Action: REFERENCE_GRID

Module	gridtools
Description	Usage
Setup a constant grid by either reading values from a file or definining a function in input
output value	type
the constant function on the grid that was specified in input	grid

Details and examples

Setup a constant grid by either reading values from a file or definining a function in input

This action allows you to create a constant function and store the values that this function takes at a grid of points. There are two ways that you can create the constant function. You can either read in the value of the function at a set of grid points from a file as is done in this example input:

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

#SETTINGS INPUTFILES=regtest/gridtools/rt-test-fib-read/kde.grid
ffgThe REFERENCE_GRID action with label ffg calculates the following quantities:
 Quantity   
 Type   
 Description  
ffg
grid
the constant function on the grid that was specified in input: REFERENCE_GRIDSetup a constant grid by either reading values from a file or definining a function in input More details FILEthe name of the file that contains the reference data=
regtest/gridtools/rt-test-fib-read/kde.grid
 Click here to see an extract from this file.
  
  ×  
FILE: regtest/gridtools/rt-test-fib-read/kde.grid
    
#! FIELDS d1n.x d1n.y d1n.z h dh_d1n.x dh_d1n.y dh_d1n.z
#! SET nbins  100
   0.1411  -0.9900   0.0000   0.0037   0.0052  -0.0364   0.0000
  -0.1793  -0.9700  -0.1642   0.0002  -0.0003  -0.0016  -0.0003
   0.0273  -0.9500   0.3111   0.0147   0.0040  -0.1401   0.0459
   0.2236  -0.9300  -0.2917   0.0007   0.0015  -0.0062  -0.0019
  -0.4083  -0.9100   0.0722   0.0002  -0.0007  -0.0016   0.0001
   0.3847  -0.8900   0.2447   0.0598   0.2301  -0.5322   0.1463
  -0.1280  -0.8700  -0.4761   0.0000  -0.0000  -0.0003  -0.0002
  -0.2428  -0.8500   0.4675   0.0063  -0.0152  -0.0532   0.0293
   0.5239  -0.8300  -0.1913   0.0049   0.0259  -0.0410  -0.0094
  -0.5421  -0.8100  -0.2238   0.0000  -0.0000  -0.0001  -0.0000
   0.2599  -0.7900   0.5553   0.1789   0.4648  -1.4132   0.9933
   0.1910  -0.7700  -0.6088   0.0001   0.0002  -0.0007  -0.0006
  -0.5723  -0.7500   0.3316   0.0002  -0.0013  -0.0018   0.0008
   0.6675  -0.7300   0.1467   0.0851   0.5683  -0.6215   0.1249
  -0.4050  -0.7100  -0.5761   0.0000  -0.0001  -0.0001  -0.0001
  -0.0930  -0.6900   0.7178   0.0487  -0.0453  -0.3362   0.3498
   0.5676  -0.6700  -0.4784   0.0006   0.0033  -0.0039  -0.0028
  -0.7593  -0.6500  -0.0314   0.0000  -0.0000  -0.0000  -0.0000
   0.5505  -0.6300   0.5478   0.5079   2.7961  -3.2001   2.7825
  -0.0366  -0.6100  -0.7916   0.0001  -0.0000  -0.0004  -0.0005
  -0.5173  -0.5900   0.6199   0.0014  -0.0071  -0.0080   0.0085
   0.8143  -0.5700  -0.1096   0.0177   0.1439  -0.1008  -0.0194
  -0.6856  -0.5500  -0.4770   0.0001  -0.0004  -0.0003  -0.0003
   0.1861  -0.5300   0.8273   0.2978   0.5542  -1.5782   2.4635
   0.4277  -0.5100  -0.7463   0.0001   0.0004  -0.0005  -0.0008
  -0.8305  -0.4900   0.2649   0.0000  -0.0001  -0.0001   0.0000
   0.8013  -0.4700   0.3702   0.3397   2.7222  -1.5968   1.2577
  -0.3448  -0.4500  -0.8238   0.0005  -0.0016  -0.0021  -0.0038
  -0.3056  -0.4300   0.8495   0.0132  -0.0403  -0.0568   0.1121
   0.8074  -0.4100  -0.4243   0.0010   0.0084  -0.0042  -0.0044
  -0.8904  -0.3900  -0.2347   0.0001  -0.0006  -0.0003  -0.0002
   0.5025  -0.3700   0.7814   0.7484   3.7603  -2.7690   5.8482
   0.1587  -0.3500  -0.9232   0.0006   0.0009  -0.0020  -0.0053
  -0.7463  -0.3300   0.5780   0.0001  -0.0007  -0.0003   0.0006
   0.9475  -0.3100   0.0785   0.0545   0.5161  -0.1689   0.0428
  -0.6499  -0.2900  -0.7025   0.0015  -0.0096  -0.0043  -0.0104
   0.0047  -0.2700   0.9628   0.0995   0.0047  -0.2687   0.9580
   0.6506  -0.2500  -0.7171   0.0002   0.0010  -0.0004  -0.0011
  -0.9690  -0.2300   0.0898   0.0000  -0.0003  -0.0001   0.0000
