From 39ac76f9ce4afe6efb65205c3f467b4881c3fe69 Mon Sep 17 00:00:00 2001
From: Brown <2mx@ornl.gov>
Date: Sat, 2 Apr 2022 11:21:12 -0400
Subject: [PATCH] add phys param writing
without changing object: CovarianceData
---
sammy/src/fin/mfin0.f90 | 5 ++-
sammy/src/fin/mfin5.f90 | 18 +++++++++--
sammy/src/fit/mfit3.f90 | 3 +-
sammy/src/io/Hdf5IO.cpp | 29 ++++++++++++-----
sammy/src/io/Hdf5IO.h | 10 +++++-
sammy/src/io/interface/cix/Hdf5IO.cpp2f.xml | 2 ++
.../src/io/interface/cpp/Hdf5IOInterface.cpp | 6 ++--
sammy/src/io/interface/cpp/Hdf5IOInterface.h | 4 +--
sammy/src/io/interface/fortran/Hdf5IO_I.f90 | 6 ++--
sammy/src/io/interface/fortran/Hdf5IO_M.f90 | 9 ++++--
sammy/src/io/tests/Hdf5IOTest.cpp | 4 ++-
sammy/src/salmon/CovToolBox.cpp | 31 +++++++++++++++++++
sammy/src/salmon/CovToolBox.h | 12 +++++++
13 files changed, 114 insertions(+), 25 deletions(-)
diff --git a/sammy/src/fin/mfin0.f90 b/sammy/src/fin/mfin0.f90
index bab45d6e2..f004ccd5c 100644
--- a/sammy/src/fin/mfin0.f90
+++ b/sammy/src/fin/mfin0.f90
@@ -6,6 +6,7 @@ module fin
!
! *** Purpose -- Convert to physical parameters, output results
!
+ ! ---- Common block modules ----------------
use over_common_m
use oops_common_m
use fixedi_m
@@ -14,6 +15,7 @@ module fin
use samxxx_common_m
use oopsch_common_m
use fixedr_m
+ ! ---- C++ interfaces ----------------------
use SammyRMatrixParameters_M
use SammyResonanceInfo_M
use EndfData_common_m
@@ -21,11 +23,12 @@ module fin
use ReadCovarianceInfo_m
use ResonanceCovariance_M
use AllocateFunctions_m
+ use SammyLptPrinting_m
+ ! ---- traditional modules -----------------
use fin1
use fin2
use fin3
use fin5
- use SammyLptPrinting_m
IMPLICIT DOUBLE PRECISION (a-h,o-z)
real(kind=8),allocatable::Ratio(:)
real(kind=8),allocatable,dimension(:)::A_Idum
diff --git a/sammy/src/fin/mfin5.f90 b/sammy/src/fin/mfin5.f90
index 334b12a96..8bba221f6 100644
--- a/sammy/src/fin/mfin5.f90
+++ b/sammy/src/fin/mfin5.f90
@@ -449,6 +449,7 @@ module fin5
!
! *** PURPOSE -- WRITE COVARIANCE (ETC) FILE
!
+ ! ---- common block modules ----------------
use fixedi_m
use ifwrit_m
use samxxx_common_m
@@ -457,6 +458,7 @@ module fin5
use namfil_common_m
use par_parameter_names_common_m
use EndfData_common_m
+ ! ---- C++ interfaces ----------------------
use SammySpinGroupInfo_M
use SammyIsoInfo_M
use SammyResonanceInfo_M
@@ -464,10 +466,13 @@ module fin5
use ReadCovarianceInfo_m
use ResonanceCovariance_M
use SammyRExternalInfo_M
+ use Hdf5IO_m
+
IMPLICIT DOUBLE PRECISION (a-h,o-z)
-!
!
type(ResonanceCovariance)::physCov
+ type(Hdf5IO)::h5
+
DIMENSION Parbrd(*), Iflbrd(*), &
Pardet(*), Ifldet(*), Igrdet(*), &
Polar(2,*), &
@@ -511,11 +516,18 @@ module fin5
integer,allocatable,dimension(:)::Ifliso
integer,allocatable,dimension(:,:,:)::Iflext
real(kind=8),allocatable,dimension(:,:,:)::Parext
- integer::nradInfo
+ integer::nradInfo,wantUparam
CHARACTER*3 Versn
DATA Versn/'M7 '/
-!
+
+! ------------------------------------------------
+! Write out the RPCM to HDF5 in physical param space
+ call h5%initialize()
+ wantUparam = 0
+ call h5%writeRPCM(covData,resParData,trim(Samcov)//".h5",wantUparam)
+ call h5%destroy()
+! ------------------------------------------------
!
nradInfo = radFitFlags%getNumRadInfo()
N = MAX0 (Nvpall, Nres*Ntotc2, Nres*Ntriag, &
diff --git a/sammy/src/fit/mfit3.f90 b/sammy/src/fit/mfit3.f90
index e48720633..9487ca02f 100644
--- a/sammy/src/fit/mfit3.f90
+++ b/sammy/src/fit/mfit3.f90
@@ -254,6 +254,7 @@ module fit3_m
Engurr(*), Aold(3,*), Iflold(3,*), Ktold(*)
type(ResonanceCovariance)::uCov, invCov
type(Hdf5IO)::h5
+ integer, parameter :: wantUparam = 1
!
