I am not sure why you are only seeing 2 generators. I was not able to duplicate 
your result. I copied and pasted the data from your e-mail into a new case file 
and get the result below (different solutions for the cases with and without 
reactive costs) …

    Ray


>> mpopt = mpoption('opf.ac.solver', 'MIPS', 'out.suppress_detail', 1);
>> mpc = loadcase('case5Stagg')

mpc = 

    version: '2'
    baseMVA: 100
        bus: [5x13 double]
        gen: [3x21 double]
     branch: [7x13 double]
    gencost: [6x7 double]

>> r = runopf(mpc, mpopt)

MATPOWER Version 5.1, 20-Mar-2015 -- AC Optimal Power Flow
MATLAB Interior Point Solver -- MIPS, Version 1.2, 20-Mar-2015
 (using built-in linear solver)
Converged!

Converged in 0.41 seconds
Objective Function Value = 2021.47 $/hr
================================================================================
|     System Summary                                                           |
================================================================================

How many?                How much?              P (MW)            Q (MVAr)
---------------------    -------------------  -------------  -----------------
Buses              5     Total Gen Capacity     250.0        -200.0 to 250.0
Generators         3     On-line Capacity       250.0        -200.0 to 250.0
Committed Gens     3     Generation (actual)    168.7              76.2
Loads              4     Load                   165.0              79.7
  Fixed            4       Fixed                165.0              79.7
  Dispatchable     0       Dispatchable          -0.0 of -0.0      -0.0
Shunts             0     Shunt (inj)             -0.0               0.0
Branches           7     Losses (I^2 * Z)         3.74             11.23
Transformers       0     Branch Charging (inj)     -               14.7
Inter-ties         0     Total Inter-tie Flow     0.0               0.0
Areas              1

                          Minimum                      Maximum
                 -------------------------  --------------------------------
Voltage Magnitude   0.991 p.u. @ bus 5          1.050 p.u. @ bus 1   
Voltage Angle      -4.74 deg   @ bus 5          0.00 deg   @ bus 1   
P Losses (I^2*R)             -                  1.34 MW    @ line 2-5
Q Losses (I^2*X)             -                  4.01 MVAr  @ line 2-5
Lambda P           14.45 $/MWh @ bus 1         15.42 $/MWh @ bus 5   
Lambda Q            0.05 $/MWh @ bus 1          0.40 $/MWh @ bus 5   

r = 

    version: '2'
    baseMVA: 100
        bus: [5x17 double]
        gen: [3x25 double]
     branch: [7x21 double]
    gencost: [6x7 double]
      order: [1x1 struct]
         om: [1x1 opf_model]
          x: [16x1 double]
         mu: [1x1 struct]
          f: 2.0215e+03
        var: [1x1 struct]
        nln: [1x1 struct]
         et: 0.4122
    success: 1
        raw: [1x1 struct]

>> mpc1 = mpc;           
>> mpc1.gencost = mpc1.gencost(1:3, :);                                
>> r = runopf(mpc1, mpopt)             

MATPOWER Version 5.1, 20-Mar-2015 -- AC Optimal Power Flow
MATLAB Interior Point Solver -- MIPS, Version 1.2, 20-Mar-2015
 (using built-in linear solver)
Converged!

Converged in 0.08 seconds
Objective Function Value = 2012.97 $/hr
================================================================================
|     System Summary                                                           |
================================================================================

How many?                How much?              P (MW)            Q (MVAr)
---------------------    -------------------  -------------  -----------------
Buses              5     Total Gen Capacity     250.0        -200.0 to 250.0
Generators         3     On-line Capacity       250.0        -200.0 to 250.0
Committed Gens     3     Generation (actual)    168.7              75.8
Loads              4     Load                   165.0              79.7
  Fixed            4       Fixed                165.0              79.7
  Dispatchable     0       Dispatchable          -0.0 of -0.0      -0.0
Shunts             0     Shunt (inj)             -0.0               0.0
Branches           7     Losses (I^2 * Z)         3.69             11.07
Transformers       0     Branch Charging (inj)     -               14.9
Inter-ties         0     Total Inter-tie Flow     0.0               0.0
Areas              1

                          Minimum                      Maximum
                 -------------------------  --------------------------------
Voltage Magnitude   1.001 p.u. @ bus 5          1.050 p.u. @ bus 1   
Voltage Angle      -4.84 deg   @ bus 5          0.00 deg   @ bus 1   
P Losses (I^2*R)             -                  1.32 MW    @ line 2-5
Q Losses (I^2*X)             -                  3.95 MVAr  @ line 2-5
Lambda P           14.45 $/MWh @ bus 1         15.38 $/MWh @ bus 5   
Lambda Q           -0.00 $/MWh @ bus 1          0.25 $/MWh @ bus 5   

r = 

    version: '2'
    baseMVA: 100
        bus: [5x17 double]
        gen: [3x25 double]
     branch: [7x21 double]
    gencost: [3x7 double]
      order: [1x1 struct]
         om: [1x1 opf_model]
          x: [16x1 double]
         mu: [1x1 struct]
          f: 2.0130e+03
        var: [1x1 struct]
        nln: [1x1 struct]
         et: 0.0820
    success: 1
        raw: [1x1 struct]





