PLUMED-NEST-TEST-SITE

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_EXPANSIONThis 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
INCLUDEIncludes an external input file, similar to #include in C preprocessor. More details FILEfile to be included=Ti-MASK.dat

# This matrix-matrix multiplication averages the spherical expansion components over all Ti atoms
The INCLUDE action with label  calculates somethingSPEX_A_T: TRANSPOSECalculate the transpose of a matrix More details ARGthe label of the vector or matrix that should be transposed=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: DOTThis 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: SUMCalculate the sum of the arguments More details ARGthe values input to this function=MASK_A PERIODICif 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 the following quantities:
 Quantity   
 Description  
NUM_A.value
the sumSUMM_A: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARG1=SUM_A ARG2=NUM_A FUNCthe function you wish to evaluate=x/y PERIODICif 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 the following quantities:
 Quantity   
 Description  
SUMM_A.value
an arbitrary functionPy_A: SELECT_COMPONENTSCreate a new value to hold a subset of the components that are in a vector or matrix More details ARGthe value from which we are selecting components=SUMM_A COMPONENTSthe 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 the following quantities:
 Quantity   
 Description  
Py_A.value
a vector containing the selected componentsPz_A: SELECT_COMPONENTSCreate a new value to hold a subset of the components that are in a vector or matrix More details ARGthe value from which we are selecting components=SUMM_A COMPONENTSthe 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 the following quantities:
 Quantity   
 Description  
Pz_A.value
a vector containing the selected componentsPx_A: SELECT_COMPONENTSCreate a new value to hold a subset of the components that are in a vector or matrix More details ARGthe value from which we are selecting components=SUMM_A COMPONENTSthe 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 the following quantities:
 Quantity   
 Description  
Px_A.value
a vector containing the selected componentsPys_A: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARG1=Py_A FUNCthe function you wish to evaluate=x*10000 PERIODICif 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 the following quantities:
 Quantity   
 Description  
Pys_A.value
an arbitrary functionPzs_A: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARG1=Pz_A FUNCthe function you wish to evaluate=x*10000 PERIODICif 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 the following quantities:
 Quantity   
 Description  
Pzs_A.value
an arbitrary functionPxs_A: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARG1=Px_A FUNCthe function you wish to evaluate=x*10000 PERIODICif 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 the following quantities:
 Quantity   
 Description  
Pxs_A.value
an arbitrary functionPmod_A: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARG1=Pxs_A ARG2=Pys_A ARG3=Pzs_A FUNCthe function you wish to evaluate=sqrt(x*x+y*y+z*z) PERIODICif 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 the following quantities:
 Quantity   
 Description  
Pmod_A.value
an arbitrary functionPtheta_A: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARG1=Pzs_A ARG2=Pmod_A FUNCthe function you wish to evaluate=acos(x/y) PERIODICif 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 the following quantities:
 Quantity   
 Description  
Ptheta_A.value
an arbitrary functionPphi_A: MATHEVALAn alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression. More details ARG1=Px_A ARG2=Py_A FUNCthe function you wish to evaluate=atan2(x,y) PERIODICif 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 the following quantities:
 Quantity   
 Description  
Pphi_A.value
an arbitrary functionPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=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 FILEthe name of the file on which to output these quantities=PVARS

# Metadynamics settings
mtd:   METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=Pmod_A PACEthe frequency for hill addition=5 SIGMAthe widths of the Gaussian hills=0.15 HEIGHTthe heights of the Gaussian hills=0.5 FILE a file in which the list of added hills is stored=HILLS BIASFACTORuse well tempered metadynamics and use this bias factor=20 TEMPthe 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 potentialPRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=Pmod_A,Pxs_A,Pys_A,Pzs_A,mtd.* STRIDE the frequency with which the quantities of interest should be output=1 FILEthe name of the file on which to output these quantities=COLVAR

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