read.plumed3d.Rd`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.
read.plumed3d(file = "fes.dat", per = c(FALSE, FALSE, FALSE))input file from PLUMED sum_hills.
logical vector specifying periodicity of collective variables.
fes3d object.
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))
#> 3D free energy surface with 3 x 3 x 3 points, maximum -0.19 and minimum -70.72