Update to v1.5.HEADmaster

  The update to version 1.5 is rather substantial, and introduces some minor
  backward-incompatibilities:
    * The header "#!symbols" has been replaced by "#!virtual_fields"
    * Multiplying polynomials using the '*' symbol is no longer supported (or,
      rather, the symbolic capabilities of meankondo were enhanced, and the
      syntax has been changed).
    * 'meantools exp' has been removed (its functionality is now handled by
      other means)
    * 'meantoolds derive' has been replaced by 'meantools differentiate'

  * The symbolic capabilities were enhanced: polynomials can now be
    multiplied, added, exponentiated, and their logarithms can be taken
    directly in the configuration file.

  * The flow equation can now be processed after being computed using the
    various "#!postprocess_*" entries.

  * Deprecated kondo_preprocess.

  * Compute the mean using an LU decomposition if possible.

  * More detailed checks for syntax errors in configuration file.

  * Check that different '#!group' entries are indeed uncorrelated.

  * New flags in meankondo: '-p' and '-A'.

  * New tool: meantools expand.

  * Improve conversion to LaTeX using meantools-convert

  * Assign terms randomly to different threads.

  * Created vim files to implement syntax highlighting for configuration
    files.

  * Multiple bug fixes

1 files changed, 69 insertions, 8 deletions

diff --git a/src/polynomial.c b/src/polynomial.c
index d082b60..fae0c08 100644
--- a/src/polynomial.c
+++ b/src/polynomial.c
@@ -1,5 +1,5 @@
 /*
-Copyright 2015 Ian Jauslin
+Copyright 2015-2022 Ian Jauslin
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
@@ -27,6 +27,7 @@ limitations under the License.
 #include "array.h"
 #include "number.h"
 #include "fields.h"
+#include "parse_file.h"
 
 
 // allocate memory
@@ -368,7 +369,7 @@ int polynomial_prod_chain_nosimplify(Polynomial input, Polynomial* inout, Fields
   Int_Array out_monomial;
   Int_Array out_factor;
   Number out_num;
-  // save length of inout (which changes during the loop
+  // save length of inout (which changes during the loop)
   int inout_length=(*inout).length;
   // first position in input which can multiply a term of inout without vanishing
   int firstpos;
@@ -630,8 +631,8 @@ int remove_unmatched_plusminus(Polynomial* polynomial, Fields_Table fields){
 	  match_internals--;
 	}
       }
-      // don't remove a term containing symbols
-      else if(type==FIELD_SYMBOL){
+      // don't remove a term containing virtual_field
+      else if(type==FIELD_VIRTUAL){
 	match_internals=0;
 	break;
       }
@@ -1093,7 +1094,7 @@ int polynomial_print(Polynomial polynomial){
   Char_Array buffer;
   init_Char_Array(&buffer, STR_SIZE);
   polynomial_sprint(polynomial, &buffer);
-  printf("%s",buffer.str);
+  printf("%s",char_array_to_str_noinit(&buffer));
   free_Char_Array(buffer);
   return(0);
 }
@@ -1104,7 +1105,7 @@ int polynomial_print(Polynomial polynomial){
 #define PP_MONOMIAL_MODE 2
 #define PP_FACTOR_MODE 3
 #define PP_NUMBER_MODE 4
-int Char_Array_to_Polynomial(Char_Array str_polynomial,Polynomial* output){
+int Char_Array_to_Polynomial(Char_Array str_polynomial, Polynomial* output){
   // buffer
   char* buffer=calloc(str_polynomial.length+1,sizeof(char));
   char* buffer_ptr=buffer;
@@ -1115,6 +1116,7 @@ int Char_Array_to_Polynomial(Char_Array str_polynomial,Polynomial* output){
   int comment=0;
   int i,j;
   int parenthesis_count=0;
+  int ret;
 
   // allocate memory
   init_Polynomial(output,POLY_SIZE);
@@ -1174,6 +1176,10 @@ int Char_Array_to_Polynomial(Char_Array str_polynomial,Polynomial* output){
 	  init_Int_Array(&factor, MONOMIAL_SIZE);
 	  num=number_one();
 	}
+	else{
+	  fprintf(stderr,"syntax error: misplaced '+' in polynomial\n");
+	  exit(-1);
+	}
 	break;
 
