Thread: Error when trying to read and process larger files

Please post your code inside code tags.

Jim

What is this weird phenomenon? What does "unable to proceed" mean? Also, I don't see any attached files.

When I run your code through the debugger it segfaults in your void thermoData(void) function at this line:

Code:

				a[k][14]=atof(buff2);

The value of k at this point was 774976307 which is clearly out of bounds for this array.

What does the smaller file that worked actually contain?

What are you trying to write to your Sthermo.dat output file in this function?

Jim

Good lord... I had a look at your code... Who on earth taught you to write code like that?

1) Try to minimize the use of global variables... that's way ridiculous.
2) Every function is void function (void) which is just crap lazy coding.
3) The layout of your source is practically unreadable... learn proper formatting and indentation
4) The only place you didn't use void was the one place you should it's... int main (void)

Really... You gotta clean that up....

Compile with warnings cranked up to the max, then make sure you fix them all. I got the following, which is definitely a problem:

file.c:731: warning: function returns address of local variable

That's in your str_replace function. You can't return "buffer", since that's basically a pointer to a local variable. Once the function returns, you have no idea what is actually at that address.

Tater is right, your code is quite a mess. I know you don't have a heavy programming background, so don't take it too hard, but you need some clean up.

• Read about why globals are evil here.
• Also, you shouldn't use goto. At least use break or continue to get out of a loop early or skip to the next iteration.
• You only have 2 functions under 100 lines. Try to split those massive functions up into smaller chunks that make it easier to read.

Originally Posted by anduril462

Compile with warnings cranked up to the max, then make sure you fix them all. I got the following, which is definitely a problem:

That's in your str_replace function. You can't return "buffer", since that's basically a pointer to a local variable. Once the function returns, you have no idea what is actually at that address.

Tater is right, your code is quite a mess. I know you don't have a heavy programming background, so don't take it too hard, but you need some clean up.

• Read about why globals are evil here.
• Also, you shouldn't use goto. At least use break or continue to get out of a loop early or skip to the next iteration.
• You only have 2 functions under 100 lines. Try to split those massive functions up into smaller chunks that make it easier to read.

Thanks for the comment. The str_replace function is actually a function I copy off from a website, of which I have credited in my code along with the link which it could be found. I do not have issues using it though. I tried to return *buffer though, but it breaks.

I tried to avoid using "goto" at first but I don't seem to get it work the way I want using break and continue, sort of a last resort. After I got everything working finally though I may go back to fix that up. Thought to breaking them out into smaller chunks as well, but as I got it working the way I want, I don't want to change it for the time being.

Other than the warnings and the messy code of which I will look them up to try to make it better, do you all face what I face, (i.e. the program breaks when I try to run it - it doesn't reach "press any key to continue." at all when I read the larger files but it does for the smaller files)? Could it be my weaker computer?

It's late here and I am about to sleep, will check back this thread the next day and also will try some cleaning up, too!

Originally Posted by tanjinjack

Yes, it indeed needs some cleaning up. I am sorry for the mess.
Some of the global variables are obsolete as I manage to find a better way for my purposes, which I could clean up later. Could the whole load of global variables be a problem as well?

Is there any reasons that I should avoid using void?

What you should do is try to minimize the use of global variables into non-existence.

Define a minimum set of variables at the top of each function.

Each function should perform a specific single task on variables passed in and return the results on it's way out... Here's a trivial example...

Code:

 
#include <stdio.h>

// calculate loop load
int LoopMultiply(int Bias, int Preload)
   { int Result = 0;  // return value
      int x;          // loop counter
      for (x = 0; x < Bias; x++)
         { Result += x * Preload; }
      return Result; }

// entry point
int main (void)
  {  int Loops = 5;       // active loop count
      int Prefactor = 6;  // preload factor
      int Load = 0;       // calculation result
     
      Load = LoopMultiply(Loops,Prefactor);
      printf("System load = %d", Load);
      
     return 0; }

The design of the lanugage is such that raw values go int the top of your function and results come out the bottom. Your programs run by passing values around and operating on them.

