-
Notifications
You must be signed in to change notification settings - Fork 0
/
MSD_unscaled_g2_Tmean.R
248 lines (189 loc) · 11.1 KB
/
MSD_unscaled_g2_Tmean.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
## MSD g2 calculation for unscaled positions
### First define a function to do the calculation for one temeprature.
MSD_unscaled_g2_one_temp_Tmean=function(path="~/Dropbox/lammps/PMMA_big/atom300",filename="atom.300_1.txt"
,molecule_atoms=602,num_mol=64,atom_type=1:10
,atom_type_mass=c(1.0079,12.011,12.011,12.011,15.9999,15.9999,12.011,12.011,1.0079,12.011),core_num=4){
setwd(path)
# record the time
timeRecordB()
# load all library
library(data.table)
library(foreach)
library(dplyr)
library(matrixStats)
library(magrittr)
### Load the data with fread
atom.300.1_fread=fread(input=filename, sep=" ", stringsAsFactors = FALSE, fill=TRUE
#,col.names = c("atom-id","type","mol","xu","yu","zu")
,colClasses = c("numeric","numeric","numeric","numeric","numeric","numeric","character","character")
,na.strings = c("ITEM:","TIMESTEP","NUMBER","OF","ATOMS","BOX","BOUNDS", "pp","id","type","mol","xu","yu","zu")
)
timeRecordB(output_message = "Load in data fread")
# select the non-NA columns
atom.300.1_fread=atom.300.1_fread[,.(V1,V2,V3,V4,V5,V6)]
# clear the rows that have NA values, V6 contains the most NAs.
atom.300.1_fread=atom.300.1_fread[complete.cases(atom.300.1_fread[,V6])]
# set the column names.
colnames(atom.300.1_fread)=c("atom.id","type","mol","xu","yu","zu")
timeRecordB(output_message = "Load in data fread")
########################################################################
# calculate total atom number and timestep.
tot_atom_num=atom.300.1_fread[,.(atom.id)]%>%max()
paste("The number of atoms:",tot_atom_num,sep="")%>%message()
timestep=dim(atom.300.1_fread)[1]/tot_atom_num
paste("The number of timestep:",timestep,sep="")%>%message()
########################################################################
# add time variable for easier data handling and safe guarding any unwanted ordering to change the ordering of time in the data.
timeRecordB()
atom.300.1_fread[,time_step:=seq(1,timestep,by=1)%>%rep(times=tot_atom_num)%>%sort()]
timeRecordB(output_message = "add time variable data.table")
# select only part of the data to release some memory.
atom.300.1_fread=atom.300.1_fread[,.(atom.id,type,time_step,xu,yu,zu)]
##########################################################################################################################################
##################################################################################
# set atom.id and timestep both as the key for the data so that the data is sorted first by atom.id then by time_step
atom.300.1_fread%>%setkey(atom.id,time_step)
message("The data is sorted by atom.id and time_step")
##################################################################################
#########################################################################################################
# add mol variable to original data frame
# Define a function to assign mol number according to the molecule size
mol_id_gen=function(atom_id,molecule_atoms){
# the minimum number for mol id is 0.
# minus 1 from the atom.id to get the last atom of each molecule to be on the correct molecule.
return(floor((atom_id-1)/molecule_atoms))
}
timeRecordB()
atom.300.1_fread[,mol:=mol_id_gen(atom_id = atom.id,molecule_atoms=molecule_atoms)]
timeRecordB(output_message = "add mol variable data.table")
#########################################################################################################
# add mass variable to original data frame
# define a function to add mass to the dataset.
decode = function(x, search, replace, default = NULL) {
# build a nested ifelse function by recursion
decode.fun <- function(search, replace, default = NULL)
if (length(search) == 0) {
function(x) if (is.null(default)) x else rep(default, length(x))
} else {
function(x) ifelse(x == search[1], replace[1],
decode.fun(tail(search, -1),
tail(replace, -1),
default)(x))
}
return(decode.fun(search, replace, default)(x))
}
timeRecordB()
atom.300.1_fread[,mass:=decode(x = type, search = atom_type, replace = atom_type_mass)]
timeRecordB(output_message = "add mass variable data.table")
gc()
#########################################################################################################
#########################################################################################################
# define functions to calculate time average
library(foreach)
library(doParallel)
library(matrixStats)
library(magrittr)
# calculate the lag difference, then squared all the values, calculate the column mean for sqaured difference, then sum the difference in x,y,z directions.
coldiff_msd=function(data,lag_val){
return(data%>%as.matrix%>%colDiffs(lag=lag_val)%>%.^2%>%colMeans%>%sum)
}
coldiff_msd=compiler::cmpfun(coldiff_msd)
# calculate the msd for a vector of lag values
vapply_lags_msd=function(data,lag_vec){
vapply(lag_vec,function(lag_val){coldiff_msd(data,lag_val = lag_val)},FUN.VALUE = numeric(1))
}
vapply_lags_msd=compiler::cmpfun(vapply_lags_msd)
