Directory branches/budaev/HEDG2_06.b2/HEDG2_06.P1V/

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sbu062 2021-06-08 12:38 Rev.: 11235

`O2` and higher optimization does not work on Windows Intel Fortran, propagate fix r11234

6 lines of code changed in 1 file:

• branches/budaev/HEDG2_06.b2/HEDG2_06.P1V: Makefile (+6 -2)

sbu062 2021-06-08 09:28 Rev.: 11233

delete dependence of living cost on smr, very small effect and potentially slow down simulation
Note: this applies changes r11231:r11232
applied diff `svn diff -r 11226:11232 m_body.f90` for all branches

2 lines of code changed in 1 file:

• branches/budaev/HEDG2_06.b2/HEDG2_06.P1V: m_body.f90 (+2 -22)

sbu062 2021-06-08 07:00 Rev.: 11229

fix exponent as in r11226

2 lines of code changed in 1 file:

• branches/budaev/HEDG2_06.b2/HEDG2_06.P1V: m_body.f90 (+2 -1)

sbu062 2021-06-03 09:47 Rev.: 11210

repeat r11209: need even longer record to fit all values

3 lines of code changed in 1 file:

• branches/budaev/HEDG2_06.b2/HEDG2_06.P1V: m_popul.f90 (+3 -3)

sbu062 2021-06-02 13:18 Rev.: 11208

need extra length for the record to avoid writing data to non-existent space beyond last character, useful against huge history crashing

1 lines of code changed in 1 file:

• branches/budaev/HEDG2_06.b2/HEDG2_06.P1V: m_popul.f90 (+1 -1)

sbu062 2021-05-28 14:30 Rev.: 11200

apply patch from simulation, worked well, Limit maximum level of sex hormones to 10.0 to avoid huge growth of it and reproductive beyond limits
Patch here:
{{{
Index: m_body.f90
===================================================================
--- m_body.f90 (revision 10934)
+++ m_body.f90 (working copy)
@@ -1439,15 +1439,15 @@
if (length_increment > TOLERANCE_LOW_DEF_SRP) then
if (this%is_male()) then
!> - If the agent is **male**, **testosterone** is incremented.
- call this%testosterone_set( &
+ call this%testosterone_set( min( 10.0_SRP, &
this%testosterone_get() + &
- this%testosterone_get() * steroid_increment_factor )
+ this%testosterone_get() * steroid_increment_factor ) )
else
!> - If the agent is **female**, **estrogen** is incremented.
!! .
- call this%estrogen_set( &
+ call this%estrogen_set( min( 10.0_SRP, &
this%estrogen_get() + &
- this%estrogen_get() * steroid_increment_factor )
+ this%estrogen_get() * steroid_increment_factor ) )
end if
!> If there was no growth and the gonadal steroids are not incremented,
!! the current values are still saved in the history stack by calling
}}}

4 lines of code changed in 1 file:

• branches/budaev/HEDG2_06.b2/HEDG2_06.P1V: m_body.f90 (+4 -4)

sbu062 2021-05-28 14:22 Rev.: 11199

fix power factor

2 lines of code changed in 2 files:

• branches/budaev/HEDG2_06.b2/HEDG2_06.P1V: m_body.f90 (new)

sbu062 2020-06-06 07:26 Rev.: 9552

white space only: fix if block indent for readability

1 lines of code changed in 1 file:

• branches/budaev/HEDG2_06.b2/HEDG2_06.P1V: m_common.f90 (+1 -1)

sbu062 2020-06-06 07:13 Rev.: 9551

gamma2gene: merged tested r9487: merged changes in (allelescale) and (gamma2gene) backends from SIGMOID_tweak_new r9486

*Patch code:*

{{{
Index: m_common.f90
===================================================================
--- m_common.f90 (.../HEDG2_06.b2/HEDG2_06.P1H) (revision 9189)
+++ m_common.f90 (.../HEDG2_06.b3/HEDG2_06.P1H) (revision 9550)
@@ -2594,6 +2594,11 @@
!! `commondata::allelescale()` functions.
integer, parameter, public :: ALLELERANGE_MAX = 10000

