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updates some one-line style defs

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This commit is contained in:
Steve Plimpton
2018-10-11 08:26:37 -06:00
parent 5f1c77ced2
commit 36a1ca7e72
6 changed files with 64 additions and 50 deletions
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2
doc/src/angle_class2.txt
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@ -7,8 +7,8 @@
:line
angle_style class2 command :h3
angle_style class2/omp command :h3
angle_style class2/kk command :h3
angle_style class2/omp command :h3
angle_style class2/p6 command :h3
[Syntax:]

24
doc/src/angle_style.txt
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@ -68,20 +68,20 @@ doc page.
"charmm"_angle_charmm.html - CHARMM angle
"class2"_angle_class2.html - COMPASS (class 2) angle
"class2/p6"_angle_class2.html -
"cosine"_angle_cosine.html - cosine angle potential
"cosine/buck6d"_angle_cosine_buck6d.html -
"cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential
"class2/p6"_angle_class2.html - COMPASS (class 2) angle expanded to 6th order
"cosine"_angle_cosine.html - angle with cosine term
"cosine/buck6d"_angle_cosine_buck6d.html - same as cosine with Buckingham term between 1-3 atoms
"cosine/delta"_angle_cosine_delta.html - angle with difference of cosines
"cosine/periodic"_angle_cosine_periodic.html - DREIDING angle
"cosine/shift"_angle_cosine_shift.html -
"cosine/shift/exp"_angle_cosine_shift_exp.html -
"cosine/squared"_angle_cosine_squared.html - cosine squared angle potential
"dipole"_angle_dipole.html -
"fourier"_angle_fourier.html -
"fourier/simple"_angle_fourier_simple.html -
"cosine/shift"_angle_cosine_shift.html - angle cosine with a shift
"cosine/shift/exp"_angle_cosine_shift_exp.html - cosine with shift and exponential term in spring constant
"cosine/squared"_angle_cosine_squared.html - angle with cosine squared term
"dipole"_angle_dipole.html - angle that controls orientation of a point dipole
"fourier"_angle_fourier.html - angle with multiple cosine terms
"fourier/simple"_angle_fourier_simple.html - angle with a single cosine term
"harmonic"_angle_harmonic.html - harmonic angle
"quartic"_angle_quartic.html -
"sdk"_angle_sdk.html -
"quartic"_angle_quartic.html - angle with cubic and quartic terms
"sdk"_angle_sdk.html - harmonic angle with repulsive SDK pair style between 1-3 atoms
"table"_angle_table.html - tabulated by angle :ul
:line

10
doc/src/bond_style.txt
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@ -76,14 +76,14 @@ bond styles is on the "Commands bond"_Commands_bond.html doc page.
"class2"_bond_class2.html - COMPASS (class 2) bond
"fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond
"fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles
"gromos"_bond_gromos.html -
"gromos"_bond_gromos.html - GROMOS force field bond
"harmonic"_bond_harmonic.html - harmonic bond
"harmonic/shift"_bond_harmonic_shift.html -
"harmonic/shift/cut"_bond_harmonic_shift_cut.html -
"harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond
"harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff
"morse"_bond_morse.html - Morse bond
"nonlinear"_bond_nonlinear.html - nonlinear bond
"oxdna/fene"_bond_oxdna.html -
"oxdna2/fene"_bond_oxdna.html -
"oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling
"oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles
"quartic"_bond_quartic.html - breakable quartic bond
"table"_bond_table.html - tabulated by bond length :ul

18
doc/src/dihedral_style.txt
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@ -90,19 +90,19 @@ doc page.
"hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul
"charmm"_dihedral_charmm.html - CHARMM dihedral
"charmmfsw"_dihedral_charmm.html -
"charmmfsw"_dihedral_charmm.html - CHARMM dihedral with force switching
"class2"_dihedral_class2.html - COMPASS (class 2) dihedral
"cosine/shift/exp"_dihedral_cosine_shift_exp.html -
"fourier"_dihedral_fourier.html -
"cosine/shift/exp"_dihedral_cosine_shift_exp.html - dihedral with exponential in spring constant
"fourier"_dihedral_fourier.html - dihedral with multiple cosine terms
"harmonic"_dihedral_harmonic.html - harmonic dihedral
"helix"_dihedral_helix.html - helix dihedral
"multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral
"nharmonic"_dihedral_nharmonic.html -
"multi/harmonic"_dihedral_multi_harmonic.html - dihedral with 5 harmonic terms
"nharmonic"_dihedral_nharmonic.html - same as multi-harmonic with N terms
"opls"_dihedral_opls.html - OPLS dihedral
"quadratic"_dihedral_quadratic.html -
"spherical"_dihedral_spherical.html -
"table"_dihedral_table.html -
"table/cut"_dihedral_table_cut.html - :ul
"quadratic"_dihedral_quadratic.html - dihedral with quadratic term in angle
"spherical"_dihedral_spherical.html - dihedral which includes angle terms to avoid singularities
"table"_dihedral_table.html - tabulated dihedral
"table/cut"_dihedral_table_cut.html - tabulated dihedral with analytic cutoff :ul
:line