> On May 31, 2016, at 2:52 AM, Saranya A <[email protected]> wrote:
> 
> Hi,
> I am using MATPOWER 5.1.
> 
> I am trying to run opf for a 5 bus system mentioned in a book by "Stagg and 
> El-Abiad".
> 
> Following is my input system data:
> 
> function mpc = case5Stagg
> %CASE5Stagg This represents the 5 bus system in Stagg El-Abiad book 
> 
> %% MATPOWER Case Format : Version 2
> mpc.version = '2';
> 
> %%-----  Power Flow Data  -----%%
> %% system MVA base
> mpc.baseMVA = 100;
> 
> %% bus data
> %     bus_i   type    Pd      Qd      Gs      Bs      area    Vm      Va      
> baseKV  zone    Vmax    Vmin
> mpc.bus = [
>       1   3   0   0   0   0   1   1.05    0   230 1   1.05    0.95;
>     2   2   20  9.7   0   0   1   1   0   230 1   1.05    0.95;
>     3   1   45  22    0   0   1   1   0  230  1   1.05    0.95;
>     4   2   40  19    0   0   1   1   0   230 1   1.05    0.95;
>     5   1   60  29    0   0   1   1   0   230 1   1.05    0.95;
> ];
> 
> %% generator data
> %     bus     Pg      Qg      Qmax    Qmin    Vg      mBase   status  Pmax    
> Pmin    Pc1     Pc2     Qc1min  Qc1max  Qc2min  Qc2max  ramp_agc        
> ramp_10 ramp_30 ramp_q  apf
> mpc.gen = [
>       1       100     20      100     -100    1       100     1       125 20  
> 0       0       0       0       0       0       0       0       0       0     
>   0;
>       2       80      20      100     -100    1       100     1       125 20  
> 0       0       0       0       0       0       0       0       0       0     
>   0;
>     4   0   50  50  0   1   100 1   0   0   0 0       0       0       0       
> 0       0       0       0       0       0;
> ];
> 
> %% branch data
> %     fbus    tbus    r       x       b       rateA   rateB   rateC   ratio   
> angle   status  angmin  angmax
> mpc.branch = [
>       1       2       0.02    0.06    0.03    180     180     180     0       
> 0       1       -360    360;
>     1   3   0.08    0.24    0.025   180 180 180 0   0   1   -360    360;
>     2   3   0.06    0.18    0.02    180 180 180 0   0   1   -360    360;
>     2   4   0.06    0.18    0.02    180 180 180 0   0   1   -360    360;
>     2   5   0.04    0.12    0.01    180 180 180 0   0   1   -360    360;
>     3   4   0.01    0.03    0.01    180 180 180 0   0   1   -360    360;
>     4   5   0.08    0.24    0.025   180 180 180 0   0   1   -360    360;      
> ];
> 
> %%-----  OPF Data  -----%%
> %% generator cost data
> %     1       startup shutdown        n       x1      y1      ...     xn      
> yn
> %     2       startup shutdown        n       c(n-1)  ...     c0
> mpc.gencost = [
>       2       0       0       3   0.0420 7.50 75;
>       2       0       0       3   0.0420 7.50 75;
>     2   0   0   3   0   0   0; 
>     2   0   0   3   0.0043  -0.0383 0.2992; 
>     2   0   0   3   0.0043  -0.0383 0.2992; 
>     2   0   0   3   0   0.1324  0;     
> ];
> 
> This system has 2 generators at bus 1 and 2 and a capacitor at bus 4.
> 
> I am also including cost of generation of reactive power from the generators 
> as well as the capacitors(refer mpc.gencost).
> 
> But after I 'runopf' , the opf results are the same with/without reactive 
> power generation cost.
> 
> results=
> 
> version: '2'
>     baseMVA: 100
>         bus: [5x17 double]
>         gen: [2x25 double]
>      branch: [7x21 double]
>     gencost: [2x7 double]
>       order: [1x1 struct]
>          om: [1x1 opf_model]
>           x: [14x1 double]
>          mu: [1x1 struct]
>           f: 2.0196e+03
>         var: [1x1 struct]
>         nln: [1x1 struct]
>          et: 0.0930
>     success: 1
>         raw: [1x1 struct]
> 
> You can see that the gencost is only a 2x7 double. Why is the program not 
> taking the other rows into account?
> 
> Please help me out.
> Thank you.
> 

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