27-Aug-2020 17:33:58
CATKINAS is running now ...
Run log in the file : D:\CATKINAS\Examples/result_single/log1 
 +------------------------------------------------------------+ 
 |                                                            | 
 |       CCC   AA   TTTTT  K  K  III  N   N   AA    SSS       | 
 |      C     A  A    T    K K    I   NN  N  A  A  S          | 
 |      C     AAAA    T    KK     I   N N N  AAAA   SSS       | 
 |      C     A  A    T    K K    I   N  NN  A  A      S      | 
 |       CCC  A  A    T    K  K  III  N   N  A  A   SSS       | 
 |                                                            | 
 +------------------------------------------------------------+ 
Written by Doctor JianFu Chen* @ ECUST since 2014/4/4 under the leadership of Professor HaiFeng Wang* and PeiJun Hu*#.
*Key Laboratory for Advanced Materials, Research Institute of Industrial Catalysis and Centre for Computational Chemistry, 
 East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China. 
 Email: jfchen@ecust.edu.cn; hfwang@ecust.edu.cn. 
#School of Chemistry and Chemical Engineering, The Queen's University of Belfast, Belfast, BT9 5AG, UK. 
 Email: p.hu@qub.ac.uk
The modified newton method are intergated by the reversibility iteration method (cite this: ACS Catal. 2016, 6, 10, 7078-7087) to improve convergence speed and stability.

See details in our website: http://www.catkinas.com ...

Find 5 recation equation(s) : 
 (1): H2 + 2#   <-> 2H#           [ 1.209  -0.757 ]                        
 (2): N2 + 2#   <-> 2N#           [ 0.658  -1.175 ]                        
 (3): N# + H#   <-> NH# + #       [ 1.429  -0.083 ]                        
 (4): NH# + H#  <-> NH2# + #      [ 1.592  -0.158 ]                        
 (5): NH2# + H# <-> NH3 + 2#      [ 1.986   1.435 ]                        
Find 1 reaction site(s) : # 
Reactant species : H2 N2 
Product species : NH3 
Intermediate species : H N NH NH2 
Find 7 reaction species : H H2 N N2 NH NH2 NH3 

Try to generate reaction kinetic rate equation now ...
Normalized reactions: 
Reaction :  1 : H2(gas) + 2 # <-> 2 H# 
                 + R1
Reaction :  2 : N2(gas) + 2 # <-> 2 N# 
                 + R2
Reaction :  3 : 1/2 H2(gas) + 1/2 N2(gas) + # <-> NH# 
                 + 1/2 R1 + 1/2 R2 + R3
Reaction :  4 : H2(gas) + 1/2 N2(gas) + # <-> NH2# 
                 + R1 + 1/2 R2 + R3 + R4
Reaction :  5 : 3/2 H2(gas) + 1/2 N2(gas) <-> NH3(gas) 
                 + 3/2 R1 + 1/2 R2 + R3 + R4 + R5

Reversibility relations: 
Inner Cycle(s): 
Total Rection(s): 
Reaction :  1 : 3 H2(gas) + N2(gas) <-> 2 NH3(gas) 
                 + 3 R1 + R2 + 2 R3 + 2 R4 + 2 R5
zt(1) = z1^3*z2*z3^2*z4^2*z5^2 = P_NH3^2/(P_H2^3*P_N2*Keq(1)^3*Keq(2)*Keq(3)^2*Keq(4)^2*Keq(5)^2)
Coverage relations: 
Reaction :  1 : 1/2 H2(gas) + # <-> H# 
                 + 1/2 R1
Q_H = P_H2^(1/2)*Q_v*(z1*Keq(1))^(1/2)
Reaction :  2 : 1/2 N2(gas) + # <-> N# 
                 + 1/2 R2
Q_N = P_N2^(1/2)*Q_v*(z2*Keq(2))^(1/2)
Reaction :  3 : 1/2 H2(gas) + 1/2 N2(gas) + # <-> NH# 
                 + 1/2 R1 + 1/2 R2 + R3
Q_NH = P_H2^(1/2)*P_N2^(1/2)*Q_v*z3*Keq(3)*(z1*Keq(1))^(1/2)*(z2*Keq(2))^(1/2)
Reaction :  4 : H2(gas) + 1/2 N2(gas) + # <-> NH2# 
                 + R1 + 1/2 R2 + R3 + R4
Q_NH2 = P_H2*P_N2^(1/2)*Q_v*z1*z3*z4*Keq(1)*Keq(3)*Keq(4)*(z2*Keq(2))^(1/2)
Reversibility relations Summary: 
zt(1) = z1^3*z2*z3^2*z4^2*z5^2 = P_NH3^2/(P_H2^3*P_N2*Keq(1)^3*Keq(2)*Keq(3)^2*Keq(4)^2*Keq(5)^2)
Coverage relations Summary: 
Q_H = P_H2^(1/2)*Q_v*(z1*Keq(1))^(1/2)
Q_N = P_N2^(1/2)*Q_v*(z2*Keq(2))^(1/2)
Q_NH = P_H2^(1/2)*P_N2^(1/2)*Q_v*z3*Keq(3)*(z1*Keq(1))^(1/2)*(z2*Keq(2))^(1/2)
Q_NH2 = P_H2*P_N2^(1/2)*Q_v*z1*z3*z4*Keq(1)*Keq(3)*Keq(4)*(z2*Keq(2))^(1/2)
Coverage expressions: 
Q_v = 1/(P_H2^(1/2)*(z1*Keq(1))^(1/2) + P_N2^(1/2)*(z2*Keq(2))^(1/2) + P_H2^(1/2)*P_N2^(1/2)*z3*Keq(3)*(z1*Keq(1))^(1/2)*(z2*Keq(2))^(1/2) + P_H2*P_N2^(1/2)*z1*z3*z4*Keq(1)*Keq(3)*Keq(4)*(z2*Keq(2))^(1/2) + 1)
Reversibility expressions: 
z1 = Q_H^2/(P_H2*Q_v^2*Keq(1))
z2 = Q_N^2/(P_N2*Q_v^2*Keq(2))
z3 = (Q_NH*Q_v)/(Q_H*Q_N*Keq(3))
z4 = (Q_NH2*Q_v)/(Q_H*Q_NH*Keq(4))
z5 = (P_NH3*Q_v^2)/(Q_H*Q_NH2*Keq(5))
Reaction rates: 
r(1) = -P_H2*Q_v^2*kf(1)*(z1 - 1)
r(2) = -P_N2*Q_v^2*kf(2)*(z2 - 1)
r(3) = -P_H2^(1/2)*P_N2^(1/2)*Q_v^2*kf(3)*(z1*Keq(1))^(1/2)*(z2*Keq(2))^(1/2)*(z3 - 1)
r(4) = -P_H2*P_N2^(1/2)*Q_v^2*z1*z3*Keq(1)*Keq(3)*kf(4)*(z2*Keq(2))^(1/2)*(z4 - 1)
r(5) = -P_H2^(3/2)*P_N2^(1/2)*Q_v^2*z1*z3*z4*Keq(1)*Keq(3)*Keq(4)*kf(5)*(z1*Keq(1))^(1/2)*(z2*Keq(2))^(1/2)*(z5 - 1)

