Navigation: Documentation / Methods / String Method / STM:Server / STM:Server Controls
The STM path setup controls the global string path handled by the STM server. The setup defines input and output files, STM iteration periods, path update intervals, termination criteria, and optimisation-method-specific parameters.
{MAIN}
[files]
| Key
|
Default value
|
Type
|
Description
|
| input
|
"{PATHS}"
|
string
|
Name of the input path file. The file defines the initial STM path.
|
| output
|
"_stm.path"
|
string
|
Name of the output path file. The current or final STM path is written to this file.
|
| trajectory
|
"_stm.traj"
|
string
|
Name of the path trajectory file. It stores the time evolution of the STM path if trajectory output is enabled.
|
| summary
|
"_stm.results"
|
string
|
Name of the output summary file containing final STM results.
|
| optlog
|
"_stm.log"
|
string
|
Name of the optimisation log file.
|
[stm]
| Key
|
Default value
|
Type
|
Description
|
| steps
|
100
|
integer
|
Maximum number of STM optimisation steps.
|
| optmethod
|
adabelif
|
string
|
Optimisation method used to update the STM path.
Allowed values are: gd, ngd, ngd-auto, adam, adabelif, amsgrad, amsgradbc.
The value determines which optimiser-specific section is used.
|
| shift2zero
|
true
|
logical
|
If enabled, the global minimum of the free energy along the path is shifted to zero.
|
| init
|
10000
|
integer
|
Length of the initialisation period, expressed in MD steps.
|
| soloinit
|
true
|
logical
|
If enabled, the initialisation period is performed as a separate stage before the regular STM cycle.
|
| accu
|
5000
|
integer
|
Length of the accumulation period, expressed in MD steps.
|
| equi
|
1000
|
integer
|
Length of the equilibration period, expressed in MD steps.
|
| soloequi
|
true
|
logical
|
If enabled, the equilibration period is performed as a separate stage before accumulation.
|
| prod
|
50000
|
integer
|
Length of the final production period, expressed in MD steps.
|
| sfac
|
0.0
|
real
|
Path smoothing factor.
|
| async
|
false
|
logical
|
Enables asynchronous STM updates. If disabled, the path is updated synchronously.
|
[termination]
| Key
|
Default value
|
Type
|
Description
|
| fplch
|
0.001
|
real
|
Termination threshold for the final relative change of the path length.
|
| maxbmove
|
0.005
|
real
|
Termination threshold for the maximum bead displacement.
|
| avebmove
|
0.005
|
real
|
Termination threshold for the average bead displacement.
|
| maxppmf
|
10.00
|
real
|
Termination threshold for the maximum perpendicular mean force.
|
| aveppmf
|
2.00
|
real
|
Termination threshold for the average perpendicular mean force.
|
| tbuflen
|
3
|
integer
|
Length of the moving-average buffer used to evaluate termination criteria.
|
[intervals]
| Key
|
Default value
|
Type
|
Description
|
| reparam
|
1
|
integer
|
Interval, in STM steps, for path reparametrisation.
|
| smooth
|
0
|
integer
|
Interval, in STM steps, for path smoothing. A value of zero disables periodic smoothing.
|
| trajectory
|
0
|
integer
|
Interval, in STM steps, for writing the path trajectory. A value of zero disables trajectory output.
|
| output
|
100
|
integer
|
Interval, in STM steps, for writing the updated path to the output file.
|
Optimiser Setup
[gd]
| Key
|
Default value
|
Type
|
Description
|
| stepsize
|
0.003
|
real
|
Step size used by the gradient descent optimiser.
|
[ngd]
| Key
|
Default value
|
Type
|
Description
|
| stepsize
|
0.003
|
real
|
Step size used by the normalised gradient descent optimiser.
|
| mingnormeps
|
1e-7
|
real
|
Minimum gradient-norm threshold used to regularise the normalised gradient.
|
| maxgnormforgd
|
5.0
|
real
|
Maximum gradient norm for switching to ordinary gradient descent. This key is used only by the ngd-auto optimisation method.
|
[adam]
| Key
|
Default value
|
Type
|
Description
|
| stepsize
|
0.003
|
real
|
Step size used by the Adam optimiser.
|
| beta1
|
0.7
|
real
|
Exponential decay factor for the first-moment estimate.
