diff --git a/doc/src/angle_class2.txt b/doc/src/angle_class2.txt index fa5e29582c..5a772f8fa9 100644 --- a/doc/src/angle_class2.txt +++ b/doc/src/angle_class2.txt @@ -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:] diff --git a/doc/src/angle_style.txt b/doc/src/angle_style.txt index 68d69d488d..a0bc47ba4c 100644 --- a/doc/src/angle_style.txt +++ b/doc/src/angle_style.txt @@ -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 diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt index c9252a8eb3..197a4fb1b6 100644 --- a/doc/src/bond_style.txt +++ b/doc/src/bond_style.txt @@ -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 diff --git a/doc/src/dihedral_style.txt b/doc/src/dihedral_style.txt index 02634c6073..d45d9b488d 100644 --- a/doc/src/dihedral_style.txt +++ b/doc/src/dihedral_style.txt @@ -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 diff --git a/doc/src/improper_style.txt b/doc/src/improper_style.txt index 28b3b440b2..f315509fe4 100644 --- a/doc/src/improper_style.txt +++ b/doc/src/improper_style.txt @@ -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 diff --git a/doc/src/prd.txt b/doc/src/prd.txt index f71f285336..43c0d309c8 100644 --- a/doc/src/prd.txt +++ b/doc/src/prd.txt @@ -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:]