This section introduces the description about the setting for the CURP. The character : after each of the keyword and the value means value types allowed. For example:
| Int: | integer value. |
|---|---|
| Float: | floating value. |
| Bool: | boolean value. yes or no. |
| File: | specify file path. |
| List[type]: | list of the value for the type given in [ and ]. |
| Choice[A|B|C]: | A, B or C must be chosen. |
vdw_cutoff_method = atom (default) : Choice[atom]
The method to cut off the van der Waals interaction.
coulomb_method = cutoff (default) : Choice[cutoff]
The method to calculate coulomb interaction.
remove_rotate = yes (default) : Bool
Remove the coordinate and velocity of rotation for the target atoms
enable_inverse_pair = no (default) : Bool
Calculate and write out inverse pairs j <- i for flux adding normal group pairs: i <- j. This option is used in the case for calculating energy flux.
decomp_group_current = no (default) : Bool
Flag whether decompose the group current into inside and outside contributions of group region.This option is used for calculating momentum current
coulomb_cutoff_method = atom (default) : Choice[atom]
The method to cut off the coulomb interaction.
group_pair_file = none (default) : File
Path to file to define group pair. If you didn’t given, all of pairs within the targets will be calculated.
target_atoms = 1- (default) : List[String]
The atom list calculated.
group_method = none (default) : Choice[united|residue|file|none]
The method to construct the group.”united” means that hydrogen atoms are included in hevy atoms covalent to them.”residue” means that the groups are calculated by residue level. If “file” is specified, the groups definition is givenby the group file in input section.
vdw_cutoff_length = 99.9 (default) : Float
The cutoff length for the van der Waals interaction.
remove_trans = yes (default) : Bool
Remove the coordinate and velocity of translation for the target atoms
log_frequency = 10 (default) : Int
Log informations will be written out every given steps.
flux_grain = group (default) : Choice[atom|group|both]
The grain to calculate the flux.”atom”, “group” and “both” values mean that the flux for atom parirs, group pairs and both of them will be calculated, respectively.
method = momentum-current (default) : Choice[energy-flux|momentum-current|microcanonical]
The method of calculation.”momentum-current” calculates the stress tensor for systems. “energy-flux” calculates the energy flow for systems. “dynamics is mainly used to verify the validity of the CURP program numerically, so its implementation is very simple
coulomb_cutoff_length = 99.9 (default) : Float
The cutoff length for the coulomb interaction.
trj_format = ascii (default) : Choice[ascii|netcdf]
The format of coordinates and velocities trajectory file.
vels_frequency = 1 (default) : Int
The interval step to write velocity trajectory.
vels_file = none (default) : File
The file path to write out the velocities trajectory. If empty, then don’t write.
integrator = vverlet (default) : Choice[vverlet|leapfrog]
The integrator to want to use with the dynamics.
num_steps = 1 (default) : Int
The number of integration steps.
crds_frequency = 1 (default) : Int
The interval step to write coordinate trajectory.
crds_file = none (default) : File
The file path to write out the coordinates trajectory. If empty, then don’t write.
dt = 0.001 (default) : Float
Time step to advance snapshots to next step, in ps unit.
group_file = group.cfg (default) : File
The group file path to define group.if curp.group_mothod == file then this definition is used.
num_chunks = 10 (default) : Int
The number of snapshots caching in reading trajectory.
first_last_interval = 0 -1 1 (default) : List[Int]
The first, last and interval step to read coordinates and velocities trajectory.
use_simtime = yes (default) : Bool
use the simulation time information in trajectory.
format = amber (default) : Choice[presto|amber|gromacs]
The format of the various files generated by other grograms.
restart_file = none (default) : File
Restart file path.
velocity_file = none (default) : File
Velocity trajectory file path.
target = trajectory (default) : Choice[trajectory|restart]
The target input file to be used.
coordinate_file = none (default) : File
Coordinate trajectory file path.
restart_format = restart (default) : Choice[restart]
The format of restart file.
dump_parameters = no (default) : Bool
Dump the parsed Amber force field parameter set.
velocity_format = ascii (default) : Choice[ascii|netcdf]
The format of velocity file.
topology_file = none (default) : File
Topology file path.
coordinate_format = ascii (default) : Choice[ascii|netcdf]
The format of coordinate file.
restart_file = none (default) : File
Restart file path.
velocity_file = none (default) : File
Velocity trajectory file path.
target = trajectory (default) : Choice[trajectory|restart]
The target input file to be used.
coordinate_file = none (default) : File
Coordinate trajectory file path.
restart_format = restart (default) : Choice[restart]
The format of restart file.
dump_parameters = no (default) : Bool
Dump the parsed Gromacs force field parameter set.
velocity_format = gro (default) : Choice[gro]
The format of velocity file.
topology_file = none (default) : File
Topology file path.
coordinate_format = gro (default) : Choice[gro]
The format of coordinate file.