+ !> Conversion parameter that defines the scaling of the integer allele
+ !! values ::ALLELERANGE_MIN to ALLELERANGE_MAX are converted to ::zero to
+ !! this parameter value as the maximum. See ::allelescale() for details.
+ real(SRP), parameter, public :: ALLELESCALE_MAX = 20.0_SRP
+
!> Number of additive allele components
integer, parameter, public :: ADDITIVE_COMPS = 3

@@ -6875,14 +6880,15 @@
!! @param[in] raw_value raw input value, integer within
!! `commondata::allelerange_min` and `commondata::allelerange_max`
!! @retval Returns the value of conversion function: integer alleles
- !! to real internal value 0 to 1
+ !! to real internal value ::zero to ::allelescale_max
!! @details Allele conversion function for the relationship between the
!! genome integer allele value and its converted real value in
!! the neuronal response function. The function rescales integer
!! allele value @f$ I_{i} @f$ within the range
!! @f$ [I_{min},I_{max}] @f$ to real values @f$ r @f$ within the
- !! range @f$ [0,1] @f$ using the formula:
- !! @f[ r = \frac{I - I_{min}}{I_{max}-I_{min}} @f]
+ !! range @f$ [0,M] @f$, where @f$ M @f$ is defined by the
+ !! ::allelescale_max parameter. Conversion is performed by the
+ !! ::rescale() backend function.
!! See implementation notes on `allele_value` component of the
!! `GENE` derived type.
!! @note Note that it is an *elemental function* that can accept both
@@ -6889,20 +6895,13 @@
!! scalar and vector arguments.
elemental function allelescale(raw_value) result(converted)

- ! @param[in] raw_value raw input value, integer within
- ! `commondata::allelerange_min` and `commondata::allelerange_max`.
integer, intent(in) :: raw_value
- ! @retval Returns the value of conversion function: integer alleles
- ! to real internal value 0 to 1
real(SRP) :: converted

- converted = (real(raw_value,SRP) - ALLELERANGE_MIN) / &
- (ALLELERANGE_MAX - ALLELERANGE_MIN)
+ converted = rescale( real(raw_value,SRP), &
+ real(ALLELERANGE_MIN,SRP), real(ALLELERANGE_MAX,SRP),&
+ ZERO, ALLELESCALE_MAX )

- !> @warning We must never accept zero values of alleles as they will
- !! result in **division by zero** in `commondata::gamma2gene()`.
- if (converted < ZERO) converted = ZERO
-
end function allelescale

!-----------------------------------------------------------------------------
@@ -7025,13 +7024,13 @@
! function.
! @note Note that the raw integer gene values are accepted by this
! function as `allelescale` is called automatically inside.
- integer, dimension(ADDITIVE_COMPS), intent(in) :: gs
+ integer, dimension(:), intent(in) :: gs

! @param[in] gh half-max effect: Gene/constant for the signal strength
! giving half max effect.
! @note Note that the raw integer gene values are accepted by this
! function as allelescale is called automatically inside.
- integer, dimension(ADDITIVE_COMPS), intent(in) :: gh
+ integer, dimension(:), intent(in) :: gh

! @param[in] signal perception: Input value of (external or internal)
! stimulus perception.
@@ -7045,7 +7044,7 @@

! Local variables:
real(SRP) :: perception
- real(SRP) :: d1
+ real(HRP) :: d1, nr
integer :: i

! Parameter that specifies the minimum perception. Can be commondata::zero
@@ -7065,7 +7064,7 @@
if (present(erpcv)) then
if (erpcv > TOLERANCE_HIGH_DEF_SRP) then
perception = max(FORCED_MIN_PERCEPT, RNORM(signal,(erpcv*signal)**2))
- else
+ else
perception = max(FORCED_MIN_PERCEPT, signal)
end if
else
@@ -7072,16 +7071,22 @@
perception = max(FORCED_MIN_PERCEPT, signal)
end if

- neuronal_response = 0.0_SRP
+ nr = 0.0_HRP

! @warning The `do concurrent` construct is F2008 and can not (yet) be
! implemented in all compilers. Use normal `do` in such a case.
- do concurrent (i=1:ADDITIVE_COMPS)
- d1 = ( perception / alleleconv( allelescale(gh(i)) ) &
- ) ** alleleconv( allelescale(gs(i)) )
- neuronal_response = neuronal_response + d1/(1.0_SRP+d1)
+ do concurrent (i=1:size(gs))
+ d1 = (real(perception, HRP) / real(alleleconv(allelescale(gh(i))),HRP)) &
+ ** real( alleleconv( allelescale(gs(i)) ), HRP )
+ nr = nr + d1/(1.0_HRP+d1)
end do