Try to generate the kinetic rate equations in myRatefun.m for checking now ...

The equations based on rate of every reaction :
dQ_H/dt = 2*r(1) - r(3) - r(4) - r(5)
dQ_N/dt = 2*r(2) - r(3)
dQ_NH/dt = r(3) - r(4)
dQ_NH2/dt = r(4) - r(5)
dQ_v/dt = r(3) - 2*r(2) - 2*r(1) + r(4) + 2*r(5)
dP_H2/dt = -Pn*(r(1) + (Fgt*P0*(P_H2 - Po_H2))/(NA*T*kB))
dP_N2/dt = -Pn*(r(2) + (Fgt*P0*(P_N2 - Po_N2))/(NA*T*kB))
dP_NH3/dt = Pn*(r(5) - (Fgt*P0*(P_NH3 - Po_NH3))/(NA*T*kB))

The rate equations of every reaction :
r(1) = P_H2*Q_v^2*kf(1) - Q_H^2*kr(1)
r(2) = P_N2*Q_v^2*kf(2) - Q_N^2*kr(2)
r(3) = Q_H*Q_N*kf(3) - Q_NH*Q_v*kr(3)
r(4) = Q_H*Q_NH*kf(4) - Q_NH2*Q_v*kr(4)
r(5) = Q_H*Q_NH2*kf(5) - P_NH3*Q_v^2*kr(5)

The equations based on P C Q kr kf :
dQ_H/dt = Q_NH*Q_v*kr(3) - Q_H*Q_N*kf(3) - Q_H*Q_NH*kf(4) - Q_H*Q_NH2*kf(5) - 2*Q_H^2*kr(1) + Q_NH2*Q_v*kr(4) + 2*P_H2*Q_v^2*kf(1) + P_NH3*Q_v^2*kr(5)
dQ_N/dt = Q_NH*Q_v*kr(3) - Q_H*Q_N*kf(3) - 2*Q_N^2*kr(2) + 2*P_N2*Q_v^2*kf(2)
dQ_NH/dt = Q_H*Q_N*kf(3) - Q_H*Q_NH*kf(4) - Q_NH*Q_v*kr(3) + Q_NH2*Q_v*kr(4)
dQ_NH2/dt = Q_H*Q_NH*kf(4) - Q_H*Q_NH2*kf(5) - Q_NH2*Q_v*kr(4) + P_NH3*Q_v^2*kr(5)
dQ_v/dt = 2*Q_H^2*kr(1) + 2*Q_N^2*kr(2) + Q_H*Q_N*kf(3) + Q_H*Q_NH*kf(4) + 2*Q_H*Q_NH2*kf(5) - Q_NH*Q_v*kr(3) - Q_NH2*Q_v*kr(4) - 2*P_H2*Q_v^2*kf(1) - 2*P_N2*Q_v^2*kf(2) - 2*P_NH3*Q_v^2*kr(5)
dP_H2/dt = -Pn*(P_H2*Q_v^2*kf(1) - Q_H^2*kr(1) + (Fgt*P0*(P_H2 - Po_H2))/(NA*T*kB))
dP_N2/dt = -Pn*(P_N2*Q_v^2*kf(2) - Q_N^2*kr(2) + (Fgt*P0*(P_N2 - Po_N2))/(NA*T*kB))
dP_NH3/dt = -Pn*(P_NH3*Q_v^2*kr(5) - Q_H*Q_NH2*kf(5) + (Fgt*P0*(P_NH3 - Po_NH3))/(NA*T*kB))

