[2696] | 1 | MODULE KPP_ROOT_Integrator |
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| 2 | |
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| 3 | USE KPP_ROOT_Parameters, ONLY : NVAR, NFIX, NREACT |
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| 4 | USE KPP_ROOT_Global, ONLY : TIME, RCONST, Volume |
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| 5 | USE KPP_ROOT_Stoichiom |
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| 6 | USE KPP_ROOT_Stochastic |
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| 7 | USE KPP_ROOT_Rates |
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| 8 | IMPLICIT NONE |
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| 9 | |
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| 10 | CONTAINS |
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| 11 | |
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| 12 | !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
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| 13 | SUBROUTINE Gillespie(Nevents, T, SCT, NmlcV, NmlcF) |
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| 14 | !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
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| 15 | ! |
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| 16 | ! Gillespie stochastic integration |
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| 17 | ! INPUT: |
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| 18 | ! Nevents = no. of individual reaction events to be simulated |
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| 19 | ! SCT = stochastic rate constants |
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| 20 | ! T = time |
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| 21 | ! NmlcV, NmlcF = no. of molecules for variable and fixed species |
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| 22 | ! OUTPUT: |
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| 23 | ! T = updated time (after Nevents reactions) |
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| 24 | ! NmlcV = updated no. of molecules for variable species |
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| 25 | ! |
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| 26 | ! |
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| 27 | !~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
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| 28 | IMPLICIT NONE |
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| 29 | KPP_REAL:: T |
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| 30 | INTEGER :: Nevents |
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| 31 | INTEGER :: NmlcV(NVAR), NmlcF(NFIX) |
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| 32 | INTEGER :: i, m, issa |
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| 33 | REAL :: r1, r2 |
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| 34 | KPP_REAL :: A(NREACT), SCT(NREACT), x |
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| 35 | |
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| 36 | DO issa = 1, Nevents |
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| 37 | |
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| 38 | ! Uniformly distributed random numbers |
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| 39 | CALL RANDOM_NUMBER(r1) |
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| 40 | CALL RANDOM_NUMBER(r2) |
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| 41 | ! Avoid log of zero |
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| 42 | r2 = MAX(r2,1.e-14) |
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| 43 | |
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| 44 | ! Propensity vector |
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| 45 | CALL Propensity ( NmlcV, NmlcF, SCT, A ) |
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| 46 | ! Cumulative sum of propensities |
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| 47 | DO i = 2, NREACT |
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| 48 | A(i) = A(i-1)+A(i); |
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| 49 | END DO |
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| 50 | |
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| 51 | ! Index of next reaction |
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| 52 | x = r1*A(NREACT) |
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| 53 | DO i = 1, NREACT |
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| 54 | IF (A(i)>=x) THEN |
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| 55 | m = i; |
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| 56 | EXIT |
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| 57 | END IF |
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| 58 | END DO |
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| 59 | |
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| 60 | ! Update time with time to next reaction |
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| 61 | T = T - LOG(r2)/A(NREACT); |
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| 62 | |
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| 63 | ! Update state vector |
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| 64 | CALL MoleculeChange( m, NmlcV ) |
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| 65 | |
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| 66 | END DO |
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| 67 | |
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| 68 | CONTAINS |
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| 69 | |
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| 70 | SUBROUTINE PropensityTemplate( T, NmlcV, NmlcF, Prop ) |
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| 71 | KPP_REAL, INTENT(IN) :: T |
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| 72 | INTEGER, INTENT(IN) :: NmlcV(NVAR), NmlcF(NFIX) |
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| 73 | KPP_REAL, INTENT(OUT) :: Prop(NREACT) |
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| 74 | KPP_REAL :: Tsave, SCT(NREACT) |
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| 75 | ! Update the stochastic reaction rates, which may be time dependent |
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| 76 | Tsave = TIME |
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| 77 | TIME = T |
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| 78 | CALL Update_RCONST() |
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| 79 | CALL StochasticRates( RCONST, Volume, SCT ) |
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| 80 | CALL Propensity ( NmlcV, NmlcF, SCT, Prop ) |
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| 81 | TIME = Tsave |
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| 82 | END SUBROUTINE PropensityTemplate |
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| 83 | |
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| 84 | END SUBROUTINE Gillespie |
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| 85 | |
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| 86 | END MODULE KPP_ROOT_Integrator |
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