix_property_atom.rst
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@ -1,10 +1,10 @@
.. index:: fix property/atom .. index:: fix property/atom
.. index:: fix property/atom/kk
fix property/atom command fix property/atom command
========================= =========================
fix property/atom/kk command Accelerator Variants: *property/atom/kk*
============================
Syntax Syntax
"""""" """"""

4
doc/src/fix_qeq.rst
View File

@ -1,4 +1,8 @@
.. index:: fix qeq/point .. index:: fix qeq/point
.. index:: fix qeq/shielded
.. index:: fix qeq/slater
.. index:: fix qeq/dynamic
.. index:: fix qeq/fire
fix qeq/point command fix qeq/point command
===================== =====================

4
doc/src/fix_qeq_comb.rst
View File

@ -1,10 +1,10 @@
.. index:: fix qeq/comb .. index:: fix qeq/comb
.. index:: fix qeq/comb/omp
fix qeq/comb command fix qeq/comb command
==================== ====================
fix qeq/comb/omp command Accelerator Variants: *qeq/comb/omp*
========================
Syntax Syntax
"""""" """"""

8
doc/src/fix_qeq_reax.rst
View File

@ -1,13 +1,11 @@
.. index:: fix qeq/reax .. index:: fix qeq/reax
.. index:: fix qeq/reax/kk
.. index:: fix qeq/reax/omp
fix qeq/reax command fix qeq/reax command
==================== ====================
fix qeq/reax/kk command Accelerator Variants: *qeq/reax/kk*, *qeq/reax/omp*
=======================
fix qeq/reax/omp command
========================
Syntax Syntax
"""""" """"""

4
doc/src/fix_reaxc_bonds.rst
View File

@ -1,10 +1,10 @@
.. index:: fix reax/c/bonds .. index:: fix reax/c/bonds
.. index:: fix reax/c/bonds/kk
fix reax/c/bonds command fix reax/c/bonds command
======================== ========================
fix reax/c/bonds/kk command Accelerator Variants: *reax/c/bonds/kk*
===========================
Syntax Syntax
"""""" """"""

4
doc/src/fix_reaxc_species.rst
View File

@ -1,10 +1,10 @@
.. index:: fix reax/c/species .. index:: fix reax/c/species
.. index:: fix reax/c/species/kk
fix reax/c/species command fix reax/c/species command
========================== ==========================
fix reax/c/species/kk command Accelerator Variants: *reax/c/species/kk*
=============================
Syntax Syntax
"""""" """"""

33
doc/src/fix_rigid.rst
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@ -1,40 +1,49 @@
.. index:: fix rigid .. index:: fix rigid
.. index:: fix rigid/omp
.. index:: fix rigid/nve
.. index:: fix rigid/nve/omp
.. index:: fix rigid/nvt
.. index:: fix rigid/nvt/omp
.. index:: fix rigid/npt
.. index:: fix rigid/npt/omp
.. index:: fix rigid/nph
.. index:: fix rigid/nph/omp
.. index:: fix rigid/small
.. index:: fix rigid/small/omp
.. index:: fix rigid/nve/small
.. index:: fix rigid/nvt/small
.. index:: fix rigid/npt/small
.. index:: fix rigid/nph/small
fix rigid command fix rigid command
================= =================
fix rigid/omp command Accelerator Variants: *rigid/omp*
=====================
fix rigid/nve command fix rigid/nve command
===================== =====================
fix rigid/nve/omp command Accelerator Variants: *rigid/nve/omp*
=========================
fix rigid/nvt command fix rigid/nvt command
===================== =====================
fix rigid/nvt/omp command Accelerator Variants: *rigid/nvt/omp*
=========================
fix rigid/npt command fix rigid/npt command
===================== =====================
fix rigid/npt/omp command Accelerator Variants: *rigid/npt/omp*
=========================
fix rigid/nph command fix rigid/nph command
===================== =====================
fix rigid/nph/omp command Accelerator Variants: *rigid/nph/omp*
=========================
fix rigid/small command fix rigid/small command
======================= =======================
fix rigid/small/omp command Accelerator Variants: *rigid/small/omp*
===========================
fix rigid/nve/small command fix rigid/nve/small command
=========================== ===========================

4
doc/src/fix_rx.rst
View File

@ -1,10 +1,10 @@
.. index:: fix rx .. index:: fix rx
.. index:: fix rx/kk
fix rx command fix rx command
============== ==============
fix rx/kk command Accelerator Variants: *rx/kk*
=================
Syntax Syntax
"""""" """"""

5
doc/src/fix_setforce.rst
View File

@ -1,10 +1,11 @@
.. index:: fix setforce .. index:: fix setforce
.. index:: fix setforce/kk
.. index:: fix setforce/spin
fix setforce command fix setforce command
==================== ====================
fix setforce/kk command Accelerator Variants: *setforce/kk*
=======================
fix setforce/spin command fix setforce/spin command
========================= =========================

1
doc/src/fix_shake.rst
View File

@ -1,4 +1,5 @@
.. index:: fix shake .. index:: fix shake
.. index:: fix rattle
fix shake command fix shake command
================= =================

4
doc/src/fix_shardlow.rst
View File

@ -1,10 +1,10 @@
.. index:: fix shardlow .. index:: fix shardlow
.. index:: fix shardlow/kk
fix shardlow command fix shardlow command
==================== ====================
fix shardlow/kk command Accelerator Variants: *shardlow/kk*
=======================
Syntax Syntax
"""""" """"""

2
doc/src/fix_smd_integrate_ulsph.rst
View File

@ -1,7 +1,7 @@
.. index:: fix smd/integrate_ulsph .. index:: fix smd/integrate_ulsph
fix smd/integrate_ulsph command fix smd/integrate_ulsph command
================================ ===============================
Syntax Syntax
"""""" """"""

2
doc/src/fix_sph.rst
View File

@ -1,7 +1,7 @@
.. index:: fix sph .. index:: fix sph
fix sph command fix sph command
================ ===============
Syntax Syntax
"""""" """"""

2
doc/src/fix_sph_stationary.rst
View File

@ -1,7 +1,7 @@
.. index:: fix sph/stationary .. index:: fix sph/stationary
fix sph/stationary command fix sph/stationary command
=========================== ==========================
Syntax Syntax
"""""" """"""

1
doc/src/fix_temp_csvr.rst
View File

@ -1,4 +1,5 @@
.. index:: fix temp/csvr .. index:: fix temp/csvr
.. index:: fix temp/csld
fix temp/csvr command fix temp/csvr command
===================== =====================

1
doc/src/fix_ttm.rst
View File

@ -1,4 +1,5 @@
.. index:: fix ttm .. index:: fix ttm
.. index:: fix ttm/mod
fix ttm command fix ttm command
=============== ===============

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