Try to read input parameters from INPUT now ...
CalcDRC = 1;
T = 673;
P_H2_FROZ = 75;
P_N2_FROZ = 25;
P_NH3_FROZ = 1;
Q_v_INIT = 1;
ThermoMode = 4;
BarrierMode = 1;
Mr_NH3 = -2;
npar = 8;
Try to initialize now ...
CalMode = [0];
parm = [1];
Q0 = [1];
BEPMode = [1];
ConsMode = [0];
TryMode = [0];
MaxTime = [3];
TimeMode = [0.02];
SaveMode = [0];
SaveFreq = [1];
CheckMode = [2];
PlotType = [1, 2, 3];
PlotMode = [1];
ProfMode = [1];
PlotList = [{}];
SimMode = [1];
SimValue = [0.01];
PathOrder = [{}];
PathCoord = [{}];
PathScale = [{}];
CompMode = [1];
SkipMode = [1];
FigMode = [2];
tspan = [0, 1];
MaxOdeTime = [60];
TryOrderList = [{'Init', 'ODE', 'PSO', 'ODEa', 'ODEm', 'Boundary', 'PSO', 'solve'}];

Try to generate the kinetic rate equations in odefun.m for ODE solver now ...
function [dy, rF, rR] = odefun_single(t, y, kf, kr, x)
rF = ...
[kf(1)*x(1)*y(5)^2;...
 kf(2)*x(2)*y(5)^2;...
 kf(3)*y(1)*y(2);...
 kf(4)*y(1)*y(3);...
 kf(5)*y(1)*y(4)];

rR = ...
[kr(1)*y(1)^2;...
 kr(2)*y(2)^2;...
 kr(3)*y(3)*y(5);...
 kr(4)*y(4)*y(5);...
 kr(5)*x(3)*y(5)^2];

r = rF - rR;

dy = ...
[2*r(1) - r(3) - r(4) - r(5);...
 2*r(2) - r(3);...
 r(3) - r(4);...
 r(4) - r(5);...
 r(3) - 2*r(2) - 2*r(1) + r(4) + 2*r(5)];

The symbol correspondence : 
[ y(1),   Q_H]
[ y(2),   Q_N]
[ y(3),  Q_NH]
[ y(4), Q_NH2]
[ y(5),   Q_v]
 
[ x(1),  P_H2]
[ x(2),  P_N2]
[ x(3), P_NH3]
 

Try to generate the kinetic rate steady-state equation now ...
2*r(1) - r(3) - r(4) - r(5)
2*r(2) - r(3)
r(3) - r(4)
r(4) - r(5)
Q_H + Q_N + Q_NH + Q_NH2 + Q_v - 1.0

Expand the equations based on P C Q :
Q_NH*Q_v*kr(3) - Q_H*Q_N*kf(3) - Q_H*Q_NH*kf(4) - Q_H*Q_NH2*kf(5) - 2*Q_H^2*kr(1) + Q_NH2*Q_v*kr(4) + 2*P_H2*Q_v^2*kf(1) + P_NH3*Q_v^2*kr(5)
Q_NH*Q_v*kr(3) - Q_H*Q_N*kf(3) - 2*Q_N^2*kr(2) + 2*P_N2*Q_v^2*kf(2)
Q_H*Q_N*kf(3) - Q_H*Q_NH*kf(4) - Q_NH*Q_v*kr(3) + Q_NH2*Q_v*kr(4)
Q_H*Q_NH*kf(4) - Q_H*Q_NH2*kf(5) - Q_NH2*Q_v*kr(4) + P_NH3*Q_v^2*kr(5)
Q_H + Q_N + Q_NH + Q_NH2 + Q_v - 1.0