+ if (nr < ZERO) then
+ neuronal_response = ZERO
+ else
+ neuronal_response = real(nr, SRP)
+ end if
+
end function gamma2gene_additive_i4

!-----------------------------------------------------------------------------
@@ -7130,13 +7135,13 @@
! function.
! @note Note that the raw integer gene values are accepted by this
! function as `allelescale` is called automatically inside.
- real(SRP), dimension(ADDITIVE_COMPS), intent(in) :: gs
+ real(SRP), dimension(:), intent(in) :: gs

! @param[in] half-max effect: Gene/constant for the signal strength giving
! half max effect.
! @note Note that the raw integer gene values are accepted by this
! function as `allelescale` is called automatically inside.
- real(SRP), dimension(ADDITIVE_COMPS), intent(in) :: gh
+ real(SRP), dimension(:), intent(in) :: gh

! @param[in] perception: Input value of (external or internal) stimulus
! perception.
@@ -7150,7 +7155,7 @@

! Local variables:
real(SRP) :: perception
- real(SRP) :: d1
+ real(HRP) :: d1, nr
integer :: i

! Parameter that specifies the minimum perception. Can be commondata::zero
@@ -7169,7 +7174,7 @@
if (present(erpcv)) then
if (erpcv > TOLERANCE_HIGH_DEF_SRP) then
perception = max(FORCED_MIN_PERCEPT, RNORM(signal,(erpcv*signal)**2))
- else
+ else
perception = max(FORCED_MIN_PERCEPT, signal)
end if
else
@@ -7176,16 +7181,22 @@
perception = max(FORCED_MIN_PERCEPT, signal)
end if

- neuronal_response = 0.0_SRP
+ nr = 0.0_HRP

! @warning The `do concurrent` construct is F2008 and can not (yet) be
! implemented in all compilers. Use normal `do` in such a case.
- do concurrent (i=1:ADDITIVE_COMPS)
- d1 = (perception / alleleconv(gh(i)) &
- ) ** alleleconv(gs(i))
- neuronal_response = neuronal_response + d1/(1.0_SRP+d1)
+ do concurrent (i=1:size(gs))
+ d1 = (real(perception,HRP) / real(alleleconv(gh(i)),HRP)) &
+ ** real( alleleconv(gs(i)),HRP )
+ nr = nr + d1/(1.0_HRP+d1)
end do

+ if (nr < ZERO) then
+ neuronal_response = ZERO
+ else
+ neuronal_response = real(nr, SRP)
+ end if
+
end function gamma2gene_additive_r4

!-----------------------------------------------------------------------------
}}}

42 lines of code changed in 1 file:

• branches/budaev/HEDG2_06.b2/HEDG2_06.P1V: m_common.f90 (+42 -31)

sbu062 2019-12-20 12:41 Rev.: 9189

portability, merged r9188, as in HEDTOOLS r9185

71 lines of code changed in 2 files:

• branches/budaev/HEDG2_06.b2/HEDG2_06.P1V: Makefile (+71 -50)

sbu062 2019-07-02 14:41 Rev.: 8487

merged r8486, save all agent data at each time step in (lifecycle_preevol)
- tests passed

52 lines of code changed in 3 files:

• branches/budaev/HEDG2_06.b2/HEDG2_06.P1V: m_common.f90 (+7), m_evolut.f90 (+45 -1)

sbu062 2019-07-01 12:36 Rev.: 8481

(population_ga_reproduce_max) include only alive
- tests pass

10 lines of code changed in 2 files:

• branches/budaev/HEDG2_06.b2/HEDG2_06.P1V: m_popul.f90 (+10 -1)

sbu062 2019-06-21 13:27 Rev.: 8461

shorter history for faster running
- separate test run with long history required for complexity analysis

1 lines of code changed in 1 file:

• branches/budaev/HEDG2_06.b2/HEDG2_06.P1V: m_common.f90 (+1 -1)

sbu062 2019-06-21 13:15 Rev.: 8460

set parameters for specific model runs

0 lines of code changed in 2 files:

• branches/budaev/HEDG2_06.b2/HEDG2_06.P1V: m_common.f90 (new)