       // enter monomial or factor mode
@@ -1181,6 +1187,10 @@ int Char_Array_to_Polynomial(Char_Array str_polynomial,Polynomial* output){
 	if(mode==PP_NULL_MODE){
 	  mode=PP_BRACKET_MODE;
 	}
+	else{
+	  fprintf(stderr,"syntax error: misplaced '[' in polynomial\n");
+	  exit(-1);
+	}
 	break;
       // factor mode
       case 'l':
@@ -1189,6 +1199,10 @@ int Char_Array_to_Polynomial(Char_Array str_polynomial,Polynomial* output){
 	  buffer_ptr=buffer;
 	  *buffer_ptr='\0';
 	}
+	else{
+	  fprintf(stderr,"syntax error: misplaced 'l' in polynomial\n");
+	  exit(-1);
+	}
 	break;
       // monomial mode
       case 'f':
@@ -1197,16 +1211,30 @@ int Char_Array_to_Polynomial(Char_Array str_polynomial,Polynomial* output){
 	  buffer_ptr=buffer;
 	  *buffer_ptr='\0';
 	}
+	else{
+	  fprintf(stderr,"syntax error: misplaced 'j' in polynomial\n");
+	  exit(-1);
+	}
 	break;
       // read monomial or factor
       case ']':
 	sscanf(buffer,"%d",&i);
+	ret=read_int(buffer,&i);
+	if(ret<0){
+	  fprintf(stderr,"syntax error: in polynomial, expected integer field or factor index, got '%s'\n",buffer);
+	  exit(-1);
+	}
+	  
 	if(mode==PP_FACTOR_MODE){
 	  int_array_append(i,&factor);
 	}
 	else if(mode==PP_MONOMIAL_MODE){
 	  int_array_append(i,&monomial);
 	}
+	else{
+	  fprintf(stderr,"syntax error: mismatched ']' in polynomial\n");
+	  exit(-1);
+	}
 	// switch back to null mode
 	mode=PP_NULL_MODE;
 	break;
@@ -1224,6 +1252,10 @@ int Char_Array_to_Polynomial(Char_Array str_polynomial,Polynomial* output){
 	  parenthesis_count++;
 	  buffer_ptr=str_addchar(buffer_ptr,str_polynomial.str[j]);
 	}
+	else{
+	  fprintf(stderr,"syntax error: misplaced '(' in polynomial\n");
+	  exit(-1);
+	}
 	break;
       case ')':
 	if(mode==PP_NUMBER_MODE){
@@ -1240,11 +1272,14 @@ int Char_Array_to_Polynomial(Char_Array str_polynomial,Polynomial* output){
 	    buffer_ptr=str_addchar(buffer_ptr,str_polynomial.str[j]);
 	  }
 	}
+	else{
+	  fprintf(stderr,"syntax error: mismatched ')' in polynomial\n");
+	  exit(-1);
+	}
 	break;
 
       // characters to ignore
       case ' ':break;
-      case '&':break;
       case '\n':break;
       
       // comments
@@ -1257,6 +1292,10 @@ int Char_Array_to_Polynomial(Char_Array str_polynomial,Polynomial* output){
 	  // write to buffer
 	  buffer_ptr=str_addchar(buffer_ptr,str_polynomial.str[j]);
 	}
+	else{
+	  fprintf(stderr,"syntax error: in polynomial, unrecognized character '%c'\n",str_polynomial.str[j]);
+	  exit(-1);
+	}
 	break;
       }
     }
@@ -1270,7 +1309,7 @@ int Char_Array_to_Polynomial(Char_Array str_polynomial,Polynomial* output){
 }
 
 // with str input
-int str_to_Polynomial(char* str_polynomial,Polynomial* output){
+int str_to_Polynomial(char* str_polynomial, Polynomial* output){
   Char_Array buffer;
   str_to_char_array(str_polynomial, &buffer);
   Char_Array_to_Polynomial(buffer, output);
@@ -1278,6 +1317,15 @@ int str_to_Polynomial(char* str_polynomial,Polynomial* output){
   return(0);
 }
 
+// check whether the polynomial is a constant
+int polynomial_is_number(Polynomial poly){
+  if(poly.length==0 || (poly.length==1 && poly.monomials[0].length==0 && poly.factors[0].length==0)){
+    return(1);
+  }
+  else{
+    return(0);
+  }
+}
 
 // -------------------- Polynomial_Matrix ---------------------
 
@@ -1307,3 +1355,16 @@ int free_Polynomial_Matrix(Polynomial_Matrix matrix){
   free(matrix.indices);
   return(0);
 }
+
+// check whether the entries are numbers
+int polynomial_matrix_is_numeric(Polynomial_Matrix matrix){
+  int i,j;
+  for(i=0;i<matrix.length;i++){
+    for(j=0;j<matrix.length;j++){
+      if(polynomial_is_number(matrix.matrix[i][j])==0){
+	return(0);
+      }
+    }
+  }
+  return(1);
+}