No thermodynamics data read-in from the provided file Thermodynamics.data or Thermodynamics_data.mat, use built-in data as default ...
% Define the default thermodynamics data in the file Thermodynamics.data
% '%' and '!' for comments
% Key words: CF, TR, AH, FQ, EF
% CF: the chemical formula, TR: the temperature range, AH: the shomate parameters [A - H]
% FQ: the frequency, EF: the experimental formation energy
CF = H2; % 1; source : bulit-in
     EF = [   -0.272839]; FQ = [ 4401.00];
     TR = [  298.00,  1000.00]; AH = [   33.066178,   -11.363417,    11.432816,    -2.772874,    -0.158558,    -9.980797,   172.707974,     0.000000];
     TR = [ 1000.00,  2500.00]; AH = [   18.563083,    12.257357,    -2.859786,     0.268238,     1.977990,    -1.147438,   156.288133,     0.000000];
     TR = [ 2500.00,  6000.00]; AH = [   43.413560,    -4.293079,     1.272428,    -0.096876,   -20.533862,   -38.515158,   162.081354,     0.000000];
CF = CH4; % 2; source : bulit-in
     EF = [   -1.865940]; FQ = [ 2917.00,  1534.00,  1534.00,  3019.00,  3019.00,  3019.00,  1306.00,  1306.00,  1306.00];
     TR = [  298.00,  1300.00]; AH = [   -0.703029,   108.477300,   -42.521570,     5.862788,     0.678565,   -76.843760,   158.716300,   -74.873100];
     TR = [ 1300.00,  1600.00]; AH = [   85.812170,    11.264670,    -2.114146,     0.138190,   -26.422210,  -153.532700,   224.414300,   -74.873100];
CF = CO; % 3; source : bulit-in
     EF = [   -1.314068]; FQ = [ 2170.00];
     TR = [  298.00,  1300.00]; AH = [   25.567590,     6.096130,     4.054656,    -2.671201,     0.131021,  -118.008900,   227.366500,  -110.527100];
     TR = [ 1300.00,  1600.00]; AH = [   35.150700,     1.300095,    -0.205921,     0.013550,    -3.282780,  -127.837500,   231.712000,  -110.527100];
CF = H2O; % 4; source : bulit-in
     EF = [   -3.034448]; FQ = [ 3657.00,  1595.00,  3756.00];
     TR = [  298.00,   500.00]; AH = [   36.303952,   -24.112320,    63.641110,   -38.952400,    -0.013850,  -252.066060,   237.394310,  -241.826400];
     TR = [  500.00,  1700.00]; AH = [   30.092000,     6.832514,     6.793435,    -2.534480,     0.082139,  -250.881000,   223.396700,  -241.826400];
     TR = [ 1700.00,  6000.00]; AH = [   41.964260,     8.622053,    -1.499780,     0.098119,   -11.157640,  -272.179700,   219.780900,  -241.826400];
CF = CO2; % 5; source : bulit-in
     EF = [   -4.385561]; FQ = [ 1333.00,  2349.00,   667.00,   667.00];
     TR = [  298.00,  1200.00]; AH = [   24.997350,    55.186960,   -33.691370,     7.948387,    -0.136638,  -403.607500,   228.243100,  -393.522400];
     TR = [ 1200.00,  6000.00]; AH = [   58.166390,     2.720075,    -0.492289,     0.038844,    -6.447293,  -425.918600,   263.612500,  -393.522400];
CF = O2; % 6; source : bulit-in
     EF = [   -0.097960]; FQ = [ 1580.00];
     TR = [  100.00,   700.00]; AH = [   31.322340,   -20.235310,    57.866400,   -36.506240,    -0.007374,    -8.903471,   246.794500,     0.000000];
     TR = [  700.00,  2000.00]; AH = [   30.032350,     8.772972,    -3.988133,     0.788313,    -0.741599,   -11.324680,   236.166300,     0.000000];
     TR = [ 2000.00,  6000.00]; AH = [   20.911110,    10.720710,    -2.020498,     0.146449,     9.245722,     5.337651,   237.618500,     0.000000];
CF = NH3; % 7; source : bulit-in
     EF = [   -1.298171]; FQ = [ 3337.00,   950.00,  3444.00,  3444.00,  1627.00,  1627.00];
     TR = [  298.00,  1400.00]; AH = [   19.995630,    49.771190,   -15.375990,     1.921168,     0.189174,   -53.306670,   203.859100,   -45.898060];
CF = N2; % 8; source : bulit-in
     EF = [   -0.146214]; FQ = [ 2359.00];
     TR = [  100.00,   500.00]; AH = [   28.986410,     1.853978,    -9.647459,    16.635370,     0.000117,    -8.671914,   226.416800,     0.000000];
     TR = [  500.00,  2000.00]; AH = [   19.505830,    19.887050,    -8.598535,     1.369784,     0.527601,    -4.935202,   212.390000,     0.000000];
CF = N2O; % 9; source : bulit-in
     EF = [    0.590717]; FQ = [ 2224.00,  1285.00,   589.00];
