Message: Updates since last commit

BondOrderScript_JKLDrives.m

@@ -1,13 +1,35 @@
-% %% DON'T RUN FROM HERE
-% 
-% while false
+%% Get already-run calcs with a given file prefix
+field = [];
+
+if (true)
+    fn = '8-merPPV-N2Optimized';
+
+
+    flist = dir('j:\NoAngle\*.mat');
+    for i = 1:length(flist)
+        fstr = regexpi(flist(i).name, ['^',fn,'-([0-9.]+)VA\.mat$'], 'tokens');
+        if (~isempty(fstr))
+            field(end+1) = str2double(fstr{1}{1});
+        end
+    end
+
+    field = sort(field,'ascend');
+
+    S = load(['j:\NoAngle\',fn,'-0VA.mat']);
 
-%% Run multiple molecules
+    mols = {fn,field(end),S.obj.axis_params};
+else
+
+
+%% If you didn't load the data from above, insert data to run here (or Run multiple molecules)
+    mols = {'15-merPPV-N2Optimized',.083,[3 118]};
+end
+
+%% Set other params and run
 
-mols = {'MeLPPP-13mer',.064,[1 186]};
 nstates = 25;
 norbs = 1000;
-poolsize = 7;
+poolsize = 3;
 
 run_energy_calcs = false;
 load_data = true;
@@ -30,10 +52,11 @@
 %     system(['subst s: "',rootdir,SFolder,'"']);
 %     system(['subst o: "',rootdir,OFolder,'"']);
 %     system(['subst p: "',rootdir,PFolder,'"']);
-
-     field = 0:0.001:mols{imol,2};
-     % field = [0:0.001:0.045, 0.0452:0.0002:0.065, 0.066:0.001:mols{imol,2}];
-
+    if (isempty(field))
+        field = 0:0.001:mols{imol,2};
+        %field = [0:0.001:0.054, 0.0542:0.0002:0.083, 0.084:0.001:mols{imol,2}];
+        %field = [0:0.001:0.054, 0.0542:0.0002:mols{imol,2}];
+    end
 
 %% Are you loading pre-existing data? Set this to false.
 if (run_energy_calcs)    

EnergyCalcExp.m

@@ -39,7 +39,8 @@
         fail_iterator;          % unsigned int: keeps track of the next index available in fail_bucket.
                                 % length(fail_bucket) = m = fail_iterator - 1
 
-        ampacexe = '"c:\Program Files\Semichem, Inc\Ampac-10.1\ampac.exe"';    % Path to the AMPAC executable, including " marks
+        sysvars;                % Contains paths to ampac and indo and other info for the system that runs this calculation
+        ampacexe;               % Ampac path with leading and trailing " marks
     end
 
     properties (SetAccess = public)
@@ -371,14 +372,8 @@
 % Output:  
 %       obj: EnergyCalcExp object. The constructed object.
 %--------------------------------------------------------------------------------------------------%
-        function obj = EnergyCalcExp(parameters, mol, axis_params, MAT, indo, ampac, load_libs, varargin)
-            if (~exist('c:\Program Files\Semichem, Inc\Ampac-10.1\ampac.exe','file'))
-                if (exist('c:\Program Files (x86)\Semichem, Inc\Ampac-10.1\ampac.exe','file'))
-                    obj.ampacexe = '"c:\Program Files (x86)\Semichem, Inc\Ampac-10.1\ampac.exe"';
-                else
-                    throw(MException('EnergyCalcExp:InvalidAmpacPath','EnergyCalcExp: Cannot find AMPAC! Update path'));
-                end
-            end
+        function obj = EnergyCalcExp(parameters, mol, axis_params, MAT, indo, ampac, load_libs, description, sysvars)
+
             if (nargin > 4)
                 % pause(0.02); % Hard drive delay catch-up...
                 if (~exist(mol,'file'))
@@ -390,10 +385,18 @@
                 obj.MATFilename = MAT;
                 obj.molecule = mol;
                 obj.axis_params = axis_params;
+                obj.description = description;
 
-                if (~isempty(varargin))
-                    obj.description = varargin{1};
+                if (~isempty(sysvars))
+                    obj.sysvars = sysvars;
+                else
+                    obj.sysvars = ECESysVars.getInstance;
+                    warning('off','ECESysVars:AlreadyInit');
+                    obj.sysvars.initialize;
+                    warning('on','ECESysVars:AlreadyInit');
                 end
+
+                obj.ampacexe = ['"',sysvars.getVars('ampac'),'"'];
 
                 if (indo(end) ~= '\')
                     indo = [indo, '\'];
@@ -665,7 +668,7 @@
                                 tmp_indo_path = tmp_indo_path(1:end-1);
                             end
 
-                            indo = Indo(indoparams, tmp_ampac_path, ampac.hash, tmp_indo_path, indo_out.hash);
+                            indo = Indo(indoparams, tmp_ampac_path, ampac.hash, tmp_indo_path, indo_out.hash, obj.sysvars);
 % 
 %                             if (indoparams.output_dm)
 %                                 movefile([obj.ampacdatapath, ampac.hash, '-dm.bin'], ...
@@ -1501,7 +1504,7 @@
                             tmp_indo_path = tmp_indo_path(1:end-1);
                         end
 