   0.7788  -0.2100   0.5911   0.5311   4.1361  -1.1153   3.1392
  -0.1757  -0.1900  -0.9659   0.0053  -0.0093  -0.0101  -0.0513
  -0.5249  -0.1700   0.8340   0.0012  -0.0063  -0.0020   0.0100
   0.9535  -0.1500  -0.2613   0.0027   0.0261  -0.0041  -0.0071
  -0.8821  -0.1300  -0.4527   0.0018  -0.0157  -0.0023  -0.0080
   0.3455  -0.1100   0.9319   0.3213   1.1102  -0.3535   2.9946
   0.3755  -0.0900  -0.9224   0.0024   0.0089  -0.0021  -0.0219
  -0.9014  -0.0700   0.4272   0.0000  -0.0002  -0.0000   0.0001
   0.9544  -0.0500   0.2943   0.0976   0.9316  -0.0488   0.2872
  -0.5054  -0.0300  -0.8624   0.0199  -0.1005  -0.0060  -0.1715
  -0.2099  -0.0100   0.9777   0.0116  -0.0243  -0.0012   0.1131
   0.8152   0.0100  -0.5791   0.0003   0.0023   0.0000  -0.0017
  -0.9919   0.0300  -0.1236   0.0010  -0.0097   0.0003  -0.0012
   0.6474   0.0500   0.7605   0.3033   1.9631   0.1516   2.3064
   0.0364   0.0700  -0.9969   0.0275   0.0100   0.0192  -0.2736
  -0.6991   0.0900   0.7094   0.0001  -0.0005   0.0001   0.0005
   0.9926   0.1100  -0.0508   0.0057   0.0564   0.0063  -0.0029
  -0.7644   0.1300  -0.6316   0.0287  -0.2191   0.0373  -0.1810
   0.1366   0.1500   0.9792   0.0487   0.0665   0.0731   0.4769
   0.5589   0.1700  -0.8116   0.0054   0.0304   0.0092  -0.0441
  -0.9568   0.1900   0.2202   0.0004  -0.0034   0.0007   0.0008
   0.8507   0.2100   0.4820   0.0747   0.6353   0.1568   0.3599
  -0.3003   0.2300  -0.9257   0.1279  -0.3840   0.2941  -1.1837
  -0.4018   0.2500   0.8809   0.0007  -0.0028   0.0017   0.0061
   0.8864   0.2700  -0.3761   0.0005   0.0046   0.0014  -0.0020
  -0.9021   0.2900  -0.3195   0.0188  -0.1697   0.0546  -0.0601
   0.4464   0.3100   0.8394   0.0603   0.2693   0.1870   0.5064
   0.2362   0.3300  -0.9140   0.0720   0.1701   0.2377  -0.6583
  -0.7854   0.3500   0.5105   0.0001  -0.0010   0.0005   0.0007
   0.9164   0.3700   0.1529   0.0057   0.0526   0.0212   0.0088
  -0.5674   0.3900  -0.7253   0.2269  -1.2873   0.8849  -1.6455
  -0.0709   0.4100   0.9093   0.0032  -0.0023   0.0133   0.0294
   0.6597   0.4300  -0.6163   0.0089   0.0589   0.0384  -0.0551
  -0.8930   0.4500   0.0087   0.0079  -0.0708   0.0357   0.0007
   0.6566   0.4700   0.5899   0.0190   0.1250   0.0895   0.1123
  -0.0847   0.4900  -0.8676   0.3773  -0.3195   1.8488  -3.2735
  -0.5167   0.5100   0.6877   0.0001  -0.0006   0.0006   0.0008
   0.8336   0.5300  -0.1558   0.0009   0.0078   0.0049  -0.0015
  -0.7090   0.5500  -0.4414   0.1790  -1.2691   0.9844  -0.7900
   0.2210   0.5700   0.7914   0.0042   0.0093   0.0241   0.0334
   0.3651   0.5900  -0.7201   0.1119   0.4085   0.6601  -0.8057
  -0.7416   0.6100   0.2791   0.0034  -0.0255   0.0210   0.0096
   0.7207   0.6300   0.2893   0.0019   0.0136   0.0119   0.0055
  -0.3288   0.6500  -0.6851   0.7096  -2.3331   4.6124  -4.8617
  -0.2153   0.6700   0.7105   0.0002  -0.0005   0.0016   0.0017
   0.6227   0.6900  -0.3690   0.0147   0.0913   0.1011  -0.0541
  -0.6892   0.7100  -0.1445   0.0894  -0.6165   0.6351  -0.1292
   0.3985   0.7300   0.5552   0.0013   0.0052   0.0096   0.0073
   0.0786   0.7500  -0.6568   0.4868   0.3826   3.6513  -3.1973
  -0.4838   0.7700   0.4159   0.0027  -0.0129   0.0206   0.0111
   0.6128   0.7900   0.0194   0.0029   0.0178   0.0230   0.0006
  -0.4197   0.8100  -0.4096   0.5239  -2.1988   4.2437  -2.1458
   0.0312   0.8300   0.5569   0.0006   0.0002   0.0052   0.0035
   0.3336   0.8500  -0.4077   0.1209   0.4033   1.0278  -0.4930
  -0.4880   0.8700   0.0705   0.0487  -0.2378   0.4239   0.0344
   0.3768   0.8900   0.2567   0.0024   0.0092   0.0217   0.0063
  -0.0949   0.9100  -0.4036   0.5007  -0.4754   4.5565  -2.0208
  -0.1796   0.9300   0.3207   0.0079  -0.0141   0.0732   0.0252
   0.2965   0.9500  -0.0978   0.0406   0.1204   0.3857  -0.0397
  -0.2217   0.9700  -0.0998   0.1596  -0.3537   1.5478  -0.1593
   0.0557   0.9900   0.1296   0.0234   0.0130   0.2312   0.0303
  