     TR = [  298.00,  1400.00]; AH = [   27.679880,    51.148980,   -30.644540,     6.847911,    -0.157906,    71.249340,   238.616400,    82.048240];
CF = NO2; % 10; source : bulit-in
     EF = [    0.152695]; FQ = [ 1318.00,  1618.00,   750.00];
     TR = [  298.00,  1200.00]; AH = [   16.108570,    75.895250,   -54.387400,    14.307770,     0.239423,    26.174640,   240.538600,    33.095020];
CF = NO; % 11; source : bulit-in
     EF = [    0.820336]; FQ = [ 1904.00];
     TR = [  298.00,  1200.00]; AH = [   23.834910,    12.588780,    -1.139011,    -1.497459,     0.214194,    83.357830,   237.121900,    90.291140];
CF = NO3; % 12; source : bulit-in
     EF = []; FQ = [ 1450.00];
     TR = [  298.00,  1100.00]; AH = [   11.223160,   166.388900,  -148.445800,    47.405980,    -0.176791,    61.008580,   221.767900,    71.128000];
     TR = [ 1100.00,  6000.00]; AH = [   82.274180,     0.487106,    -0.098769,     0.006853,    -6.264954,    29.223110,   326.252800,    71.128000];
CF = HNO2; % 13; source : bulit-in
     EF = []; FQ = [];
     TR = [  298.00,  1200.00]; AH = [   24.899740,    91.375630,   -64.846140,    17.920070,    -0.134737,   -88.135960,   254.267100,   -76.734980];
CF = HNO3; % 14; source : bulit-in
     EF = []; FQ = [];
     TR = [  298.00,  1200.00]; AH = [   19.632290,   153.959900,  -115.837800,    32.879550,    -0.249114,  -146.881800,   247.704900,  -134.306000];
CF = HCN; % 15; source : bulit-in
     EF = [    0.948927]; FQ = [ 3311.00,   712.00,   712.00,  2097.00];
     TR = [  298.00,  1200.00]; AH = [   32.693730,    22.592050,    -4.369142,    -0.407697,    -0.282399,   123.481100,   233.259700,   135.143200];
CF = C2H4; % 16; source : bulit-in
     EF = [   -0.705013]; FQ = [ 3026.00,  1623.00,  1342.00,  1023.00,  3103.00,  1236.00,   949.00,   943.00,  3106.00,   826.00,  2989.00,  1444.00];
     TR = [  298.00,  1200.00]; AH = [   -6.387880,   184.401900,  -112.971800,    28.495930,     0.315540,    48.173320,   163.156800,    52.466940];
CF = CH2O; % 17; source : bulit-in
     EF = [   -1.786501]; FQ = [ 2783.00,  1746.00,  1500.00,  2843.00,  1249.00,  1167.00];
     TR = [  298.00,  1500.00]; AH = [    5.193767,    93.232490,   -44.854570,     7.882279,     0.551175,  -119.359100,   202.466300,  -115.897200];
CF = CH3OH; % 18; source : bulit-in
     EF = [   -3.315495]; FQ = [ 3681.00,  3000.00,  2844.00,  1477.00,  1455.00,  1345.00,  1060.00,  1033.00,  2960.00,  1477.00,  1165.00,   200.00];
     TR = [  298.00,  1500.00]; AH = [   -1.084581,   153.246357,   -79.530504,    16.471302,     0.522033,  -205.897417,   199.189375,  -201.000000];
CF = CH3CH2OH; % 19; source : bulit-in
     EF = [   -4.325727]; FQ = [ 3653.00,  2984.00,  2939.00,  2900.00,  1490.00,  1464.00,  1412.00,  1371.00,  1256.00,  1091.00,  1028.00,   888.00,   417.00,  2991.00,  2910.00,  1446.00,  1275.00,  1161.00,   812.00];
     TR = [  298.00,  1500.00]; AH = [   -4.736788,   271.961816,  -169.349465,    43.738602,     0.246434,  -244.628281,   203.332562,  -234.800000];
CF = CH3CHO; % 20; source : bulit-in
     EF = [   -3.115742]; FQ = [ 3005.00,  2917.00,  2822.00,  1743.00,  1441.00,  1400.00,  1352.00,  1113.00,   919.00,   509.00,  2967.00,  1420.00,   867.00,   763.00,   150.00];
     TR = [  298.00,  1500.00]; AH = [    4.803739,   185.920024,   -99.108461,    20.614739,     0.277080,  -174.756600,   220.002447,  -166.190000];
CF = HCOOH; % 21; source : bulit-in
     EF = [   -4.736916]; FQ = [ 3570.00,  2943.00,  1770.00,  1387.00,  1229.00,  1105.00,   625.00,  1033.00,   638.00];
     TR = [  298.00,  1500.00]; AH = [    3.802752,   153.662179,   -84.640468,    16.297378,     0.277206,  -385.165270,   212.969897,  -379.000000];
CF = H2O2; % 22; source : bulit-in
     EF = [   -2.034197]; FQ = [ 3617.95,  1393.50,   877.93,   370.89,  3560.00,  1273.68];
     TR = [  298.00,  1500.00]; AH = [   34.256670,   555.184450,   -35.154430,     9.087440,    -0.422157,  -149.909800,  -257.060600,  -136.106400];

