encoding debug & upgrade

encoding debug & upgrade

chemi_mechanism/Deconvolu_SysConvert.m

@@ -1,11 +1,12 @@
 %This function is used to transform a number to decimal system.
 function num_10base = Deconvolu_SysConvert(given_num_char,base)
-num_table = {'1','2','3','4','5','6','7','8','9','a','b','c','d',...
-    'e','f','g','h','i','j','k','l','m','n','o','p','q','r','s','t','u','v','w','x','y','z'};
+num_table = {'0','1','2','3','4','5','6','7','8','9',...
+    'a','b','c','d','e','f','g','h','i','j','k','l','m','n','o','p','q','r','s','t','u','v','w','x','y','z',...
+    'A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z'};
 [~,matches] = strsplit(given_num_char,num_table,'CollapseDelimiters',false);
 num_10base = 0;
 for i = 1:length(matches)
     [~,num_true] = ismember(matches{i},num_table);
-    num_10base = num_10base + num_true*base^(length(matches)-i);
+    num_10base = num_10base + (num_true-1)*base^(length(matches)-i);
 end
 end

chemi_mechanism/SysConvert.m

@@ -1,13 +1,15 @@
 %scrit file name SysConvert
 %purpose:
 %This function is used to convert a given number into an expected number
-%system. ASCII is used
+%system. ASCII is used.
 function target_num=SysConvert(given_num,base)
-if given_num==round(given_num) && given_num>0 && base==round(base) && base>0
+if base > 62
+    error('The base for atom id encoding is larger than 62, unrecognizable char except 0-9£¬a-z£¬A-Z may be used. Please check it')
+end
+if given_num == round(given_num) && given_num > 0 && base == round(base) && base > 0
     control=1;remaindermat=[];
 else
-    control=0;
-    error('\nConversion of number system should be with an integer!!!');
+    error('\nThe base and atom id must be positive integer!');
 end
 
 while control
@@ -24,12 +26,15 @@
 
 atomid='';i=size(remaindermat,1);
 while i
-    if remaindermat(i,2)<=9
+    if remaindermat(i,2) <= 9 %0-9
         atomid=strcat(atomid,num2str(remaindermat(i,2)));
-    else
+    elseif remaindermat(i,2) > 9 && remaindermat(i,2) <= 35 %a-z
         atomid=strcat(atomid,char(remaindermat(i,2)+87));
+    elseif remaindermat(i,2) > 35 && remaindermat(i,2) <= 61 %A-Z
+        atomid=strcat(atomid,char(remaindermat(i,2)+29));
     end
     i=i-1;
 end
+
 target_num=atomid;
 

chemi_mechanism/car_mdf_filemaker.m

@@ -42,7 +42,35 @@
             elementname=eleswap{lib,2};
         end
         atomid_conv=SysConvert(tarBOinform{readline,1},base);
-        atomname=strcat(elementname,atomid_conv);
+        if elemax==2
+            if formatout==1 || formatout==2
+                if 238327>=atomnum
+                    atomname=strcat(elementname,atomid_conv);
+                else
+                    atomname=atomid_conv;
+                end
+            elseif formatout==3
+                if 3843>=atomnum
+                    atomname=strcat(elementname,atomid_conv);
+                else
+                    atomname=atomid_conv;
+                end
+            end
+        elseif elemax==1
+            if formatout==1 || formatout==2
+                if 14776335>=atomnum
+                    atomname=strcat(elementname,atomid_conv);
+                else
+                    atomname=atomid_conv;
+                end
+            elseif formatout==3
+                if 238327>=atomnum
+                    atomname=strcat(elementname,atomid_conv);
+                else
+                    atomname=atomid_conv;
+                end
+            end
+        end
 