-                        indo = Indo(indoparams, tmp_ampac_path, ampac.hash, tmp_indo_path, indo_out.hash);
+                        indo = Indo(indoparams, tmp_ampac_path, ampac.hash, tmp_indo_path, indo_out.hash, obj.sysvars);
 
                         indo_out.indo = indo;
 

Indo.m

@@ -31,8 +31,7 @@
         ehsci       % (i,1) hole of the ith SCI basis function (0 if GS)
         % (i,2) = elec of the ith SCI basis function (0 if GS)
 
-        indoExe = '"c:\mscpp\demo-dci-working.exe"';
-        % indoExe = '"c:\mscpp\demo-dci\Release\demo-dci.exe"';
+        indoExe;    % Path to INDO exe
     end % properties
     properties (Transient)
         osc         % (1,i) oscillator strength from gs to state i
@@ -159,7 +158,8 @@ function readIndo(obj, inputfile)
         end
     end
     methods       
-        function res = Indo(ConfigIn, dataPathIn, jobNameIn, varargin)
+        function res = Indo(ConfigIn, dataPathIn, jobNameIn, dataPathOut, jobNameOut, sysvars)
+
             if (nargin < 1)
                 res.config = Indo.defaultConfig();
             else
@@ -178,13 +178,21 @@ function readIndo(obj, inputfile)
             if (nargin < 4)
                 res.dataPathOut = res.dataPathIn;
             else
-                res.dataPathOut = varargin{1};
+                res.dataPathOut = dataPathOut;
             end
             if (nargin < 5)
                 res.jobNameOut = res.jobNameIn;
             else
-                res.jobNameOut = varargin{2};
+                res.jobNameOut = jobNameOut;
+            end
+            if (nargin < 6)
+                sysvars = ECESysVars.getInstance;
+                warning('off','ECESysVars:AlreadyInit');
+                sysvars.initialize;
+                warning('on','ECESysVars:AlreadyInit');
             end
+            res.indoExe = ['"',sysvars.getVars('indo'),'"'];
+
             if (nargin > 0)
 %                 jobstring = [res.indoExe,' "',res.dataPath,'\',res.jobName,'"', ...
 %                     ' ',num2str(res.config.charge), ...

LoadPPVData.m

@@ -2,58 +2,58 @@
 
 %% 6-mer PPV Unrelaxed
 
-rootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\6-merPPV\';
+loadrootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\6-merPPV\';
 mat_file_path = {'..\6-merPPV-EvsF.mat'};
 
 %% 7-mer PPV Unrelaxed
 
-rootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\7-merPPV\';
+loadrootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\7-merPPV\';
 mat_file_path = {'..\7-merPPV-EvsF.mat'};
 
 %% 8-mer PPV Unrelaxed
 
-rootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\8-merPPV\';
+loadrootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\8-merPPV\';
 mat_file_path = {'..\8-merPPV-EvsF.mat'};
 
 %% 9-mer PPV Unrelaxed
 
-rootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\9-merPPV\';
+loadrootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\9-merPPV\';
 mat_file_path = {'..\9-merPPV-EvsF.mat'};
 
 %% 10-mer PPV Unrelaxed
 
-rootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\10-merPPV\';
+loadrootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\10-merPPV\';
 mat_file_path = {'..\10-merPPV-EvsF.mat'};
 
 %% 13-mer PPV Unrelaxed
 
-rootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\13-merPPV\';
+loadrootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\13-merPPV\';
 mat_file_path = {'..\13-merPPV-EvsF.mat'};
 
 %% 15-mer PPV Unrelaxed
 
-rootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\15-merPPV\';
+loadrootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\15-merPPV\';
 mat_file_path = {'..\15-merPPV-EvsF.mat'};
 
 
 %% 17-mer PPV Unrelaxed
 
-rootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\17-merPPV\';
+loadrootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\17-merPPV\';
 mat_file_path = {'..\17-merPPV-EvsF.mat'};
 
 %% 20-mer PPV Unrelaxed
 
-rootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\20-merPPV\';
+loadrootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\20-merPPV\';
 mat_file_path = {'..\20-merPPV-EvsF.mat'};
 
 %% Load data here
 
-if (rootdir(end) ~= '\')
-    rootdir = [rootdir, '\'];
+if (loadrootdir(end) ~= '\')
+    loadrootdir = [loadrootdir, '\'];
 end
 
 for i = 1:length(mat_file_path)
-    load([rootdir, mat_file_path{i}]);
+    load([loadrootdir, mat_file_path{i}]);
 end
 
 if (strcmpi(myexp.ampacdatapath, 'p:\'))
@@ -70,10 +70,10 @@
 OFolder = 'INDOLib';
 PFolder = 'GSLib';
 
-system('subst ',expt,': /d');
-system('subst ',indo,': /d');
-system('subst ',ampac,': /d');
+system(['subst ',expt,': /d']);
+system(['subst ',indo,': /d']);
+system(['subst ',ampac,': /d']);
 