# calculate lagged msd for different atom.id.
# This the most outerloop per se. So that we could use foreach to do things in parallel.
#================================= This function assumes that the dataset contains a mol column. ==================================#
foreach_datas_lags_para_msd=function(data,lag_vec,mol_id,mol_min,core_num=core_num){
registerDoParallel(cores = core_num)
para_foreach_result=foreach(i=seq_along(mol_id),.combine = rbind)%dopar%{
mol_center_of_mass=data[mol==mol_id[i],]%>%vapply_lags_msd(lag_vec = lag_vec)
# if(i%%100==0 ){paste0("atom number",i,"/",length(mol_id))%>%message()} # echo the progress since I am a control freak.
return(mol_center_of_mass)
}
# getDoParWorkers()%>%print()
stopImplicitCluster()
gc()
return(para_foreach_result)
}
foreach_datas_lags_para_msd=compiler::cmpfun(foreach_datas_lags_para_msd)
# atom_id_1[,.(diff(xu,lag=2),diff(yu,lag=2),diff(zu,lag=2))]%>%head()%>%.^2%>%sum()
####################################################################################################################
MSD_g2_matrix=function(data,timestep,totmass,mol_min,mol_max,core_num){
# calculate the center of mass for every timestep and every mol
center_of_mass=data[,.(xu=sum(xu*mass)/totmass,yu=sum(yu*mass)/totmass,zu=sum(zu*mass)/totmass),by=.(mol,time_step)]
# reorder the data first by mol then by the timestep
center_of_mass%>%setkey(mol,time_step)
# calculate the time average for MSD for each mol.
MSD_g2_empty_matrix=center_of_mass[,.(mol,xu,yu,zu)]%>%foreach_datas_lags_para_msd(lag_vec = 1:timestep,mol_id = mol_min:mol_max,core_num = core_num)
return(MSD_g2_empty_matrix)
}
#########################################################################################################
# mass of molecule 1
totmass= atom.300.1_fread[time_step==1,]%>%.[mol==1,.(mass)]%>%sum
# calculate mol_min number
mol_min=atom.300.1_fread[time_step==1,.(mol)]%>%min()
mol_max=atom.300.1_fread[time_step==1,.(mol)]%>%max()
# do it for every mol and combine the results by rbind
timeRecordB()
MSD.all.matrix=atom.300.1_fread%>%MSD_g2_matrix(timestep=timestep,totmass=totmass,mol_min=mol_min,mol_max=mol_max,core_num=core_num)
gc()
timeRecordB(output_message = paste("cores:",core_num,"total mols:",num_mol, "MSD matrix calculation"))
timeRecordR()%>%filter(output_message!="None")
########################
# calculate non-gaussian parameter.
timeRecordB()
NGP.600=(0.6)*colMeans(MSD.all.matrix^2)/(colMeans(MSD.all.matrix))^2-1
timeRecordB(output_message = "NGP calculation")
# write the NGP into a txt file.
timeRecordB()
NGP.600%>%write.table(file="NGP.g2.Tmean.1.txt", sep=",")
timeRecordB(output_message = "NGP Write")
# calculation the MSD averagd over all atoms and write it to a txt file.
timeRecordB()
MSD.all.matrix%>%colMeans%>%write.table(file="MSD.g2.colmean.Tmean.1.txt", sep=",")
timeRecordB(output_message = "MSD average Write")
gc()
return(timeRecordR(ignore=0.1)%>%filter(output_message!="None")%>%select(output_message,run_time) )
}
# example use.
# # load the timeRecord functions from my github account.
# source("https://raw.githubusercontent.com/edwardcooper/mlmodel_select/master/timeRecord_functions.R")
# MSD_unscaled_g2_one_temp_Tmean(path="~/Dropbox/lammps/PMMA_big/atom300",filename="atom.300_1.txt"
# ,molecule_atoms=602,num_mol=64,atom_type=1:10
# ,atom_type_mass=c(1.0079,12.011,12.011,12.011,15.9999,15.9999,12.011,12.011,1.0079,12.011),core_num=4)
# # stopping a parallel computation could only be done from htop. Not from the Rstudio.
## echo the current calculation and percentage of entire calculation.
MSD_unscaled_g2_Tmean=function(Path="~/Dropbox/lammps/",polymer="PMMA_big",temperatures=seq(300,600,by=20)
,molecule_atoms=602,num_mol=64,atom_type=1:10
,atom_type_mass=c(1.0079,12.011,12.011,12.011,15.9999,15.9999,12.011,12.011,1.0079,12.011)
,core_num=4){
# load the timeRecord functions from my github account.
source("https://raw.githubusercontent.com/edwardcooper/mlmodel_select/master/timeRecord_functions.R")
library(magrittr)
# the loop to calculate the same thing in all temepratures defined above.
for (i in seq_along(temperatures)){
# echo beginning of calculation
paste("Begin calculation of temperature:",temperatures[i],sep="")%>%message
# set correct path for the data file
path=paste(Path,"/", polymer,"/atom",temperatures[i], sep='')
# find the correct file to read and calculate.
filename=paste("atom.",temperatures[i],"_1.txt",sep="")
# calculation for MSD
MSD_unscaled_g2_one_temp_Tmean(path=path,filename =filename
,molecule_atoms=molecule_atoms,num_mol=num_mol,
atom_type=atom_type,atom_type_mass=atom_type_mass,core_num=core_num )
# echo end of calculation
paste("End calculation of temperature:",temperatures[i],sep="")%>%message
paste(i,"/",length(temperatures))%>%message
gc()
}
return( timeRecordR(ignore=0.1)%>%filter(output_message!="None")%>%select(output_message,run_time) )
}
# example use
# MSD_unscaled_g2_Tmean(Path="~/Dropbox/lammps/",polymer="PMMA_big",temperatures=seq(300,600,by=20)
# ,molecule_atoms=602,num_mol=64,atom_type=1:10
# ,atom_type_mass=c(1.0079,12.011,12.011,12.011,15.9999,15.9999,12.011,12.011,1.0079,12.011)
# ,core_num=4)