classdef ML_inpt_att2 %UNTITLED Summary of this class goes here % Detailed explanation goes here %HISTORY: %2016- working version of code finished (dunno excacter date) %Feb 2017: Added %July 2017: Made mac friendly version (Nowj ust better code in general % too). No more reliance on '\' for path delimiting properties energies; %nx1(row) vector containing energies of MOs (in eV) intensities; %nxm matrix containing contributions to the MO with energy given by energies(n,1). DOES NOT INCLUDE THE TDOS (you have to sum the row to get this) fragment_labels; %list of fragment labels (1 label per position) used to extract x_sections later (e.g S3D N2D) m_factor; %factor to multiply a fragments contribution by (in case calc. system stoichiometry doesnt match experimental) frag_tdos; %Sum of the intensities row. essentially the pDoS for this fragment. WARNING: OBVIOUSLY NOT UPDATED AUTOMATICALLY IF YOU UPDATE DIFF FIELD numb_MOs; %Simply number of rows in energies/intensities. But i like to be explicit %Properties below are all related to creating a new MLinpt.txt file easily(write_new_file_method) first_line; %first_line and second_line are literally the 1st and 2nd lines of input file. Purpoes of having them here is that a new input file can easily be created from this object. second_line; base_fname; %As input file is *_MLinpt.txt format,base_fname is the * part of that (e.g cheese_MLinpt.txt, base_fname = 'cheese') base_path; %Path to foldere containng the original *_MLinpt.txt file end methods %filename = obbviously the full path of file to import %max_e = cutoff for orbital BINDING energy (orbitals with higher B.E will be deleted)(OPTIONAL ARGUMENT) %min_e = cutoff for orbital BINDING energy (orbitals with lower B.E will be deleted)(OPTIONAL ARGUMENT) function obj = ML_inpt_att2(filename) %NOTE: CANT GIVE AN ERROR FOR 0 arguments, otherwise i cant %initialise an object array (gj matlab.....) %if nargin==0 % error('Need at least a filepath argument for ML_inpt Class') %end if nargin>0 if nargin==1 min_e = -10000000; max_e = 100000000; end [obj.base_path , obj.base_fname] = fileparts(filename); obj.base_fname = strrep(obj.base_fname,'_MLinpt.txt',''); %temp = strrep(strsplit(filename,'\'),'_MLinpt.txt',''); obj.base_fname=temp{end}; %would probably work(but might need two lines) %obj.base_path = strjoin(temp(1:end-1),'\'); inp_file = fileread(filename); inp_file = strsplit(inp_file,'\n'); %String list/cell array containing lines of input file obj.first_line = inp_file{1}; obj.second_line = inp_file{2}; obj.m_factor = str2num ( strrep(inp_file{1},'# M_FACTOR=','') ); fragment_labels = strsplit(inp_file{2},','); fragment_labels = fragment_labels(3:end); %All fragment labels,NOT TDOS and energies though obj.fragment_labels = fragment_labels; numb_cols = size(fragment_labels,2) + 1; %Columns in data matrix, 1 more than frag_labels as it includes energy data_array = zeros(size(inp_file,2)-3,numb_cols); %POSSIBLE ERROR:inp_file has empty column@end, hence the -1 in loop. May cause problems somehow. %Putting energies+intensities into 1 grid (data_array-not TDOS column tho) for cls_loopvar1=3:size(inp_file,2)-1 temp_list = strsplit(inp_file{cls_loopvar1},','); counter=1; for cls_loopvar2=1:size(temp_list,2) if cls_loopvar2~=2 %Gets rid of the TDOS column data_array(cls_loopvar1-2,counter) = str2num(temp_list{cls_loopvar2}); counter=counter+1; end end end %Converting energies to binding energies and removing energies %above/below threshold %POSSIBLE ERROR:code assumes highest value=1st entry (as it should be but..) data_array(:,1) = data_array(:,1)*-1; e_upper=1; %index of highest energy MO we want e_lower=size(data_array,1); for cls_loopvar1=1:size(data_array,1) if data_array(cls_loopvar1,1) > max_e e_upper = cls_loopvar1 +1; end if data_array(size(data_array,1)-cls_loopvar1+1,1) < min_e e_lower = size(data_array,1)-cls_loopvar1; end end obj.energies = data_array(e_upper:e_lower,1); obj.intensities = data_array(e_upper:e_lower,2:end); obj.frag_tdos = NaN(size(obj.intensities,1),1); for cls_loopvar1=1:size(obj.intensities,1) obj.frag_tdos(cls_loopvar1,1) = sum(obj.intensities(cls_loopvar1,:)); end obj.numb_MOs = size(obj.energies,1); end end %Writes *MLinpt.txt file with current object attributes %(energies/intensities/base_fname/base_path/m_factor) %Modify object properties to modify output ldo function [] = write_file(obj) %Preparing the delimited data (energies/intensities) output_data = [obj.energies*-1 NaN(size(obj.energies,1),1) obj.intensities]; for i =1:size(output_data,1) output_data(i,2) = sum(obj.intensities(i,:)); end save_path = fullfile(obj.base_path,obj.base_fname); %Writing header output_filename = [save_path '_MLinpt.txt']; %Full path to output file fobject1 = fopen(output_filename,'w'); fprintf(fobject1,['# M_FACTOR=' num2str(obj.m_factor) '\n']); fprintf(fobject1,['# Energy (eV),TDOS,' strjoin(obj.fragment_labels,',') '\n']); fclose(fobject1); %Writing data dlmwrite(output_filename,output_data,'-append','precision','%.6f'); end end methods (Static) %Takes folder as an argument and returns object array contaning an %MLinpt object for each *MLinpt.txt file in folder %INput argument is obviously just full path to folder of interest function [MLinpt_obj_array] = create_MLinpt_obj_array_folder(folder) % file_list = dir([folder '\*MLinpt*.txt']); %nx1 structure containing all relevant file names file_list = dir(fullfile(folder,'*MLinpt.txt')); MLinpt_obj_array(size(file_list,1),1) = ML_inpt_att2; for i =1:size(MLinpt_obj_array,1) MLinpt_obj_array(i,1) = ML_inpt_att2( fullfile(folder,file_list(i,1).name) ); end end end end