The problem with using void function (void) for everything is that all those global variables are at risk of being modified in ways you won't understand... a buffer overflow, an integer overflow, bad memory management etc. can all affect the validity of global values. The more encapsulated your code is the less the risk of catastrophic failure for untraceable reasons.

The extensive use of global variables has been frowned upon since GWBASIC was largely replaced by Pascal... in the late 1970s.

Moreover... indentation, a simple text setup operation --typing skill-- can go a very long way towards making code more readable. It is a worthwhile skill and should be a habit... especially if it's likely you're going to have to come back to this code in a couple of years and update it.

Indent style - Wikipedia, the free encyclopedia

The same is true of commenting... don't be afraid to type a line or two to say what a section of code is doing. *Especially* if it's effect is not entirely obvious.

Never in my life have I seen so many arrays. Why do I think you really need to make use of some structs here?

The code, indented:

Code:

#include <stdio.h>
#include <stdlib.h>
#include <string.h>

#define nSpecies  160
#define numForwardRxn 1540

void fetchRxn(void);
void processRxn(void);
void thermoData(void);
char *replace_str(char *str, char *orig); //credit to itsme86 from linuxquestions.org "http://goo.gl/F3YpH"//

char speciesName[nSpecies][25];
double ArrhFac[numForwardRxn];
double tempN[numForwardRxn];
double energyAct[numForwardRxn];
double thermo[nSpecies][15];
int numRxnThisSpc[nSpecies];
int rxnID_SpcN[nSpecies][numForwardRxn];
int stoichioNum[nSpecies][numForwardRxn];
int numReactSpc[numForwardRxn];
int numProdtSpc[numForwardRxn];
int reactSpcIDNum[numForwardRxn][5];
int prodtSpcIDNum[numForwardRxn][5];
double cpCoeff4EqmConst[nSpecies][15];
int numPressuDpdRxn=0;
int rxnID_PrDpdRxn[numForwardRxn];
double koa[numForwardRxn];
double kotn[numForwardRxn];
double koe[numForwardRxn];
double alfa[numForwardRxn];
double tts[numForwardRxn];
double ts[numForwardRxn];
double tss[numForwardRxn];

int nn[numForwardRxn];
char speciesTBSR[numForwardRxn][nSpecies][30];
double lpl[numForwardRxn][3];
double troe[numForwardRxn][4];
char rxnFormula[numForwardRxn][110];

char buff[256];

FILE *fp;


int main()
{
    fetchRxn();
    puts("past here?");
    processRxn();

    thermoData();

    return 0;
}


void fetchRxn(void)
{
    int i=0,j[numForwardRxn],k=0, TBSRcount[numForwardRxn], LPLcount[numForwardRxn],
        n=0,numTBSRonly=0, numLPLonly=0,
        b=0,c=0,LPLcheck=0,
        e=0;
    int RxnTBSR[numForwardRxn];
    FILE *fRxn, *fatne,*frcpm, *ftbsr;
    int RxnLPL[numForwardRxn];


    double coeffTBSR[numForwardRxn][nSpecies];
    char dummy[30];
    for(c=0;c<numForwardRxn;c++)
    {
        j[c]=0;
        RxnTBSR[c]=0;
        LPLcount[c]=0;
        TBSRcount[c]=0;
        for(e=0;e<nSpecies;e++)
            coeffTBSR[c][e]=0;

    }


    fp=fopen("try2.out","r");
    while ( fgets( buff, sizeof(buff)-1, fp ) != NULL )
    {


        if(sscanf(buff,"%d. %s %lf %lf %lf",&nn[i],rxnFormula[i],&ArrhFac[i],&tempN[i],&energyAct[i])==5)
        {

            sprintf(rxnFormula[i],"%s",(replace_str((replace_str(rxnFormula[i], "(+M)")),"(+M)")));
            sprintf(rxnFormula[i],"%s",(replace_str((replace_str(rxnFormula[i], "+M")),"+M")));
            // sprintf(rxnFormula[i],"%s",(replace_str((replace_str(rxnFormula[i], "<")),"<")));
            // sprintf(rxnFormula[i],"%s",(replace_str((replace_str(rxnFormula[i], ">")),">")));