Thermodynamic summary:
    (eV)       H2       N2      NH3 
     dGc  -1.0773  -1.5043  -1.5760 
       G  -0.9638  -1.3891  -1.8903 
       H   0.1135   0.1151  -0.3143 
      H0   0.0000  -0.0008  -0.4757 
     CpT   0.1131   0.1189   0.1616 
     TdS   1.0773   1.5043   1.5760 
     ZPE   0.2728   0.1462   0.8944 
      Ef  -0.2728  -0.1462  -1.2982 

Total rection(s): 
Reaction :  1 : 3 H2(gas) + N2(gas) <-> 2 NH3(gas) 
type:     dGc       dG       dH      dH0    d(CpT)   d(TdS)     dZPE     dEf 
(eV):    1.584    0.500   -1.084   -0.951   -0.135   -1.584    0.824   -1.632

 
Simplify the labels:
[ H2(gas), N2(gas), NH3(gas)]
[   gas01,   gas02,    gas03]
 

Solve the reaction kinetics ...

Run the sample 1 now ...
Type                              Original      |           Corrected      |             Corrected           |     TS mode
Reactions               Ea/for   Ea/rev    G0   |  Ea/for   Ea/rev    G0   |    k/for      k/rev      Keq    | forward reverse
(1):H2+2#<->2H#         1.209    1.966   -0.757    2.286    1.966    0.320    1.06e-04   2.66e-02   3.99e-03    TST     TST
(2):N2+2#<->2N#         0.658    1.833   -1.175    2.162    1.833    0.329    9.01e-04   2.63e-01   3.42e-03    TST     TST
(3):N#+H#<->NH#+#       1.429    1.512   -0.083    1.429    1.512   -0.083    2.79e+02   6.67e+01   4.18e+00    TST     TST
(4):NH#+H#<->NH2#+#     1.592    1.750   -0.158    1.592    1.750   -0.158    1.68e+01   1.10e+00   1.52e+01    TST     TST
(5):NH2#+H#<->NH3+2#    1.986    0.551    1.435    1.986    2.127   -0.141    1.88e-02   1.66e-03   1.14e+01    ORI     TST
Inner cycle(s):
Total rection(s):
Reaction :  1 : 3 H2(gas) + N2(gas) <-> 2 NH3(gas) 
dG =   0.526 eV :  + 3 R1 + R2 + 2 R3 + 2 R4 + 2 R5

Try numeric solution with arbitrary precision now ...
Elapsed time: 00:00:03.054. Time's up, return with the residue |dy/dt| ~= 10^-0001, |dlog(y)/dt| ~= 10^00000.
Try Reversibility Newton Iteration Method failed ... Elapsed time: 00:00:03.231

Try Reversibility Newton Iteration Method at state from ODE15S solver (yInit) now ...
  try time: 01, ydiff: 2.0000e+00, norm(slop): 2.6406e+00; Elapsed time: 00:00:00.482;
  try time: 02, ydiff: 1.9851e+00, norm(slop): 2.5192e+00; Elapsed time: 00:00:00.253;
  try time: 03, ydiff: 1.9850e+00, norm(slop): 2.5183e+00; Elapsed time: 00:00:00.214;
  try time: 04, ydiff: 1.9850e+00, norm(slop): 2.5204e+00; Elapsed time: 00:00:00.228;
  try time: 05, ydiff: 1.9849e+00, norm(slop): 2.6506e+00; Elapsed time: 00:00:00.273;
  try time: 06, ydiff: 1.9819e+00, norm(slop): 2.3617e+00; Elapsed time: 00:00:00.373;
  try time: 07, ydiff: 2.0353e+00, norm(slop): 9.2800e-01; Elapsed time: 00:00:00.501;
  try time: 08, ydiff: 6.7206e-01, norm(slop): 7.6224e-03; Elapsed time: 00:00:00.422;
  try time: 09, ydiff: 1.9891e-15, norm(slop): 1.9278e-16; Elapsed time: 00:00:00.197;
Elapsed time: 00:00:00.062. Converged, return with the residue |dy/dt| ~= 10^-1001, |dlog(y)/dt| ~= 10^-1001. Succeed!! 
Extract individual solutions by Reversibility Newton Iteration Method
Q_H      =   8.5506231311e-02
Q_N      =   9.2153951324e-02
Q_NH     =   9.9719104288e-02
Q_NH2    =   3.9210552902e-01
Q_v      =   3.3051518406e-01
Elapsed time: 00:00:00.035. Converged, return with the residue |dy/dt| ~= 10^-1001, |dlog(y)/dt| ~= 10^-1001. Succeed!! 
Extract individual solutions by Reversibility Newton Iteration Method
 No.                    Rforward                   Rreverse                       Rnet              Reversibility    Reactions                  Ea       G0     Eapp         kf         kr        Keq
1    :    8.6952023818972373e-04     1.9427308892775157e-04     6.7524714926197216e-04     2.2342560919825588e-01    (1):H2+2#<->2H#         2.286    0.320    2.103   1.06e-04   2.66e-02   3.99e-03 
2    :    2.4608048233328572e-03     2.2357224402455335e-03     2.2508238308732405e-04     9.0853302100469813e-01    (2):N2+2#<->2N#         2.162    0.329    2.103   9.01e-04   2.63e-01   3.42e-03 
3    :    2.1991903594472588e+00     2.1987401946810841e+00     4.5016476617464811e-04     9.9979530431995534e-01    (3):N#+H#<->NH#+#       1.429   -0.083    2.103   2.79e+02   6.67e+01   4.18e+00 
4    :    1.4318543805690809e-01     1.4273527329073343e-01     4.5016476617464811e-04     9.9685607159300837e-01    (4):NH#+H#<->NH2#+#     1.592   -0.158    2.103   1.68e+01   1.10e+00   1.52e+01 
5    :    6.3102634808051203e-04     1.8086158190586390e-04     4.5016476617464811e-04     2.8661494477372912e-01    (5):NH2#+H#<->NH3+2#    1.986   -0.141    2.103   1.88e-02   1.66e-03   1.14e+01 

Base on reactants/products : 
 No.      	 gas01                    	 gas02                    	 gas03                    	
Species   	 H2(gas)                  	 N2(gas)                  	 NH3(gas)                 	
Rate : 	   -6.7524714926197216e-04	   -2.2508238308732405e-04	    4.5016476617464811e-04	
Eapp : 	                     2.103	                     2.103	                     2.103	

Elapsed time: 00:00:07.018. Try numeric solution with arbitrary precision finished ...

