diff --git a/doc/min_style.html b/doc/min_style.html index 2e6fdc5da0..59735c8377 100644 --- a/doc/min_style.html +++ b/doc/min_style.html @@ -55,15 +55,18 @@ some situations.

Style quickmin is a damped dynamics method described in (Sheppard), where the damping parameter is related to the projection of the velocity vector along the current force vector for -each atom. +each atom. The velocity of each atom is initialized to 0.0 by this +style, at the beginning of a minimization.

Style fire is a damped dynamics method described in (Bitzek), which is similar to quickmin but adds a variable timestep and alters the projection operation to maintain components of -the velocity non-parallel to the current force vector. +the velocity non-parallel to the current force vector. The velocity +of each atom is initialized to 0.0 by this style, at the beginning of +a minimization.

Either the quickmin and fire styles are useful in the context of -nudged elastic band (NEB calculations via the neb command. +nudged elastic band (NEB) calculations via the neb command.

IMPORTANT NOTE: The quickmin and fire styles do not yet support the use of the fix box/relax command or @@ -90,7 +93,7 @@ Jonsson, Mills, Jacobsen.

-

Bitzek Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett, +

(Bitzek) Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett, 97, 170201 (2006).

diff --git a/doc/min_style.txt b/doc/min_style.txt index dcfee4270d..7463024bdd 100755 --- a/doc/min_style.txt +++ b/doc/min_style.txt @@ -51,15 +51,18 @@ some situations. Style {quickmin} is a damped dynamics method described in "(Sheppard)"_#Sheppard, where the damping parameter is related to the projection of the velocity vector along the current force vector for -each atom. +each atom. The velocity of each atom is initialized to 0.0 by this +style, at the beginning of a minimization. Style {fire} is a damped dynamics method described in "(Bitzek)"_#Bitzek, which is similar to {quickmin} but adds a variable timestep and alters the projection operation to maintain components of -the velocity non-parallel to the current force vector. +the velocity non-parallel to the current force vector. The velocity +of each atom is initialized to 0.0 by this style, at the beginning of +a minimization. Either the {quickmin} and {fire} styles are useful in the context of -nudged elastic band (NEB} calculations via the "neb"_neb.html command. +nudged elastic band (NEB) calculations via the "neb"_neb.html command. IMPORTANT NOTE: The {quickmin} and {fire} styles do not yet support the use of the "fix box/relax"_fix_box_relax.html command or @@ -84,6 +87,6 @@ min_style cg :pre Jonsson, Mills, Jacobsen. :link(Bitzek) -[{Bitzek}] Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett, +[(Bitzek)] Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett, 97, 170201 (2006). diff --git a/doc/minimize.html b/doc/minimize.html index 8b225887b6..0921d1bf86 100644 --- a/doc/minimize.html +++ b/doc/minimize.html @@ -66,6 +66,12 @@ damped dynamics using an Euler integration step. Thus they require a timestep be defined, typically the same value used for running dynamics with the system.

+

IMPORTANT NOTE: Etol should be set to 0.0 when using the quickmin +or fire minimization styles. This is because they +periodically reset velocities to 0.0 and take a zero-length step which +will appear as a 0.0 energy change, stopping the minimizer if etol +is finite. +

The objective function being minimized is the total potential energy of the system as a function of the N atom coordinates:

diff --git a/doc/minimize.txt b/doc/minimize.txt index 59809e3467..9b203f1820 100644 --- a/doc/minimize.txt +++ b/doc/minimize.txt @@ -63,6 +63,12 @@ damped dynamics using an Euler integration step. Thus they require a "timestep"_timestep.html be defined, typically the same value used for "running dynamics"_run.html with the system. +IMPORTANT NOTE: {Etol} should be set to 0.0 when using the {quickmin} +or {fire} "minimization styles"_min_style.html. This is because they +periodically reset velocities to 0.0 and take a zero-length step which +will appear as a 0.0 energy change, stopping the minimizer if {etol} +is finite. + The objective function being minimized is the total potential energy of the system as a function of the N atom coordinates: diff --git a/doc/neb.html b/doc/neb.html index bd7a14928b..fb4f91127f 100644 --- a/doc/neb.html +++ b/doc/neb.html @@ -30,8 +30,8 @@ neb 1.0e-6 0.001 1000 500 50 coords.final

Description:

Perform a nudged elastic band (NEB) calculation using multiple -replicas of a system. Three or more replicas must be used, two of -which are the end points of the transition path. +replicas of a system. Two or more replicas must be used, two of which +are the end points of the transition path.