            // printf("%2d - %25s - %10.3e %10.3e %10.3e\n",nn[i],rxnFormula[i],ArrhFac[i],tempN[i],energyAct[i]);
            // system("PAUSE");
            i++;
            j[i]=0;
            LPLcheck=0;

        }

        else if(strstr(buff,"Enhanced")!=NULL)
        {
            if(j[i]==0)//&&LPLcheck==0)
            {

                RxnTBSR[numTBSRonly]=i;
//printf("%d,%d\n",numTBSRonly,RxnTBSR[numTBSRonly]);
                numTBSRonly++;
                //printf("%d:TBSR includes %d\n",numTBSRonly-1,RxnTBSR[numTBSRonly-1]);
            }
            //else if(j==0&&LPLcheck==1)

            sscanf(buff,"%s %*s %*s %s",speciesTBSR[i][j[i]],dummy); //coeffTBSR[RxnID][j]
            {
                coeffTBSR[i][j[i]]=atof(dummy);
                //if(LPLcheck==0)
                //printf("3rd body surface rxn for rxn %d, %s species with enhancement of %e\n",RxnTBSR[numTBSRonly-1],speciesTBSR[i][j],coeffTBSR[i][j]);

                //if(LPLcheck==0)

                j[i]++;
                TBSRcount[numTBSRonly-1]=j[i];
                // if(i==43)
                //printf("j %d in TBSRRxn %d\n",TBSRcount[numTBSRonly-1],numTBSRonly-1);

            }


        }
        else if(strstr(buff,"Low pressure limit")!=NULL)
        {
            sscanf(buff,"%*s %*s %*s\t%lf\t%lf\t%lf",&lpl[i][0],&lpl[i][1],&lpl[i][2]);
            //printf("Low pressure limit: %e %e %e\n",lpl[i][0],lpl[i][1],lpl[i][2]);
//tell "Enhanced by" to delete the LPL off//
//LPLcheck=1;
            {
                RxnLPL[numLPLonly]=i;
                // LPLcount[numLPLonly]=TBSRcount[numTBSRonly-1];
                LPLcount[numLPLonly]=j[i];
                numTBSRonly--;

                numLPLonly++;

//            goto skip;
            }


        }


        else if(strstr(buff,"TROE centering")!=NULL)
        {

            numLPLonly--;
            sscanf(buff,"%*s %*s\t%lf\t%lf\t%lf\t%lf",&troe[i][0],&troe[i][1],&troe[i][2],&troe[i][3]);
            // printf("%E %E %E %E\n",troe[i][0],troe[i][1],troe[i][2],troe[i][3]);
            //printf("Low pressure limit: %e %e %e\n",lpl[i][0],lpl[i][1],lpl[i][2]);
            koa[numPressuDpdRxn]=lpl[i][0]; lpl[i][0]=0; //zero to avoid messing up
            kotn[numPressuDpdRxn]=lpl[i][1]; lpl[i][1]=0;
            koe[numPressuDpdRxn]=lpl[i][2]; lpl[i][2]=0;
            alfa[numPressuDpdRxn]=troe[i][0];
            tts[numPressuDpdRxn]=troe[i][1];
            ts[numPressuDpdRxn]=troe[i][2];
            tss[numPressuDpdRxn]=troe[i][3];
            rxnID_PrDpdRxn[numPressuDpdRxn]=(i); //first i is zero, may need i instead of (i-1)//
            // printf("%d. pressure dependent rxn is %d\n",numPressuDpdRxn,i);
            numPressuDpdRxn++;

