dox
(13 files, 44003 lines)
pfunit
(0 files, 0 lines)
tests
(3 files, 1722 lines)
[root]/branches/budaev/HEDG2_04
dox
(13 files, 44003 lines)
pfunit
(0 files, 0 lines)
tests
(3 files, 1722 lines)
| Author | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| sbu062 | 162 (100.0%) | 3450 (100.0%) | 21.2 |
`O2` and higher optimization does not work on Windows Intel Fortran, propagate fix r11234
6 lines of code changed in 1 file:
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:
fix exponent as in r11226
2 lines of code changed in 1 file:
repeat r11209: need even longer record to fit all values
3 lines of code changed in 1 file:
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:
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:
fix power factor
2 lines of code changed in 2 files:
white space only: fix if block indent for readability
1 lines of code changed in 1 file:
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:
portability, merged r9188, as in HEDTOOLS r9185
71 lines of code changed in 1 file:
enable generate doxygen output in RFT, pdflatex makefile seems broken in new versions
1 lines of code changed in 1 file:
merged r8486, save all agent data at each time step in (lifecycle_preevol)
- default disabled ENABLE_SAVE_AGENTS_EACH_TIMESTEP FALSE
- tests pass
52 lines of code changed in 2 files:
merged r8481, (population_ga_reproduce_max) include only alive
- tests pass
10 lines of code changed in 1 file:
foxed global bug causing GA_REPRODUCE_N_MIN reproducing sub-population in all cases
2 lines of code changed in 2 files:
(LOG_IEEE): log IEEE signalling, backport from r8442:r8443
54 lines of code changed in 1 file:
shorter log message
1 lines of code changed in 1 file:
backported r8427:r8428 IPO now works in ifort
3 lines of code changed in 1 file:
backported (ieee_error_reporting) r8421:r8423 to older models
43 lines of code changed in 2 files:
backported reverse sorfing in (qsort) as in r8409
13 lines of code changed in 1 file:
backported fixes and tests r8333:r8348 from model **06**
33 lines of code changed in 1 file:
fix doxygen comments after backporting
- forgotten on parameters descriptions
4 lines of code changed in 1 file:
more conformant explanations for (do_sanitise) and (ieee_error_reporting)
- more correct doxygen style
45 lines of code changed in 1 file:
backported parameter change for (fitness_energy_reprfact_mass) from r8233
2 lines of code changed in 1 file:
backported (fitness_energy_reprfact_mass) r8234
- tests pass
99 lines of code changed in 2 files:
backported latest changes from HEDG2_06 r8320
- tests pass
195 lines of code changed in 3 files:
**compiler bug**, debug: fix for intel **ifort 19** compiler bug
- accessor function `is_available()` is not accessible
resulting in crashing in high cpu-optimised build
(`-O3` etc)
5 lines of code changed in 1 file:
debug: more information logging
- log value `distance` and `visrange` in `LOG_DBG` because
they occur quite often, need checking actual values if
they are really not very much different, small
differences can be ignored in log WARNINGs
2 lines of code changed in 1 file:
fix merged r8280 for (average), test pass all
17 lines of code changed in 1 file:
(population_load_data_all_genomes): implemented procedure to load genome data
- merged after further testing r8121 from 06
- merged from feature branch as in r8119
386 lines of code changed in 1 file:
merged workaround against intel fortran 19 compiler bugs r7726:r7740 from HEDG2_06: crashes due to (a) loss of non-fixed log file unit while running and (b) loss of access to dynamic derived objects from other modules with O3 and -parallel optimisation flags
176 lines of code changed in 2 files:
merged xmpp notifications r7693 and r7736
8 lines of code changed in 1 file:
(food_resource_replenish_food_items_all): merged latest changes from model 06, r7676:r7687, tests pass
65 lines of code changed in 1 file:
merged r7671, default vcs
3 lines of code changed in 1 file:
merged r7669, version control info error fix
13 lines of code changed in 1 file:
merged r7665: confusing UNIVERSE added _NOTUSE
6 lines of code changed in 1 file:
backported r7653, intro doc on new stop file signal control
23 lines of code changed in 1 file:
stop file code r7651 merged to other models
27 lines of code changed in 2 files:
doc: fix wrong doc statement on relative visual range in (predator_capture_risk_calculate_fish)
1 lines of code changed in 1 file:
memory leak check using libasan breaks debug build on most Windows installations, enable libasan only on non-Windows platforms
6 lines of code changed in 1 file:
we have new tegsvn server and fixed Makefile path in generated doxygen output
0 lines of code changed in 2 files:
(84 more)