10
doc/src/improper_style.txt
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@ -69,13 +69,13 @@ doc page.
"hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul
"class2"_improper_class2.html - COMPASS (class 2) improper
"cossq"_improper_cossq.html -
"cossq"_improper_cossq.html - improper with a cosine squared term
"cvff"_improper_cvff.html - CVFF improper
"distance"_improper_distance.html -
"fourier"_improper_fourier.html -
"distance"_improper_distance.html - improper based on distance between atom planes
"fourier"_improper_fourier.html - improper with multiple cosine terms
"harmonic"_improper_harmonic.html - harmonic improper
"inversion/harmonic"_improper_inversion_harmonic.html -
"ring"_improper_ring.html -
"inversion/harmonic"_improper_inversion_harmonic.html - harmonic improper with Wilson-Decius out-of-plane definition
"ring"_improper_ring.html - improper which prevents planar conformations
"umbrella"_improper_umbrella.html - DREIDING improper :ul
:line

50
doc/src/prd.txt
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@ -48,11 +48,12 @@ replicas of a system. One or more replicas can be used. The total
number of steps {N} to run can be interpreted in one of two ways; see
discussion of the {time} keyword below.
PRD is described in "this paper"_#Voter1998 by Art Voter. It is a method
for performing accelerated dynamics that is suitable for
infrequent-event systems that obey first-order kinetics. A good
overview of accelerated dynamics methods for such systems in given in
"this review paper"_#Voter2002prd from the same group. To quote from the
PRD is described in "(Voter1998)"_#Voter1998 by Art Voter. Similar to
global or local hyperdynamics (HD), PRD is a method for performing
accelerated dynamics that is suitable for infrequent-event systems
that obey first-order kinetics. A good overview of accelerated
dynamics methods for such systems in given in this review paper
"(Voter2002)"_#Voter2002prd from Art's group. To quote from the
paper: "The dynamical evolution is characterized by vibrational
excursions within a potential basin, punctuated by occasional
transitions between basins." The transition probability is
@ -61,15 +62,27 @@ Running multiple replicas gives an effective enhancement in the
timescale spanned by the multiple simulations, while waiting for an
event to occur.
Each replica runs on a partition of one or more processors. Processor
partitions are defined at run-time using the "-partition command-line
switch"_Run_options.html. Note that if you have MPI installed, you
can run a multi-replica simulation with more replicas (partitions)
than you have physical processors, e.g you can run a 10-replica
simulation on one or two processors. However for PRD, this makes
little sense, since running a replica on virtual instead of physical
processors,offers no effective parallel speed-up in searching for
infrequent events. See the "Howto replica"_Howto_replica.html doc
Both PRD and HD produce a time-accurate trajectory that effectively
extends the timescale over which a system can be simulated, but they
do it differently. PRD creates Nr replicas of the system and runs
dynamics on each independently with a normal unbiased potential until
an event occurs in one of the replicas. The time between events is
reduced by a factor of Nr replicas. HD uses a single replica of the
system and accelerates time by biasing the interaction potential in a
manner such that each timestep is effectively longer. For both
methods, per wall-clock second, more physical time elapses and more
events occur. See the "hyper"_hyper.html doc page for more info about
HD.
In PRD, each replica runs on a partition of one or more processors.
Processor partitions are defined at run-time using the "-partition
command-line switch"_Run_options.html. Note that if you have MPI
installed, you can run a multi-replica simulation with more replicas
(partitions) than you have physical processors, e.g you can run a
10-replica simulation on one or two processors. However for PRD, this
makes little sense, since running a replica on virtual instead of
physical processors,offers no effective parallel speed-up in searching
for infrequent events. See the "Howto replica"_Howto_replica.html doc
page for further discussion.
When a PRD simulation is performed, it is assumed that each replica is
@ -78,8 +91,8 @@ I.e. the simulation domain, the number of atoms, the interaction
potentials, etc should be the same for every replica.
A PRD run has several stages, which are repeated each time an "event"
occurs in one of the replicas, as defined below. The logic for a PRD
run is as follows:
occurs in one of the replicas, as explained below. The logic for a
PRD run is as follows:
while (time remains):
dephase for n_dephase*t_dephase steps
@ -129,7 +142,8 @@ Minimization parameters may be set via the
PRD command. The latter are the settings that would be used with the
"minimize"_minimize.html command. Note that typically, you do not
need to perform a highly-converged minimization to detect a transition
event.
event, though you may need to in order to prevent a set of atoms in
the system from relaxing to a saddle point.
The event check is performed by a compute with the specified
{compute-ID}. Currently there is only one compute that works with the
@ -307,7 +321,7 @@ deposit"_fix_deposit.html.
"min_modify"_min_modify.html, "min_style"_min_style.html,
"run_style"_run_style.html, "minimize"_minimize.html,
"velocity"_velocity.html, "temper"_temper.html, "neb"_neb.html,
"tad"_tad.html
"tad"_tad.html, "hyper"_hyper.html
[Default:]