 VALUEthe name of the value that should be read from the grid=h
DUMPGRIDOutput the function on the grid to a file with the PLUMED grid format. More details ARGthe label for the grid that you would like to output=ffg FILE the file on which to write the grid=output.grid

The input file in this case has the format for grids that is discussed in the documentation for DUMPGRID.

The second way you can create these constant functions is illustrated below.

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

d2The REFERENCE_GRID action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
grid
the constant function on the grid that was specified in input: REFERENCE_GRIDSetup a constant grid by either reading values from a file or definining a function in input More details GRID_MIN the lower bounds for the grid=0 GRID_MAX the upper bounds for the grid=10 GRID_BINthe number of bins for the grid=20 FUNCthe function to compute on the grid=d1*d1 VARthe names to give each of the grid directions in the function=d1 PERIODICare the grid directions periodic=NO
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
ffThe EVALUATE_FUNCTION_FROM_GRID action with label ff calculates the following quantities:
 Quantity   
 Type   
 Description  
ff
scalar
interpolation of the input grid to get the value of the function at the input arguments: EVALUATE_FUNCTION_FROM_GRIDCalculate the function stored on the input grid at an arbitrary point More details GRIDthe name of the grid that we are using to evaluate the function=d2
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,ff FMT the format that should be used to output real numbers=%8.4f FILEthe name of the file on which to output these quantities=colvar

This input illustrates a rather elaborate (and approximate) method for evaluating the square of the distance between atoms 1 and 2. As you can see, the option involves using the GRID_MIN, GRID_MAX and GRID_BIN options to create a grid of points. You can then use the FUNC option to specify the function that should be evaluated at each of those grid points. If you use this option the lepton library that is discussed in the documentation for CUSTOM is used to evaluate the function at the various grid points.

N.B. This method with lepton was implemented to facilitate the implementation of the normalisation in the implementation of the RDF shortcut.

Lastly note that you can specify the grid spacing in the input to this action rather than the number of bins as shown below:

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

d2The REFERENCE_GRID action with label d2 calculates the following quantities:
 Quantity   
 Type   
 Description  
d2
grid
the constant function on the grid that was specified in input: REFERENCE_GRIDSetup a constant grid by either reading values from a file or definining a function in input More details GRID_MIN the lower bounds for the grid=0 GRID_MAX the upper bounds for the grid=10 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.5 FUNCthe function to compute on the grid=d1*d1 VARthe names to give each of the grid directions in the function=d1 PERIODICare the grid directions periodic=NO
d1The DISTANCE action with label d1 calculates the following quantities:
 Quantity   
 Type   
 Description  
d1
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2
ffThe EVALUATE_FUNCTION_FROM_GRID action with label ff calculates the following quantities:
 Quantity   
 Type   
 Description  
ff
scalar
interpolation of the input grid to get the value of the function at the input arguments: EVALUATE_FUNCTION_FROM_GRIDCalculate the function stored on the input grid at an arbitrary point More details GRIDthe name of the grid that we are using to evaluate the function=d2
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=d1,ff FMT the format that should be used to output real numbers=%8.4f FILEthe name of the file on which to output these quantities=colvar

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
GRID_MIN	compulsory	auto	the lower bounds for the grid
GRID_MAX	compulsory	auto	the upper bounds for the grid
PERIODIC	compulsory	none	are the grid directions periodic
FILE	compulsory	none	the name of the file that contains the reference data
VALUE	compulsory	none	the name of the value that should be read from the grid
FUNC	optional	not used	the function to compute on the grid
GRID_BIN	optional	not used	the number of bins for the grid
GRID_SPACING	optional	not used	the approximate grid spacing (to be used as an alternative or together with GRID_BIN)
VAR	optional	not used	the names to give each of the grid directions in the function