        }

    }

    remove("Reaction.txt");
    fRxn=fopen("Reaction.txt","a+");
    for(i=0;i<numForwardRxn;i++)  fprintf(fRxn,"%s\n",rxnFormula[i]);
    fclose(fRxn);
    remove("atne.txt");
    fatne=fopen("atne.txt","a+");
    for(i=0;i<numForwardRxn;i++) fprintf(fatne,"%E\n",ArrhFac[i]);
    for(i=0;i<numForwardRxn;i++) fprintf(fatne,"%E\n",tempN[i]);
    for(i=0;i<numForwardRxn;i++) fprintf(fatne,"%E\n",energyAct[i]);
    fclose(fatne);

    remove("rcpm.txt");
    frcpm=fopen("rcpm.txt","a+");
    for(i=0;i<numPressuDpdRxn;i++) fprintf(frcpm,"%d\n",rxnID_PrDpdRxn[i]);
    fclose(frcpm);
    remove("Pm.txt");
    frcpm=fopen("Pm.txt","a+");
    for(i=0;i<numPressuDpdRxn;i++) fprintf(frcpm,"%E\n",koa[i]);
    for(i=0;i<numPressuDpdRxn;i++) fprintf(frcpm,"%E\n",kotn[i]);
    for(i=0;i<numPressuDpdRxn;i++) fprintf(frcpm,"%E\n",koe[i]);
    for(i=0;i<numPressuDpdRxn;i++) fprintf(frcpm,"%E\n",alfa[i]);
    for(i=0;i<numPressuDpdRxn;i++) fprintf(frcpm,"%E\n",tts[i]);
    for(i=0;i<numPressuDpdRxn;i++) fprintf(frcpm,"%E\n",ts[i]);
    for(i=0;i<numPressuDpdRxn;i++) fprintf(frcpm,"%E\n",tss[i]);

    remove("tbsr.txt");
    ftbsr=fopen("tbsr.txt","a+");
    for(i=0;i<numTBSRonly;i++)
    {
        fprintf(ftbsr,"%d\n",RxnTBSR[i]);
//printf("TBSR includes %d \n",RxnTBSR[i]);

    }
    fclose(ftbsr);
    remove("tbsrcount.txt");
    ftbsr=fopen("tbsrcount.txt","a+");
    for(i=0;i<numTBSRonly;i++)
    {
        fprintf(ftbsr,"%d\n",j[RxnTBSR[i]]);
    }
    remove("Stbsr.txt");
    ftbsr=fopen("Stbsr.txt","a+");
    for(i=0;i<numTBSRonly;i++)
    {
        //for(j=0;j<TBSRcount[i];j++)
        //printf("i=%d, TBSRcount=%d\n",RxnTBSR[i],TBSRcount[i]);
        for(k=0;k<TBSRcount[i];k++) fprintf(ftbsr,"%s\n",speciesTBSR[RxnTBSR[i]][k]);
    }
    for(i=0;i<numTBSRonly;i++)
    {

        for(k=0;k<TBSRcount[i];k++) fprintf(ftbsr,"%E\n",coeffTBSR[RxnTBSR[i]][k]);
    }
    fclose(ftbsr);

    FILE *flpl;
    remove("lpl.txt");
    remove("lplcount.txt");
    remove("Slpl.txt");
    flpl=fopen("lpl.txt","a+");
    for(i=0;i<numLPLonly;i++)
    {
        fprintf(flpl,"%d\n",RxnLPL[i]);
        //printf("%d,LPLcount = %d\n",RxnLPL[i],LPLcount[numLPLonly]);
    }
    fclose(flpl);
    flpl=fopen("lplcount.txt","a+");
    for(i=0;i<numLPLonly;i++)
        fprintf(flpl,"%d\n",j[RxnLPL[i]]);
    fclose(flpl);
    flpl=fopen("Slpl.txt","a+");
    for(i=0;i<numLPLonly;i++)
    {
        //for(k=0;j<LPLcount[i];k++)
        //printf("i=%d, LPLcount=%d\n",RxnLPL[i],LPLcount[i]);
        for(k=0;k<LPLcount[i];k++) fprintf(flpl,"%s\n",speciesTBSR[RxnLPL[i]][k]);
    }
    for(i=0;i<numLPLonly;i++)
    {

        for(k=0;k<LPLcount[i];k++) fprintf(flpl,"%E\n",coeffTBSR[RxnLPL[i]][k]);
    }
    fclose(flpl);
    remove("coefflpl.txt");
    flpl=fopen("coefflpl.txt","a+");
    for(i=0;i<numLPLonly;i++) fprintf(flpl,"%E\n",lpl[RxnLPL[i]][0]);
    for(i=0;i<numLPLonly;i++) fprintf(flpl,"%E\n",lpl[RxnLPL[i]][1]);
    for(i=0;i<numLPLonly;i++) fprintf(flpl,"%E\n",lpl[RxnLPL[i]][2]);
    fclose(flpl);

