PLUMED-NEST

Project ID: plumID:23.043
Source: metad-example/plumed.dat
Originally used with PLUMED version: 2.10-mod
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

# This section computes the spherical expansion features for a 6x6x6 BaTiO3 structure (modify the number of atoms if the structure changes)
SPEX_A: 
SPHERICAL_EXPANSION
This action is not part of PLUMED and was included by using a LOAD command More details
 ...
  SPECIES1=1-216 SPECIES2=217-432 SPECIES3=433-1080
  HYPERPARAMS={
    "max_radial": 6,
    "max_angular": 1,
    "compute_gradients": false,
    "cutoff_function": {"type": "ShiftedCosine", "cutoff": {"value": 3.0, "unit": "AA"} smooth_width value 05 unit AA
    gaussian_density type Constant gaussian_sigma value 05 unit AA
    radial_contribution type GTO
  
...


# This instruction includes a mask contained in a separate .dat file that selects out the Ti atoms
INCLUDE
Includes an external input file, similar to #include in C preprocessor. More details. Show included file
 
FILE
file to be included
=Ti-MASK.dat
# The command:
# INCLUDE FILE=Ti-MASK.dat
# ensures PLUMED loads the contents of the file called Ti-MASK.dat
# The contents of this file are shown below (click the red comment to hide them).
The INCLUDE action with label Ti-MASK.dat calculates somethingMASK_A: 
CONSTANT_VALUE
This action is not part of PLUMED and was included by using a LOAD command More details
 VALUES=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0

# --- End of included input --- 
# This matrix-matrix multiplication averages the spherical expansion components over all Ti atoms
SPEX_A_T: 
TRANSPOSE
Calculate the transpose of a matrix More details
 
ARG
the input for this action is the scalar output from one or more other actions
=SPEX_A
The TRANSPOSE action with label SPEX_A_T calculates the following quantities:
 Quantity   
 Description  
SPEX_A_T.value
the transpose of the input matrixSUM_A: 
DOT
This action is not part of PLUMED and was included by using a LOAD command More details
 ARG1=SPEX_A_T ARG2=MASK_A
NUM_A: 
SUM
Calculate the sum of the arguments More details
 
ARG
the input to this function
=MASK_A 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO

# This gives a polarization vector that is roughly of order 1 modulus for a fully polar phase - we here divide by the number of Ti atoms and multiply by 10000 
The SUM action with label NUM_A calculates somethingSUMM_A: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG1
the input to this function
=SUM_A 
ARG2
the input to this function
=NUM_A 
FUNC
the function you wish to evaluate
=x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO   
The MATHEVAL action with label SUMM_A calculates somethingPy_A: 
SELECT_COMPONENTS
Create a new value to hold a subset of the components that are in a vector or matrix More details
 
ARG
the argument we are using to build the shortcut
=SUMM_A 
COMPONENTS
the components in the input value that you woul like to build a new vector from
=50
The SELECT_COMPONENTS action with label Py_A calculates somethingPz_A: 
SELECT_COMPONENTS
Create a new value to hold a subset of the components that are in a vector or matrix More details
 
ARG
the argument we are using to build the shortcut
=SUMM_A 
COMPONENTS
the components in the input value that you woul like to build a new vector from
=51
The SELECT_COMPONENTS action with label Pz_A calculates somethingPx_A: 
SELECT_COMPONENTS
Create a new value to hold a subset of the components that are in a vector or matrix More details
 
ARG
the argument we are using to build the shortcut
=SUMM_A 
COMPONENTS
the components in the input value that you woul like to build a new vector from
=52
The SELECT_COMPONENTS action with label Px_A calculates somethingPys_A: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG1
the input to this function
=Py_A 
FUNC
the function you wish to evaluate
=x*10000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The MATHEVAL action with label Pys_A calculates somethingPzs_A: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG1
the input to this function
=Pz_A 
FUNC
the function you wish to evaluate
=x*10000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO 
The MATHEVAL action with label Pzs_A calculates somethingPxs_A: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG1
the input to this function
=Px_A 
FUNC
the function you wish to evaluate
=x*10000 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO  

# The following section computes the polarization modulus and its orientation (theta and phi angles) with respect to the z-axis taken as reference
The MATHEVAL action with label Pxs_A calculates somethingPmod_A: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG1
the input to this function
=Pxs_A 
ARG2
the input to this function
=Pys_A 
ARG3
the input to this function
=Pzs_A 
FUNC
the function you wish to evaluate
=sqrt(x*x+y*y+z*z 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The MATHEVAL action with label Pmod_A calculates somethingPtheta_A: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG1
the input to this function
=Pzs_A 
ARG2
the input to this function
=Pmod_A 
FUNC
the function you wish to evaluate
=acos(x/y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=NO
The MATHEVAL action with label Ptheta_A calculates somethingPphi_A: 
MATHEVAL
An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details
 
ARG1
the input to this function
=Px_A 
ARG2
the input to this function
=Py_A 
FUNC
the function you wish to evaluate
=atan2(x,y 
PERIODIC
if the output of your function is periodic then you should specify the periodicity of the function
=-PI,PI

# This instruction prints the polarization data to a file PVARS
The MATHEVAL action with label Pphi_A calculates something
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=Pxs_A,Pys_A,Pzs_A,Pmod_A,Ptheta_A,Pphi_A 
STRIDE
 the frequency with which the quantities of interest should be output
=1 
FILE
the name of the file on which to output these quantities
=PVARS

# Metadynamics settings
The PRINT action with label  calculates somethingmtd:   
METAD
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=Pmod_A 
PACE
the frequency for hill addition
=5 
SIGMA
the widths of the Gaussian hills
=0.15 
HEIGHT
the heights of the Gaussian hills
=0.5 
FILE
 a file in which the list of added hills is stored
=HILLS 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=20 
TEMP
the system temperature - this is only needed if you are doing well-tempered metadynamics
=200

The METAD action with label mtd calculates the following quantities:
 Quantity   
 Description  
mtd.bias
the instantaneous value of the bias potential
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=Pmod_A,Pxs_A,Pys_A,Pzs_A,mtd 
STRIDE
 the frequency with which the quantities of interest should be output
=1 
FILE
the name of the file on which to output these quantities
=COLVAR

FLUSH
This command instructs plumed to flush all the open files with a user specified frequency. More details
 
STRIDE
the frequency with which all the open files should be flushed
=1