         [trjrow,~]=size(trjdata);tartrjdata=[];
         for i=1:trjrow

chemi_mechanism/chemi_mechanism.m

@@ -69,61 +69,69 @@
 if elemax==2
     if formatout==1 || formatout==2
         fprintf('\nDifferent number system is adopted according to the atom number (ASCII)\n');
-        if 262143>=atomnum && atomnum>32767
-            fprintf('64 base number system is recommended for atom id');base=64;
+        if 238327>=atomnum && atomnum>32767
+            fprintf('62 base number system is recommended for atom id');base=62;
         elseif 32767>=atomnum && atomnum>4095
             fprintf('32 base number system is recommended for atom id');base=32;
         elseif 4095>=atomnum && atomnum>999
             fprintf('16 base number system is recommended for atom id');base=16;
         elseif 999>=atomnum
             fprintf('10 base number system (decimalism) is recommended for atom id');
-        elseif atomnum<0 || atomnum>32767
-            error('Atom number is less than 0 or larger than  262143. If larger, please check it and modify code accordingly!')
+        elseif atomnum<=916132831 || atomnum>238327
+            fprintf('\nAtom number is no more than 916132831 but larger than  238327. If larger, no element name is list in the number system, indicating 5 ASCII chars are used to encode\n')
+			base=62;
+		elseif atomnum > 916132831
+            error('Atom number exceeds 916132831, which can not be encoded. Please check it or contact the developer!')
         end
     elseif formatout==3
         fprintf('\nDifferent number system is adopted according to the atom number (ASCII)\n');
-        if 65535>=atomnum && atomnum>16383
-            fprintf('256 base number system is recommended for atom id');base=256;
-        elseif 16383>=atomnum && atomnum>4095
-            fprintf('128 base number system is recommended for atom id');base=128;
-        elseif 4095>=atomnum && atomnum>1023
-            fprintf('64 base number system is recommended for atom id');base=64;
+        if 3843>=atomnum && atomnum>1023
+            fprintf('62 base number system is recommended for atom id');base=62;
         elseif 1023>=atomnum && atomnum>255
             fprintf('32 base number system is recommended for atom id');base=32;
         elseif 255>=atomnum && atomnum>99
             fprintf('16 base number system is recommended for atom id');base=16;
         elseif 99>=atomnum
             fprintf('10 base number system (decimalism) is recommended for atom id');
-        elseif atomnum<0 || atomnum>65535
-            error('Atom number is less than 0 or larger than  65535. If larger, please check it and modify code accordingly!')
+        elseif atomnum<=14776335 || atomnum>3843
+            fprintf('\nAtom number is no more than 14776335 but larger than 3843. If larger, no element name is list in the number system, indicating 4 ASCII chars are used to encode\n')
+			base=62;
+		elseif atomnum > 14776335
+            error('Atom number exceeds 14776335, which can not be encoded. Please check it or contact the developer!')
         end
     end
 elseif elemax==1
     if formatout==1 || formatout==2
         fprintf('\nDifferent number system is adopted according to the atom number (ASCII)\n');
-        if 16777215>=atomnum && atomnum>1048575
-            fprintf('64 base number system is recommended for atom id');base=64;
+        if 14776335>=atomnum && atomnum>1048575
+            fprintf('62 base number system is recommended for atom id');base=62;
         elseif 1048575>=atomnum && atomnum>65535
             fprintf('32 base number system is recommended for atom id');base=32;
         elseif 65535>=atomnum && atomnum>9999
             fprintf('16 base number system is recommended for atom id');base=16;
         elseif 9999>=atomnum
             fprintf('10 base number system (decimalism) is recommended for atom id');
-        elseif atomnum<0 || atomnum>16777215
-            error('Atom number is less than 0 or larger than 16777215. If larger, please check it and modify code accordingly!')
+        elseif atomnum<=916132831 || atomnum>14776335
+            fprintf('\nAtom number is no more than 916132831 but larger than 14776335. If larger, no element name is list in the number system, indicating 5 ASCII chars are used to encode\n')
+			base=62;
+		elseif atomnum > 916132831
+            error('Atom number exceeds 916132831, which can not be encoded. Please check it or contact the developer!')
         end
     elseif formatout==3
         fprintf('\nDifferent number system is adopted according to the atom number (ASCII)\n');
-        if 262143>=atomnum && atomnum>32767
-            fprintf('64 base number system is recommended for atom id');base=64;
+        if 238327>=atomnum && atomnum>32767
+            fprintf('64 base number system is recommended for atom id');base=62;
         elseif 32767>=atomnum && atomnum>4095
             fprintf('32 base number system is recommended for atom id');base=32;
         elseif 4095>=atomnum && atomnum>999
             fprintf('16 base number system is recommended for atom id');base=16;
         elseif 999>=atomnum
             fprintf('10 base number system (decimalism) is recommended for atom id');
-        elseif atomnum<0 || atomnum>262143
-            error('Atom number is less than 0 or larger than 262143. If larger, please check it and modify code accordingly!')
+        elseif atomnum<= 14776335 || atomnum>238327
+            fprintf('Atom number is no more than 14776335 but larger than 238327. If larger, no element name is list in the number system, indicating 4 ASCII chars are used to encode')
+			base=62;
+		elseif atomnum > 14776335
+            error('Atom number exceeds 14776335, which can not be encoded. Please check it or contact the developer!')
         end
     end
 else

chemi_mechanism/xyz_car_pdb_filemaker.m

@@ -75,7 +75,35 @@
             elementname=eleswap{lib,2};
         end
         atomid_conv=SysConvert(tarBOinform{readline,1},base);
-        atomname=strcat(elementname,atomid_conv);
+        if elemax==2
+            if formatout==1 || formatout==2
+                if 238327>=atomnum
+                    atomname=strcat(elementname,atomid_conv);
+                else
+                    atomname=atomid_conv;
+                end
+            elseif formatout==3
+                if 3843>=atomnum
+                    atomname=strcat(elementname,atomid_conv);
+                else
+                    atomname=atomid_conv;
+                end
+            end
+        elseif elemax==1
+            if formatout==1 || formatout==2
+                if 14776335>=atomnum
+                    atomname=strcat(elementname,atomid_conv);
+                else
+                    atomname=atomid_conv;
+                end
+            elseif formatout==3
+                if 238327>=atomnum
+                    atomname=strcat(elementname,atomid_conv);
+                else
+                    atomname=atomid_conv;
+                end
+            end
+        end
 