}


void processRxn(void)
{
    puts("here?");
    int hh[nSpecies];
    int i=0,j=0,k=0,
        n=0,p=0,a=0,
        b=0,c=0,d=0,
        e=0;
    char buffer[80];
    char temp[2*numForwardRxn][60];
    char *sep;
    char *sep2;
    FILE *fp,*fp2;
    remove("Species.txt");
    remove("nva.dat");
    remove("va1.dat");
    remove("va2.dat");
    remove("sre.dat");
    remove("spr.dat");
    int countspecies[nSpecies];
    int countspecies2[nSpecies];
    int va1[nSpecies][2*numForwardRxn];
    int va2[nSpecies][2*numForwardRxn];
    int va2temp;
    double rateRxnOA[numForwardRxn];
    double concS[nSpecies];
    double kRxn[2*numForwardRxn];
    char rxnstring[2*numForwardRxn];
    int srepr[2*numForwardRxn];
    int sre[numForwardRxn];
    int spr[numForwardRxn];
    int srepr2[2*numForwardRxn];
    int sre2[3*numForwardRxn];
    int spr2[3*numForwardRxn];

    for(i=0;i<nSpecies;i++)
    {
        countspecies[i]=0;
        countspecies2[i]=countspecies[i];
        hh[i]=0;

        for(j=0;j<numForwardRxn;j++)
        {
            rxnID_SpcN[i][j]=0;
            stoichioNum[i][j]=0;

        }
    }

    for(i=0;i<2*numForwardRxn;i++)
        srepr[i]=0;
    j=0;
    fp=fopen("Reaction.txt","r");
    while ((fgets(buffer,sizeof(buffer)-1,fp))!=NULL)
    {

        //printf("something: %s\n",rxnFormula[i]);
        //system("PAUSE");
        sep=strtok(buffer,"<=>\n"); //seperate the strings with delimiter, '=' and '\n'//

//assign buffer into temporary array//
        while(sep!=NULL)
        {

            strcpy(temp[n],sep);
//printf("%3d)%s\n",n,temp[n]);
            n++;
            sep=strtok(NULL,"<=>\n");
        }

    }
    fclose(fp);
//splitting temporary array into species//
    for(p=0;p<n;p++)
    {
//printf("splitting <%s>\n",temp[p]);

        sep2=strtok(temp[p],"+");
        while(sep2!=NULL)
        {
            va2temp=1;
            if(sscanf(sep2,"%d%s", &va2temp,sep2)==2)
            {
                //printf("va2temp %d\t",va2temp);
                //printf("va2 correct\n");
            }
            //else
            {

            }

            //check for duplicate//
            for(i=0;i<j;i++)
            {


                if(strcmp(sep2,speciesName[i])==0) //compare strings,0 indicates same strings//
                {

                    //add counter to know how many times the species participate in the mechanism//
                    countspecies[i]++;
                    //printf("in strcmp: j=%3d,%7s participate in rxn ID: %d\n",i,species[i],p);
                    //assign this duplicate species[i] into va1[i][h[i]]//
                    va1[i][hh[i]]=p;

                    //if (va2temp!=1)
                    {
                        va2[i][hh[i]]=va2temp;
                    }
                    //else va2[i][h[i]]=1;

                    for(k=0;k<hh[i];k++)
                    {
                        if(va1[i][hh[i]]==va1[i][k])
                        {
                            goto skipwriteva1;
                        }
                    }

                    hh[i]++;
                  skipwriteva1:

                    //printf(">>>>duplicate found<<<<\n");
                    //printf("add one counter to %s\n",species[i]);

                    // srepr2[c++]=i;

                    goto skipcopy; //skip writing in the species if there is duplicate//
                }

            }
            //check for duplicate end//

            strcpy(speciesName[j],sep2);  //assign the splitted token as species after checking for duplicate//

            countspecies[j]++;