-system(['subst ',expt,': "',rootdir,SFolder,'"']);
-system(['subst ',indo,': "',rootdir,OFolder,'"']);
-system(['subst ',ampac,': "',rootdir,PFolder,'"']);
+system(['subst ',expt,': "',loadrootdir,SFolder,'"']);
+system(['subst ',indo,': "',loadrootdir,OFolder,'"']);
+system(['subst ',ampac,': "',loadrootdir,PFolder,'"']);

OptExcStateStructure.m

@@ -4,10 +4,12 @@
 
 % ampac_pathonly = 'C:\Users\Christian\Documents\Research\Yaron\dyes2\data\DMG-8mer\';
 % ampac_nameonly = '8-merPPVampac';
-
-    % EXECUTABLE PATHWAYS, NO QUOTES
-    AmpacEXE = 'C:\Program Files\Semichem, Inc\Ampac-10.1\ampac.exe';
-    OpenBabelEXE = 'C:\Program Files (x86)\OpenBabel-2.3.2\babel.exe';
+    if (~ECE_system_vars('check'))
+        ECE_system_vars('setall');
+    end
+
+    global AMPACEXE;
+    AmpacEXE = AMPACEXE;
 
 
     indoidx = find(cellfun(@(x)isequal(lower(x),'indo'), varargin));

SetUpSubstDrives.m

@@ -8,7 +8,8 @@
 
 %% Load substituted drives
 
-rootdir = fullfile(pwd,'data\8-merPPV-newampac\Coupling');
+rootdir = fullfile(pwd,'..\data\17-merPPV\');
+% rootdir = fullfile('C:\Users\clegaspi\Documents\MATLAB\data\13-merPPV\');
 SFolder = 'Exp';
 OFolder = 'INDOLib';
 PFolder = 'GSLib';
@@ -18,7 +19,12 @@
 end
 
 if (~exist(rootdir,'dir'))
-    mkdir(rootdir);
+    response = questdlg('This directory does not exist. Create?','Dir DNE','Yes','No','Yes');
+    if (strcmp(response,'Yes'))
+        mkdir(rootdir);
+    else
+        return;
+    end
 end
 if (~exist([rootdir,SFolder],'dir'))
     mkdir([rootdir,SFolder]);
@@ -46,7 +52,7 @@
 
 %% Load substituted drives
 
-rootdir = 'C:\Users\clegaspi\Documents\MATLAB\data\MeLPPP-13mer\';
+rootdir = fullfile(pwd,'..\data\PFH-13mer-N2Opt\');
 SFolder = 'Exp';
 OFolder = 'INDOLib';
 PFolder = 'GSLib';
@@ -56,7 +62,12 @@
 end
 
 if (~exist(rootdir,'dir'))
-    mkdir(rootdir);
+    response = questdlg('This directory does not exist. Create?','Dir DNE','Yes','No','Yes');
+    if (strcmp(response,'Yes'))
+        mkdir(rootdir);
+    else
+        return;
+    end
 end
 if (~exist([rootdir,SFolder],'dir'))
     mkdir([rootdir,SFolder]);

ampac_to_xyz.m

@@ -2,16 +2,8 @@
 %AMPAC_TO_XYZ Summary of this function goes here
 %   Detailed explanation goes here
 
-    % OpenBabelEXE = 'C:\Program Files (x86)\OpenBabel-2.3.2\babel.exe';
-    ampacexe = 'C:\Program Files\Semichem, Inc.\Ampac-10.1\ampac.exe';
-
-    if (~exist(ampacexe, 'file'))
-        if (exist('C:\Program Files (x86)\Semichem, Inc.\Ampac-10.1\ampac.exe', 'file'))
-            ampacexe = 'C:\Program Files (x86)\Semichem, Inc.\Ampac-10.1\ampac.exe';
-        else
-            throw(MException('ampac_to_xyz:AmpacNotFound', 'ampac_to_xyz: AMPAC EXE not found. Please edit.'));
-        end
-    end
+    sysvars = ECESysVars.getInstance;
+    ampacexe = sysvars.getVars('ampac');
 
     if (iscell(input))
         zmatrix = input;

closest_member.m

@@ -15,9 +15,9 @@
     [b,ix] = sort(myset,'ascend');
 
     for i = 1:length(b)
-        if (b(i) < a)
+        if (b(i) < a && i < length(b))
             continue;
-        elseif (b(i) == a)
+        elseif (b(i) == a || (b(i) < a && i == length(b)))
             varargout{1} = b(i);
             switch nargout
                 case 2

distort_geometry.m

@@ -1,5 +1,11 @@
 function newzmatrix = distort_geometry(zmatrix, ring_info, newblsbyatom, varargin)
-    AmpacEXE = 'C:\Program Files\Semichem, Inc\Ampac-10.1\ampac.exe';    
+    if (~ECE_system_vars('check'))
+        ECE_system_vars('setall');
+    end
+
+    global AMPACEXE;
+    AmpacEXE = AMPACEXE;
+
     newzmatrix = zmatrix;
     natoms = size(zmatrix, 1);
     rings = {ring_info.rings};