Calculate the degree of rate control of barrier of reaction ((1):H2+2#<->2H#)
Elapsed time: 00:00:00.027. Converged, return with the residue |dy/dt| ~= 10^-1001, |dlog(y)/dt| ~= 10^-1001. Succeed!! 
Extract individual solutions by Reversibility Newton Iteration Method
4.93e-01	4.93e-01	4.93e-01	4.93e-01	4.93e-01	
Calculate the degree of rate control of barrier of reaction ((2):N2+2#<->2N#)
Elapsed time: 00:00:00.028. Converged, return with the residue |dy/dt| ~= 10^-1001, |dlog(y)/dt| ~= 10^-1001. Succeed!! 
Extract individual solutions by Reversibility Newton Iteration Method
-2.15e-02	-2.15e-02	-2.15e-02	-2.15e-02	-2.15e-02	
Calculate the degree of rate control of barrier of reaction ((3):N#+H#<->NH#+#)
Elapsed time: 00:00:00.027. Converged, return with the residue |dy/dt| ~= 10^-1001, |dlog(y)/dt| ~= 10^-1001. Succeed!! 
Extract individual solutions by Reversibility Newton Iteration Method
-4.97e-05	-4.97e-05	-4.97e-05	-4.97e-05	-4.97e-05	
Calculate the degree of rate control of barrier of reaction ((4):NH#+H#<->NH2#+#)
Elapsed time: 00:00:00.028. Converged, return with the residue |dy/dt| ~= 10^-1001, |dlog(y)/dt| ~= 10^-1001. Succeed!! 
Extract individual solutions by Reversibility Newton Iteration Method
-1.36e-04	-1.36e-04	-1.36e-04	-1.36e-04	-1.36e-04	
Calculate the degree of rate control of barrier of reaction ((5):NH2#+H#<->NH3+2#)
Elapsed time: 00:00:00.027. Converged, return with the residue |dy/dt| ~= 10^-1001, |dlog(y)/dt| ~= 10^-1001. Succeed!! 
Extract individual solutions by Reversibility Newton Iteration Method
5.29e-01	5.29e-01	5.29e-01	5.29e-01	5.29e-01	
Summary : 
   R001	   R002	   R003	   R004	   R005	
   0.49	   0.49	   0.49	   0.49	   0.49		(1):H2+2#<->2H#     
  -0.02	  -0.02	  -0.02	  -0.02	  -0.02		(2):N2+2#<->2N#     
  -0.00	  -0.00	  -0.00	  -0.00	  -0.00		(3):N#+H#<->NH#+#   
  -0.00	  -0.00	  -0.00	  -0.00	  -0.00		(4):NH#+H#<->NH2#+# 
   0.53	   0.53	   0.53	   0.53	   0.53		(5):NH2#+H#<->NH3+2#
Base on reactants/products : 
   gas01   	 gas02   	 gas03   	
   4.93e-01	 4.93e-01	 4.93e-01		(1):H2+2#<->2H#     
  -2.15e-02	-2.15e-02	-2.15e-02		(2):N2+2#<->2N#     
  -4.97e-05	-4.97e-05	-4.97e-05		(3):N#+H#<->NH#+#   
  -1.36e-04	-1.36e-04	-1.36e-04		(4):NH#+H#<->NH2#+# 
   5.29e-01	 5.29e-01	 5.29e-01		(5):NH2#+H#<->NH3+2#
Simplification : 
  gas01	  gas02	  gas03	
   0.49	   0.49	   0.49		(1):H2+2#<->2H#     
  -0.02	  -0.02	  -0.02		(2):N2+2#<->2N#     
   0.53	   0.53	   0.53		(5):NH2#+H#<->NH3+2#

Calculate the degree of rate control of intermediate of species (Q_H)
Elapsed time: 00:00:00.027. Converged, return with the residue |dy/dt| ~= 10^-1001, |dlog(y)/dt| ~= 10^-1001. Succeed!! 
Extract individual solutions by Reversibility Newton Iteration Method
-1.71e-01	-1.71e-01	-1.71e-01	-1.71e-01	-1.71e-01	
Calculate the degree of rate control of intermediate of species (Q_N)
Elapsed time: 00:00:00.027. Converged, return with the residue |dy/dt| ~= 10^-1001, |dlog(y)/dt| ~= 10^-1001. Succeed!! 
Extract individual solutions by Reversibility Newton Iteration Method
-1.84e-01	-1.84e-01	-1.84e-01	-1.84e-01	-1.84e-01	
Calculate the degree of rate control of intermediate of species (Q_NH)
Elapsed time: 00:00:00.028. Converged, return with the residue |dy/dt| ~= 10^-1001, |dlog(y)/dt| ~= 10^-1001. Succeed!! 
Extract individual solutions by Reversibility Newton Iteration Method
-1.99e-01	-1.99e-01	-1.99e-01	-1.99e-01	-1.99e-01	
Calculate the degree of rate control of intermediate of species (Q_NH2)
Elapsed time: 00:00:00.028. Converged, return with the residue |dy/dt| ~= 10^-1001, |dlog(y)/dt| ~= 10^-1001. Succeed!! 
Extract individual solutions by Reversibility Newton Iteration Method
-7.84e-01	-7.84e-01	-7.84e-01	-7.84e-01	-7.84e-01	
Calculate the degree of rate control of intermediate of species (Q_v)
Elapsed time: 00:00:00.027. Converged, return with the residue |dy/dt| ~= 10^-1001, |dlog(y)/dt| ~= 10^-1001. Succeed!! 
Extract individual solutions by Reversibility Newton Iteration Method
-6.61e-01	-6.61e-01	-6.61e-01	-6.61e-01	-6.61e-01	
Summary : 
   R001	   R002	   R003	   R004	   R005	
  -0.17	  -0.17	  -0.17	  -0.17	  -0.17		Q_H  
  -0.18	  -0.18	  -0.18	  -0.18	  -0.18		Q_N  
  -0.20	  -0.20	  -0.20	  -0.20	  -0.20		Q_NH 
  -0.78	  -0.78	  -0.78	  -0.78	  -0.78		Q_NH2
  -0.66	  -0.66	  -0.66	  -0.66	  -0.66		Q_v  
Base on reactants/products : 
   gas01   	 gas02   	 gas03   	
  -1.71e-01	-1.71e-01	-1.71e-01		Q_H  
  -1.84e-01	-1.84e-01	-1.84e-01		Q_N  
  -1.99e-01	-1.99e-01	-1.99e-01		Q_NH 
  -7.84e-01	-7.84e-01	-7.84e-01		Q_NH2
  -6.61e-01	-6.61e-01	-6.61e-01		Q_v  
Simplification : 
  gas01	  gas02	  gas03	
  -0.17	  -0.17	  -0.17		Q_H  
  -0.18	  -0.18	  -0.18		Q_N  
  -0.20	  -0.20	  -0.20		Q_NH 
  -0.78	  -0.78	  -0.78		Q_NH2
  -0.66	  -0.66	  -0.66		Q_v  