            //assign this species[j] into the va1[species j][h[j]]//
            //printf("           j=%3d,%7s participate in rxn ID: %d\n",j,species[j],p);
            va1[j][hh[j]]=p;

            //if (va2temp!=1)
            {
                va2[i][hh[j]]=va2temp;
            }
            //else va2[i][h[j]]=1;

            //srepr2[c++]=j;
            hh[j]++;
            j++;
          skipcopy:

//assign va2 value//

//for sre and spr, count how many reactants/products//




            if(va2temp!=1)
            {
                srepr[p]+=(va2temp-1);


            }
            srepr[p]++;

            sep2=strtok(NULL,"+");

        }



//ensure all counter will add up to ONE only//
        for(i=0;i<j;i++)
        {
            if(countspecies[i]>(countspecies2[i]+1))
            {
                countspecies[i]=countspecies2[i]+1;
            }
            countspecies2[i]=countspecies[i];

        }

    }

//printf("\n");

//print out the species//
    fp=fopen("Species.txt","a+");
    for (i=0;i<j;i++)
    {
        fprintf(fp,"%s\n",speciesName[i]);
        //printf("species %2d: <%s>\n",i+1,speciesName[i]);
    }
    fclose(fp);
//printf("\n");
//print out the number of times each species occurs in//

    fp=fopen("nva.dat","a+");
    for(i=0;i<j;i++)
    {
        fprintf(fp,"%d\n",countspecies[i]);
//printf("%3d: %7s found %3d times in total\n",i+1,speciesName[i],countspecies[i]);
        numRxnThisSpc[i]=countspecies[i];
    }
    fclose(fp);

//print va1//
    fp=fopen("va1.dat","a+");
//adjust va1, from say 1,2,3,4,5,6,7,8,9,10 into 1,3,5,7,9,2,4,6,8,10//
    for(i=0;i<j;i++)
    {
        for(k=0;k<hh[i];k++)
        {
            va1[i][k]=va1[i][k]+1;
            if((va1[i][k])%2==0)
            {
                //even//

                (va1[i][k])=(va1[i][k]+1)/2+numForwardRxn;
            }
            else
            {
                //odd//
                (va1[i][k])=va1[i][k]/2+1;
            }
            rxnID_SpcN[i][k]=va1[i][k];
//printf("%4d",va1[i][k]);
            fprintf(fp,"%d\t",va1[i][k]);
        }
        fprintf(fp,"\n");
//printf("\n");
    }
    fclose(fp);
//printf("\n\n");
    fp=fopen("va2.dat","a+");
    for(i=0;i<j;i++)
    {
        for(k=0;k<hh[i];k++)
        {
            if(va1[i][k]<=numForwardRxn) //adjust, give negative for those at the LHS of a reaction//
                va2[i][k]=-va2[i][k];
            stoichioNum[i][k]=va2[i][k];
            //printf("%4d",va2[i][k]);
            fprintf(fp,"%d\t",va2[i][k]);
        }
        fprintf(fp,"\n");
        //printf("\n");
    }
    fclose(fp);

//building the rateRxnOA=kRxn*conc-kRxn*conc
    for(i=0;i<2*numForwardRxn;i++)
    {
        // printf("species involved in rxn ID %d includes:\t",i+1);

        for(k=0;k<nSpecies;k++)
        {
            //while (va1[k][a]!=NULL)
            for(a=0;a<hh[k];a++)
            {
                if(va1[k][a]==i+1)
                {
                    c=0;
                    while(c<abs(va2[k][a]))
                    {
                        //printf("%s\t",speciesName[k]);
                        c++;

                        if(i<numForwardRxn)
                            sre2[d++]=k;
                        else
                            spr2[e++]=k;
                    }
                }
            }
        }
        //printf("\n");
    }



    b=0;
//fixing spr and sre, 1st part//
    fp=fopen("sre.dat","a+");
    fp2=fopen("spr.dat","a+");
    for(i=0;i<numForwardRxn;i++)
    {
        sre[i]=srepr[b]; //here got problem!!, or up there for srepr there//
        spr[i]=srepr[b+1];
        b+=2;