NEB is a method for finding both the atomic configurations and height of the energy barrier associated with a transition state, e.g. for an @@ -72,14 +72,13 @@ procedure, but they will not be part of the barrier finding procedure.

The "starting configuration" for NEB should be a state with the NEB atoms (and all other atoms) having coordinates on one side of the energy barrier. These coordinates will be assigned to the first -replica #1. The coordinates should be close to a local energy minimum -and the velocities should be zeroed. A perfect energy minimum is not -required (nor are zero velocities), since NEB runs via damped dynamics -which will tend to drive the configuration of replica #1 to a true -energy minimum, but you will typically get better convergence if the -initial state is already at a minimum. For example, for a system with -a free surface, the surface should be fully relaxed before attempting -a NEB calculation. +replica #1. The coordinates should be close to a local energy +minimum. A perfect energy minimum is not required, since NEB runs via +damped dynamics which will tend to drive the configuration of replica +#1 to a true energy minimum, but you will typically get better +convergence if the initial state is already at a minimum. For +example, for a system with a free surface, the surface should be fully +relaxed before attempting a NEB calculation.

The final configuration is specified in the input filename, which is formatted as described below. Only coordinates for NEB atoms or a @@ -167,11 +166,6 @@ some cases, but if those atoms move too far (e.g. because the initial state of your system was not well-minimized), it can cause problems for the NEB procedure.

-

Similarly, you should initialize the velocity of all NEB atoms (and -non-NEB atoms if they are free to move) in your system to 0.0 before -invoking the neb command. This gives the minimizer a consistent zero -velocity to start its damped dynamics with. -

The damped dynamics minimizers, such as quickmin and fire), adjust the position and velocity of the atoms via an Euler integration step. Thus you must define an appropriate diff --git a/doc/neb.txt b/doc/neb.txt index f5d679a14a..b815e19d70 100644 --- a/doc/neb.txt +++ b/doc/neb.txt @@ -27,8 +27,8 @@ neb 1.0e-6 0.001 1000 500 50 coords.final :pre [Description:] Perform a nudged elastic band (NEB) calculation using multiple -replicas of a system. Three or more replicas must be used, two of -which are the end points of the transition path. +replicas of a system. Two or more replicas must be used, two of which +are the end points of the transition path. NEB is a method for finding both the atomic configurations and height of the energy barrier associated with a transition state, e.g. for an @@ -69,14 +69,13 @@ procedure, but they will not be part of the barrier finding procedure. The "starting configuration" for NEB should be a state with the NEB atoms (and all other atoms) having coordinates on one side of the energy barrier. These coordinates will be assigned to the first -replica #1. The coordinates should be close to a local energy minimum -and the velocities should be zeroed. A perfect energy minimum is not -required (nor are zero velocities), since NEB runs via damped dynamics -which will tend to drive the configuration of replica #1 to a true -energy minimum, but you will typically get better convergence if the -initial state is already at a minimum. For example, for a system with -a free surface, the surface should be fully relaxed before attempting -a NEB calculation. +replica #1. The coordinates should be close to a local energy +minimum. A perfect energy minimum is not required, since NEB runs via +damped dynamics which will tend to drive the configuration of replica +#1 to a true energy minimum, but you will typically get better +convergence if the initial state is already at a minimum. For +example, for a system with a free surface, the surface should be fully +relaxed before attempting a NEB calculation. The final configuration is specified in the input {filename}, which is formatted as described below. Only coordinates for NEB atoms or a @@ -164,11 +163,6 @@ some cases, but if those atoms move too far (e.g. because the initial state of your system was not well-minimized), it can cause problems for the NEB procedure. -Similarly, you should initialize the velocity of all NEB atoms (and -non-NEB atoms if they are free to move) in your system to 0.0 before -invoking the neb command. This gives the minimizer a consistent zero -velocity to start its damped dynamics with. - The damped dynamics "minimizers"_min_style.html, such as {quickmin} and {fire}), adjust the position and velocity of the atoms via an Euler integration step. Thus you must define an appropriate