Calculate the degree of rate control of pressure of species (P_H2)
Elapsed time: 00:00:00.027. Converged, return with the residue |dy/dt| ~= 10^-1001, |dlog(y)/dt| ~= 10^-1001. Succeed!! 
Extract individual solutions by Reversibility Newton Iteration Method
-6.35e-01	-6.35e-01	-6.35e-01	-6.35e-01	-6.35e-01	
Calculate the degree of rate control of pressure of species (P_N2)
Elapsed time: 00:00:00.028. Converged, return with the residue |dy/dt| ~= 10^-1001, |dlog(y)/dt| ~= 10^-1001. Succeed!! 
Extract individual solutions by Reversibility Newton Iteration Method
2.35e-01	2.35e-01	2.35e-01	2.35e-01	2.35e-01	
Calculate the degree of rate control of pressure of species (P_NH3)
Elapsed time: 00:00:00.028. Converged, return with the residue |dy/dt| ~= 10^-1001, |dlog(y)/dt| ~= 10^-1001. Succeed!! 
Extract individual solutions by Reversibility Newton Iteration Method
2.12e-01	2.12e-01	2.12e-01	2.12e-01	2.12e-01	
Summary : 
   R001	   R002	   R003	   R004	   R005	
  -0.63	  -0.63	  -0.63	  -0.63	  -0.63		P_H2 
   0.24	   0.24	   0.24	   0.24	   0.24		P_N2 
   0.21	   0.21	   0.21	   0.21	   0.21		P_NH3
Base on reactants/products : 
   gas01   	 gas02   	 gas03   	
  -6.35e-01	-6.35e-01	-6.35e-01		P_H2 
   2.35e-01	 2.35e-01	 2.35e-01		P_N2 
   2.12e-01	 2.12e-01	 2.12e-01		P_NH3
Simplification : 
  gas01	  gas02	  gas03	
  -0.63	  -0.63	  -0.63		P_H2 
   0.24	   0.24	   0.24		P_N2 
   0.21	   0.21	   0.21		P_NH3

    
Progress : [====================================================================================================]
Ratio    :     1/    1; Percent : 100.00%; Used Time :      00:00:10; Left Time :      00:00:00

Plot the reaction results ...

    
Progress : [====================================================================================================] 
Ratio    :    13/   13; Percent : 100.00%; Used Time :      00:00:06; Left Time :      00:00:00

The possible reaction pathways : 
Total Rection(s): 
Reaction :  1 : 3 H2(gas) + N2(gas) <-> 2 NH3(gas) 
                 + 3 R1 + R2 + 2 R3 + 2 R4 + 2 R5

Plot the reaction energy profile ...

    
Progress : [====================================================================================================] 
Ratio    :     1/    1; Percent : 100.00%; Used Time :      00:00:00; Left Time :      00:00:00

Plot the reaction flow diagram ...

    
Progress : [====================================================================================================] 
Ratio    :     1/    1; Percent : 100.00%; Used Time :      00:00:01; Left Time :      00:00:00

Make the htmls files for the figure results ...

    
Progress : [====================================================================================================] 
Ratio    :    15/   15; Percent : 100.00%; Used Time :      00:00:00; Left Time :      00:00:00

Elapsed time: 00:00:25.085
27-Aug-2020 17:34:23
CATKINAS is finished now ...
Written by Doctor JianFu Chen* @ ECUST since 2014/4/4 under the leadership of Professor HaiFeng Wang* and PeiJun Hu*#.
*Key Laboratory for Advanced Materials, Research Institute of Industrial Catalysis and Centre for Computational Chemistry, 
 East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, P.R. China. 
 Email: jfchen@ecust.edu.cn; hfwang@ecust.edu.cn. 
#School of Chemistry and Chemical Engineering, The Queen's University of Belfast, Belfast, BT9 5AG, UK. 
 Email: p.hu@qub.ac.uk
Run log in the file : D:\CATKINAS\Examples/result_single/log1 


