metadynminer3d (version 0.0.2)

read.plumed3d: Read 3D free energy surface from PLUMED sum_hills

Description

`read.plumed3d` reads 3D free energy surface from PLUMED sum_hills. The grid in the inputfile must contain the same number of points for CV1, CV2 and CV3. It does not use the header of the file. Periodicity must be specified.

Usage

read.plumed3d(file = "fes.dat", per = c(FALSE, FALSE, FALSE))

Arguments

file

input file from PLUMED sum_hills.

per

logical vector specifying periodicity of collective variables.

Value

fes3d object.

Examples

# NOT RUN {
l1<-" -3.14 -3.14 -3.14 -61.13 -47.43  19.00   2.04"
l2<-" -1.05 -3.14 -3.14 -70.72  25.95  25.78   2.43"
l3<-"  1.05 -3.14 -3.14 -65.58   8.34   2.82  -3.09"
l4<-" -3.14 -1.05 -3.14 -51.31 -43.88 -19.91   1.51"
l5<-" -1.05 -1.05 -3.14 -66.43   7.67 -22.45  -0.39"
l6<-"  1.05 -1.05 -3.14 -61.08  -7.50  -7.36  -0.83"
l7<-" -3.14  1.05 -3.14 -53.07 -55.12   0.19  -0.28"
l8<-" -1.05  1.05 -3.14 -62.81  36.19   1.65   0.45"
l9<-"  1.05  1.05 -3.14 -65.28  22.84  11.47   0.59"
l10<-" -3.14 -3.14 -1.05 -13.03 -32.17   8.24 -35.25"
l11<-" -1.05 -3.14 -1.05 -21.88  17.89  21.91 -51.20"
l12<-"  1.05 -3.14 -1.05 -14.49   3.60   6.04 -44.05"
l13<-" -3.14 -1.05 -1.05  -2.26  -7.00  -7.01 -10.65"
l14<-" -1.05 -1.05 -1.05  -8.21   3.69 -22.89 -28.48"
l15<-"  1.05 -1.05 -1.05  -1.10   0.52   3.59  -1.99"
l16<-" -3.14  1.05 -1.05  -3.75 -11.70  -5.65 -15.36"
l17<-" -1.05  1.05 -1.05  -1.15   5.75   1.05  -2.42"
l18<-"  1.05  1.05 -1.05 -10.67   8.23 -10.42 -36.77"
l19<-" -3.14 -3.14  1.05  -4.64 -13.79  10.51  14.96"
l20<-" -1.05 -3.14  1.05  -7.80  12.24  20.59  23.03"
l21<-"  1.05 -3.14  1.05  -5.32   3.46   3.17  21.99"
l22<-" -3.14 -1.05  1.05  -2.06  -6.59   0.17  10.04"
l23<-" -1.05 -1.05  1.05  -9.69   8.43  -0.97  36.97"
l24<-"  1.05 -1.05  1.05  -0.19  -0.44  -0.26   0.91"
l25<-" -3.14  1.05  1.05  -7.98 -23.02   3.97  26.98"
l26<-" -1.05  1.05  1.05  -4.64  13.66  -9.74  10.15"
l27<-"  1.05  1.05  1.05 -13.42  15.78  16.36  41.60"
twentysevenpoints<-c(l1,l2,l3,l4,l5,l6,l7,l8,l9,l10,
                     l11,l12,l13,l14,l15,l16,l17,l18,l19,l20,
                     l21,l22,l23,l24,l25,l26,l27)
tf <- tempfile()
writeLines(twentysevenpoints, tf)
read.plumed3d(tf, per=c(TRUE,TRUE,TRUE))
# }