        // printf("sre:%d\tspre:%d\n",sre[i],spr[i]);
        numReactSpc[i]=sre[i];
        numProdtSpc[i]=spr[i];
        fprintf(fp,"%d\n",sre[i]);
        //printf("%d\t",spr[i]);
        fprintf(fp2,"%d\n",spr[i]);

    }

//printf("\n\n");


    for(i=0;i<d;i++)
//printf("%d\t",sre2[i]+1)
        ;
    k=0;
    for(i=0;i<numForwardRxn;i++)
        for(j=0;j<numReactSpc[i];j++)
        {
			reactSpcIDNum[i][j]=(sre2[k++]+1);
			//printf("%d\t",reactSpcIDNum[i][j]);
            fprintf(fp,"%d\n",reactSpcIDNum[i][j]);
        }
//printf("\n\n");

    for(i=0;i<numForwardRxn;i++)
        for(j=0;j<numProdtSpc[i];j++)
        {
			prodtSpcIDNum[i][j]=(spr2[k++]+1);
            fprintf(fp2,"%d\n",prodtSpcIDNum[i][j]);
        }
    fclose(fp);
    fclose(fp2);


}
//processRxn end.




void thermoData(void)
{

    char buff[82];
    char buff2[30];
    char tspecies[nSpecies][10];
    int n=0,m=0;
    int i=0,k=0;
    double a[nSpecies][15];

    int len;
    //FILE *fp;
    fp=fopen("thermo30.dat","r");

    while ( fgets( buff, sizeof(buff)-1, fp ) != NULL)
    {
//printf("something %d\n",m++);
        len=strlen(buff);
        if(len>75)
        {
            if(i%4==0)
            {
                sscanf(buff,"%s",tspecies[k]);
                //printf("%s\n",temp[k]);
                strncpy(buff2,&buff[67],11);
                a[k][14]=atof(buff2);

            }



            if(i%4==1)
            {
//puts(buff);

                {

                    for(n=0;n<5;n++)
                    {
                        sscanf(&buff[n*15],"%lf",&a[k][n]);
                        //  printf("%e\n",a[k][n]);
                    }

                }

//printf("\n\n");
            }



            if(i%4==2)
            {
//puts(buff);

                {

                    for(n=0;n<5;n++)
                    {
                        sscanf(&buff[n*15],"%lf",&a[k][n+5]);
                        // printf("%e\n",a[k][n+5]);
                    }

                }

//printf("\n\n");
            }




            if(i%4==3)
            {
//puts(buff);
                for(n=0;n<4;n++)
                {
                    sscanf(&buff[n*15],"%lf",&a[k][n+10]);
                    //printf("%e\n",a[k][n+10]);
                }
                k++;
//printf("\n\n");
            }
            i++;

        }

    }

    fclose(fp);
    remove("Sthermo.dat");
    fp=fopen("Sthermo.dat","a+");
    for(m=0;m<nSpecies;m++)
    {
        for(i=0;i<nSpecies;i++)
            if(strcmp(speciesName[m],tspecies[i])==0)
            {
                for(k=0;k<15;k++)
                    thermo[m][k]=a[i][k];
            }
//printf("%s has the following coeffs:\n",speciesName[m]);
        for(k=0;k<15;k++)
//printf("%e\n", thermo[m][k]);
            if(k<14)
                fprintf(fp,"%.8E\n",thermo[m][k]);
        cpCoeff4EqmConst[m][k]=thermo[m][k];
    }
    for(m=0;m<nSpecies;m++)
        fprintf(fp,"%.8E\n",thermo[m][14]);
    fclose(fp);



}


char *replace_str(char *str, char *orig)
{
    char buffer[4096];
    char *pp;

    if(!(pp = strstr(str, orig)))  // Is 'orig' even in 'str'?
        return str;

    strncpy(buffer, str, pp-str); // Copy characters from 'str' start to 'orig' st$
    buffer[pp-str] = '\0';

    sprintf(buffer+(pp-str), "%s", pp+strlen(orig));

    return buffer;
}