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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,142 @@ | ||
| %scrit file name bonds_analysis_speedup | ||
| %purpose: | ||
| %This program is used to analyze bonds file and is more fast than | ||
| %bonds_analysis program | ||
| %version 1;2018.6.25 | ||
| disp('##################################################################################################################################') | ||
| disp('Welcome!--by Qiang Liu @Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics; Email: liubinqiang@163.com'); | ||
| disp('Repository adress of the Source code on github: https://github.com/dadaoqiuzhi/RMD_Digging'); | ||
| disp('References: 1.Fuel 287 (2021) 119484. 2.ACS Appl. Mat. Interfaces 13(34) (2021) 41287-41302. More work is coming!') | ||
| disp('##################################################################################################################################') | ||
| fprintf('This program will read the BO information of a specified or all (not recommended) trajectories, the text in the 2-4 rows of each trajectory is omitted.\n') | ||
| dataname=input('Please input the file name to be processed: \n','s'); | ||
| trajper=input('Please input the output frequency of BO information (Positive integer): \n'); | ||
| tartrajectory=input('\nPlease input the timestep of the specified trajectory: \n'); | ||
| atomnum=input('Please input atom number: \n'); | ||
| disp('bonds_analysis_speedup is running, please wait...') | ||
| tartrajectory={tartrajectory(1)}; | ||
| if mod(tartrajectory{1},trajper)~=0 | ||
| control=0; | ||
| fprintf('\nThis trajectory is not existed, please check it!!!\n') | ||
| return; | ||
| else | ||
| control=1; | ||
| end | ||
|
|
||
|
|
||
| readline=0; | ||
| gap=8+atomnum; | ||
| rawdata=fopen(dataname,'r'); | ||
| dataline=fgetl(rawdata); | ||
| readline=readline+1; | ||
| datacell=textscan(dataline,'%s','delimiter','\n'); | ||
| datacellchar=char(datacell{1}); | ||
| datadel=strrep(datacellchar,'#',''); | ||
| datarep=strtrim(datadel); | ||
| datasplit=strsplit(datarep); | ||
| if str2num(datasplit{1,2})==tartrajectory{1} | ||
| control=0; | ||
| else | ||
| while control | ||
| i=1; | ||
| unfound=1; | ||
| while unfound | ||
| dataline=fgetl(rawdata); | ||
| readline=readline+1; | ||
| i=i+1; | ||
| if i==gap+1 | ||
| unfound=0; | ||
| break; | ||
| end | ||
| end | ||
| if mod(readline-1,gap)==0 | ||
| datacell=textscan(dataline,'%s','delimiter','\n'); | ||
| datacellchar=char(datacell{1}); | ||
| datadel=strrep(datacellchar,'#',''); | ||
| datarep=strtrim(datadel); | ||
| datasplit=strsplit(datarep); | ||
| if str2num(datasplit{1,2})==tartrajectory{1} | ||
| control=0; | ||
| end | ||
| else | ||
| disp('not timestep row, please check it!!!') | ||
| return; | ||
| end | ||
| end | ||
| end | ||
|
|
||
| found=6; | ||
| while found | ||
| dataline=fgetl(rawdata); | ||
| readline=readline+1; | ||
| found=found-1; | ||
| end | ||
|
|
||
| bondoutdata={}; | ||
| bondoutdata{1,1}='Timestep'; | ||
| bondoutdata{1,2}=tartrajectory{1}; | ||
| for i=3:15 | ||
| bondoutdata{1,i}=[]; | ||
| end | ||
|
|
||
| line=2; | ||
| while atomnum | ||
| dataline=fgetl(rawdata); | ||
| readline=readline+1; | ||
| atomnum=atomnum-1; | ||
| if atomnum<=0 | ||
| break; | ||
| end | ||
| datacell=textscan(dataline,'%s','delimiter','\n'); | ||
| datacellchar=char(datacell{1}); | ||
| datarep=strtrim(datacellchar); | ||
| datasplit=strsplit(datarep); | ||
| bondnumdata={}; | ||
| bondnumdata(1,1:3)=datasplit(1,1:3); | ||
| if ~strcmp(datasplit{1,3},'0') | ||
| for i=1:str2num(datasplit{1,3}) | ||
| bondnumdata(1,i+3)=datasplit(1,i+3); | ||
| end | ||
| bondnumdata(1,8)=datasplit(1,i+4); | ||
| k=i+5; | ||
| for j=1:str2num(datasplit{1,3}) | ||
| bondnumdata(1,j+8)=datasplit(1,k); | ||
| k=k+1; | ||
| end | ||
| bondnumdata(1,13:15)=datasplit(1,k:k+2); | ||
| else | ||
| bondnumdata(1,8)=datasplit(1,4); | ||
| bondnumdata(1,13)=datasplit(1,5); | ||
| bondnumdata(1,14)=datasplit(1,6); | ||
| bondnumdata(1,15)=datasplit(1,7); | ||
| end | ||
| for kk=1:length(bondnumdata) | ||
| if isempty(bondnumdata{kk}) | ||
| bondnumdata{kk}='NaN'; | ||
| else | ||
| bondnumdata{kk}=str2num(bondnumdata{kk}); | ||
| end | ||
| end | ||
| for kk=1:length(bondnumdata) | ||
| bondoutdata{line,kk}=bondnumdata{kk}; | ||
| end | ||
| line=line+1; | ||
| end | ||
| fclose(rawdata); | ||
| fprintf('\nbonds_analysis is successfully finished, BO information is saved inbondoutdata') | ||
|
|
||
| outputans=input('Export results? y/n?: \n','s'); | ||
| outputans=lower(outputans); | ||
| if outputans=='y' | ||
| [dataoutrow,dataoutcol]=size(bondoutdata); | ||
| dataoutputrow=strcat('A','1'); | ||
| dataoutcolchar=char(65+dataoutcol-1); | ||
| dataoutputcol=strcat(dataoutcolchar,num2str(dataoutrow)); | ||
| filename='output_mydata.xlsx'; | ||
| xlswrite(filename,bondoutdata,dataoutputrow:dataoutputcol) | ||
| fprintf('\nbonds_analysis is successfully finished. BO information is exported into the excel:output_mydata\n') | ||
| end | ||
| fprintf('\nbonds_analysis is successfully finished. BO information is saved inbondoutdata.\n') | ||
|
|
||
| clear ans atomnum bondnumdata control datacell datacellchar datadel dataline dataname datarep datasplit found gap i j k kk line | ||
| clear outputans rawdata tartrajectory trajper unfound dataoutrow dataoutcol dataoutputrow dataoutcolchar dataoutputcol filename |
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