energy_decomp = no (default) : Bool
Flag whether decompose the total energy to bonded, coulomb, and van der Waals interaction.
energy_freqency = 0 (default) : Int
The frequency to write the energy information.
format = ascii (default) : Choice[ascii|netcdf]
The format of flux data.
compress = no (default) : Bool
Flag whether compress with gnu zip, then the extension of the file name became ”.gz”.
filename = current.dat (default) : File
The file name to output the current or flux information.
frequency = 0 (default) : Int
The frequency to create new file to write the additional file.
energy_compress = yes (default) : Bool
Flag whether compress with gnu zip for energy_file, then the extension of the file name became ”.gz”.
energy_file = energy.dat (default) : File
The file path to output the energy information.
output_energy = no (default) : Bool
Flag whether output the energy information or not.
decomp = no (default) : Bool
Flag whether decompose the total current or flux to bonded, coulomb, and van der Waals interaction.
voronoi_solvation = none (default) : Choice[none|RANDOM20]
The kind of solvation system to sink the target system in vacuum for the voronoi method. The density value of the water under NPT ensemble is 0.99651 [g/cm^3] at 27 [Kelvin]
output_gvolume_file = none (default) : File
The file path to write out the group volumes trajectory. If this value is not given, writing out is not performed.The file written by this option can be used in the optionsgroup_trajectory_file.
atomic_trajectory_file = none (default) : File
Atomic volumes trajectory file path for outer method.
group_trajectory_file = none (default) : File
Group volumes trajectory file path for outer method.
voronoi_no_hydrogen = no (default) : Bool
Flag to determine whether include hydrogen atomsfor the voronoi calculation.
voronoi_output_solvation_file = none (default) : File
The file path to write out the solvation pdb data in the case of voronoi_solvation == “none”.If the file path is not given, writing out is not performed.
voronoi_cutoff = 6.0 (default) : Float
The cutoff length that the voronoi calculation finds outneighbour candidate particles.
output_volume_file = none (default) : File
The file path to write out the atomic volumes trajectory. If this value is not given, writing out is not performed.The file written by this option can be used in the options,atomic_trajectory_file.
voronoi_probe_length = 2.4 (default) : Float
The probe length of the solvation for the voronoi method.The water molecules within the probe length from the system are removed.
method = none (default) : Choice[none|vdw|voronoi|outer]
Algorithm to calculate the atomic volumes.
Please visit NetCDF website to use NetCDF format file for more information.
Please visit NetCDF website to use NetCDF format file for more information.
Note
Note that there isn’t ncomponent variable in time-correlation data unlike energy flux data file
For example, you can separate the main chain and the side chain parts by using the following specification:
[01_ALA_M]
1-6 11-12
[01_ALA_S]
7-10
[02_ALA_M]
13-16 21-22
[02_ALA_S]
17-20
[03_ALA_M]
23-26 31-33
[03_ALA_S]
27-30
The group names are surrounded by [ and ]. Then the range of the constituent atoms are provided. You can spacify the range by using - symbol. You can provide multiple data saparated by space, empty line, or tab.
usage: simplify_tensor.py [-h] -i DATA_FILENAME [-l LABEL_LINE] [-s]
[fns [fns ...]]
Show and make figure for stress ratio.
positional arguments:
fns specify additive filenames. ex.) label_data1,
label_data2, ...
optional arguments:
-h, --help show this help message and exit
-i DATA_FILENAME, --input-data DATA_FILENAME
specify input filename for the stress data.
-l LABEL_LINE, --label-line LABEL_LINE
specify additive label string. ex.)
"label1,label2,..."
-s, --every-snapshot specify flog to average the magnitude for every
snapshot.
usage: get_ncdata.py [-h] -r [FRIST:LAST [FRIST:LAST ...]] [-n DATANAME]
[-o PREFIX]
ACF_FILE
Get simple text data from file in netcdf format by given arguments.
positional arguments:
ACF_FILE The filepath of auto-correlation function data.
optional arguments:
-h, --help show this help message and exit
-r [FRIST:LAST [FRIST:LAST ...]], --group-ranges [FRIST:LAST [FRIST:LAST ...]]
The pair range list to want to gain.
-n DATANAME, --dataname DATANAME
The name of the netcdf data you want to gain.
-o PREFIX, --output-prefix PREFIX
The prefix of the files to want to write, that
includes directory path.
The commands in the $CURP_HOME/bin directory are performed in the CURP environment. But, the scripts in the $CURP_HOME/script directory are performed in the system environment. This script realizes that you use the script in the CURP enviromnet, which is not in the bin directory. For example, please use as follows:
$ $CURP_HOME/bin/ana-curp simplify_tensor.py arg1 arg2 ...
Takahisa YAMATO, Dr. Sci.
Graduate School of Science, Nagoya University,
Furo-cho, Chikusa-ku, Nagoya, 4648602, Japan.
Email: yamato@nagoya-u.jp