         [trjrow,~]=size(trjdata);tartrjdata=[];
         for i=1:trjrow

lammpstrj2xyz_arc_pdb/Deconvolu_SysConvert.m

@@ -0,0 +1,12 @@
+%This function is used to transform a number to decimal system.
+function num_10base = Deconvolu_SysConvert(given_num_char,base)
+num_table = {'0','1','2','3','4','5','6','7','8','9',...
+    'a','b','c','d','e','f','g','h','i','j','k','l','m','n','o','p','q','r','s','t','u','v','w','x','y','z',...
+    'A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z'};
+[~,matches] = strsplit(given_num_char,num_table,'CollapseDelimiters',false);
+num_10base = 0;
+for i = 1:length(matches)
+    [~,num_true] = ismember(matches{i},num_table);
+    num_10base = num_10base + (num_true-1)*base^(length(matches)-i);
+end
+end

lammpstrj2xyz_arc_pdb/SysConvert.m

@@ -1,13 +1,15 @@
 %scrit file name SysConvert
 %purpose:
 %This function is used to convert a given number into an expected number
-%system. ASCII is used¡£
+%system. ASCII is used.
 function target_num=SysConvert(given_num,base)
-if given_num==round(given_num) && given_num>0 && base==round(base) && base>0
+if base > 62
+    error('The base for atom id encoding is larger than 62, unrecognizable char except 0-9£¬a-z£¬A-Z may be used. Please check it')
+end
+if given_num == round(given_num) && given_num > 0 && base == round(base) && base > 0
     control=1;remaindermat=[];
 else
-    control=0;
-    error('\nConversion of number system should be with an integer!!!');
+    error('\nThe base and atom id must be positive integer!');
 end
 
 while control
@@ -24,12 +26,15 @@
 
 atomid='';i=size(remaindermat,1);
 while i
-    if remaindermat(i,2)<=9
+    if remaindermat(i,2) <= 9 %0-9
         atomid=strcat(atomid,num2str(remaindermat(i,2)));
-    else
+    elseif remaindermat(i,2) > 9 && remaindermat(i,2) <= 35 %a-z
         atomid=strcat(atomid,char(remaindermat(i,2)+87));
+    elseif remaindermat(i,2) > 35 && remaindermat(i,2) <= 61 %A-Z
+        atomid=strcat(atomid,char(remaindermat(i,2)+29));
     end
     i=i-1;
 end
+
 target_num=atomid;
 

lammpstrj2xyz_arc_pdb/xyz_arc_filemaker_speedupMOLE.m

@@ -440,7 +440,35 @@
               elementname=eleswap{lib,2};
           end
           atomid_conv=SysConvert(tarBOinform{trjreadline,1},base);
-          atomname=strcat(elementname,atomid_conv);
+          if elemax==2
+            if formatout==1 || formatout==2
+                if 238327>=atomnum
+                    atomname=strcat(elementname,atomid_conv);
+                else
+                    atomname=atomid_conv;
+                end
+            elseif formatout==3
+                if 3843>=atomnum
+                    atomname=strcat(elementname,atomid_conv);
+                else
+                    atomname=atomid_conv;
+                end
+            end
+        elseif elemax==1
+            if formatout==1 || formatout==2
+                if 14776335>=atomnum
+                    atomname=strcat(elementname,atomid_conv);
+                else
+                    atomname=atomid_conv;
+                end
+            elseif formatout==3
+                if 238327>=atomnum
+                    atomname=strcat(elementname,atomid_conv);
+                else
+                    atomname=atomid_conv;
+                end
+            end
+        end
 
           [trjrow,~]=size(trjdata);tartrjdata=[];
           for i=1:trjrow

lammpstrj2xyz_arc_pdb/xyz_arc_pdb_filemaker.m

@@ -610,7 +610,35 @@
               elementname=eleswap{lib,2};
           end
           atomid_conv=SysConvert(tarBOinform{trjreadline,1},base);
-          atomname=strcat(elementname,atomid_conv);%
+          if elemax==2
+            if formatout==1 || formatout==2
+                if 238327>=atomnum
+                    atomname=strcat(elementname,atomid_conv);
+                else
+                    atomname=atomid_conv;
+                end
+            elseif formatout==3
+                if 3843>=atomnum
+                    atomname=strcat(elementname,atomid_conv);
+                else
+                    atomname=atomid_conv;
+                end
+            end
+        elseif elemax==1
+            if formatout==1 || formatout==2
+                if 14776335>=atomnum
+                    atomname=strcat(elementname,atomid_conv);
+                else
+                    atomname=atomid_conv;
+                end
+            elseif formatout==3
+                if 238327>=atomnum
+                    atomname=strcat(elementname,atomid_conv);
+                else
+                    atomname=atomid_conv;
+                end
+            end
+        end
 
           [trjrow,~]=size(trjdata);tartrjdata=[];
           for i=1:trjrow