|
| beta2
|
0.99
|
real
|
Exponential decay factor for the second-moment estimate.
|
| mingnormeps
|
1e-7
|
real
|
Minimum gradient-norm threshold used to regularise the optimisation step.
|
| maxresets
|
0
|
integer
|
Maximum number of optimiser resets. A value of zero disables this limit.
|
| memsteps
|
0
|
integer
|
Number of steps after which the optimiser memory is reset. A value of zero disables periodic memory resets.
|
[adabelif]
| Key
|
Default value
|
Type
|
Description
|
| stepsize
|
0.003
|
real
|
Step size used by the AdaBelief optimiser.
|
| beta1
|
0.7
|
real
|
Exponential decay factor for the first-moment estimate.
|
| beta2
|
0.99
|
real
|
Exponential decay factor for the second-moment estimate.
|
| mingnormeps
|
1e-7
|
real
|
Minimum gradient-norm threshold used to regularise the optimisation step.
|
| maxresets
|
0
|
integer
|
Maximum number of optimiser resets. A value of zero disables this limit.
|
| memsteps
|
0
|
integer
|
Number of steps after which the optimiser memory is reset. A value of zero disables periodic memory resets.
|
[amsgrad]
| Key
|
Default value
|
Type
|
Description
|
| stepsize
|
0.003
|
real
|
Step size used by the AMSGrad optimiser.
|
| beta1
|
0.7
|
real
|
Exponential decay factor for the first-moment estimate.
|
| beta2
|
0.99
|
real
|
Exponential decay factor for the second-moment estimate.
|
| mingnormeps
|
1e-7
|
real
|
Minimum gradient-norm threshold used to regularise the optimisation step.
|
| maxresets
|
0
|
integer
|
Maximum number of optimiser resets. A value of zero disables this limit.
|
| memsteps
|
0
|
integer
|
Number of steps after which the optimiser memory is reset. A value of zero disables periodic memory resets.
|
[amsgradbc]
| Key
|
Default value
|
Type
|
Description
|
| stepsize
|
0.003
|
real
|
Step size used by the bias-corrected AMSGrad optimiser.
|
| beta1
|
0.7
|
real
|
Exponential decay factor for the first-moment estimate.
|
| beta2
|
0.99
|
real
|
Exponential decay factor for the second-moment estimate.
|
| mingnormeps
|
1e-7
|
real
|
Minimum gradient-norm threshold used to regularise the optimisation step.
|
| maxresets
|
0
|
integer
|
Maximum number of optimiser resets. A value of zero disables this limit.
|
| memsteps
|
0
|
integer
|
Number of steps after which the optimiser memory is reset. A value of zero disables periodic memory resets.
|
{LAUNCHER}
The presence of the {LAUNCHER} group enables the job launcher. If the group is missing, no jobs are submitted or monitored by the launcher.
[setup]
| Key
|
Default value
|
Type
|
Description
|
| jobs
|
"jobs.in"
|
string
|
Name of the job specification file. If the value is enclosed in curly braces, for example "{JOBS}", the job specification is read from the corresponding control-file group instead of an external file.
|
| log
|
"launcher.log"
|
string
|
Name of the launcher log file.
|
| resubmit
|
false
|
logical
|
Enables resubmission of dead bead jobs.
|
| keytime
|
0
|
integer
|
Sleep time, in milliseconds, after distributing the server key. The value must be non-negative.
|
| submittime
|
0
|
integer
|
Sleep time, in milliseconds, after submitting a job. The value must be non-negative.
|
| statustime
|
0
|
integer
|
Sleep time, in milliseconds, after checking the status of a job. The value must be non-negative.
|
| rechecktime
|
10000
|
integer
|
Sleep time, in milliseconds, before repeating the job-status check. The value must be non-negative.
|
[wrappers]
| Key
|
Default value
|
Type
|
Description
|
| distribute-key
|
"distribute-key"
|
string
|
Name or path of the wrapper used to distribute the STM server key to bead jobs.
|
| submit-job
|
"submit-job"
|
string
|
Name or path of the wrapper used to submit bead jobs.
|
| job-status
|
"job-status"
|
string
|
Name or path of the wrapper used to check the status of submitted jobs.
|