!
CALL Newopn (62, Samcov, 1)
@@ -314,7 +315,7 @@ module fit3_m
! Write simple res param covariance matrix
! to HDF5 file (u-param & u-covar)
! -----------------------------------------
- call h5%writeRPCM(covData,trim(Samcov)//".h5")
+ call h5%writeRPCM(covData,resParData,trim(Samcov)//".h5",wantUparam)
RETURN
END
diff --git a/sammy/src/io/Hdf5IO.cpp b/sammy/src/io/Hdf5IO.cpp
index baac8ff06..b65a43dfb 100644
--- a/sammy/src/io/Hdf5IO.cpp
+++ b/sammy/src/io/Hdf5IO.cpp
@@ -1,5 +1,4 @@
#include "Hdf5IO.h"
-#include <cmath>
namespace sammy {
@@ -102,23 +101,37 @@ namespace sammy {
}
}
- void Hdf5IO::writeRPCM(CovarianceData & cov,std::string hdf5Filename){
+ void Hdf5IO::writeRPCM(CovarianceData & cov,
+ SammyRMatrixParameters & resParData,
+ std::string hdf5Filename,
+ int rpcmIsReduced){
+ if( rpcmIsReduced < 0 || rpcmIsReduced > 1 ){
+ std::string errmsg("integer rpcmIsReduced must be 0 || 1");
+ throw std::runtime_error(errmsg);
+ }
std::cout << "--------------------------------------------" << std::endl;
std::cout << "writing resonance covariance to HDF5 file..." << std::endl;
std::cout << "--------------------------------------------" << std::endl;
- // get parameter covariance out
- endf::ResonanceCovariance * parCov = cov.getUCovariance();
+ std::vector<double> param;
int numParam = cov.getNumTotalParam();
+ endf::ResonanceCovariance * parCov;
+ // ---- get parameter covariance and parameters out ---------
+ if( rpcmIsReduced ){
+ parCov = cov.getUCovariance();
+ for( int i=0; i<numParam; ++i ) param.push_back(cov.getUParamValue(i));
+ }
+ else{
+ CovToolBox ctb;
+ param = ctb.getPhysParam(resParData);
+ parCov = cov.getCovariance();
+ }
+ // ---- check if length of params match covariance ----------
int numRows = parCov->getNumRows();
if( numParam != numRows ) {
std::cerr << "numParam != numRows of covariance!" << std::endl;
}
- // get parameters out
- std::vector<double> param;
- for( int i=0; i<numParam; ++i ) param.push_back(cov.getUParamValue(i));
-
double data[numRows][numRows];
for( int i=0; i<numRows; ++i ){
for( int j=0; j<numRows; ++j ){
diff --git a/sammy/src/io/Hdf5IO.h b/sammy/src/io/Hdf5IO.h
index 396439e51..fce378ccb 100644
--- a/sammy/src/io/Hdf5IO.h
+++ b/sammy/src/io/Hdf5IO.h
@@ -1,14 +1,19 @@
#ifndef SAMMY_HDF5IO_H
#define SAMMY_HDF5IO_H
+// ---- std ---------------------------
#include <vector>
#include <fstream>
#include <iostream>
#include <cstring>
#include <stdexcept>
+#include <cmath>
+// ---- sammy -------------------------
#include "OdfIO.h"
#include "H5Cpp.h"
#include "../endf/CovarianceData.h"
+#include "../endf/SammyRMatrixParameters.h"
+#include "../salmon/CovToolBox.h"
namespace sammy{
@@ -60,7 +65,10 @@ namespace sammy{
* @param cov class that contains all param. covariance info
* @param hdf5Filename the string specifying the H5 file name
************************************************************/
- void writeRPCM(CovarianceData & cov,std::string hdf5Filename);
+ void writeRPCM(CovarianceData & cov,
+ SammyRMatrixParameters & resParData,
+ std::string hdf5Filename,
+ int rpcmIsReduced);
/*************************************************************
* Read the resonance parameter covariance matrix from an HDF5
diff --git a/sammy/src/io/interface/cix/Hdf5IO.cpp2f.xml b/sammy/src/io/interface/cix/Hdf5IO.cpp2f.xml
index 87b2cf43e..c86a09b1f 100644
--- a/sammy/src/io/interface/cix/Hdf5IO.cpp2f.xml
+++ b/sammy/src/io/interface/cix/Hdf5IO.cpp2f.xml
@@ -5,7 +5,9 @@
<class name="Hdf5IO">
<method name="writeRPCM">
<param name="cov" type="CovarianceData"/>
+ <param name="resParData" type="SammyRMatrixParameters"/>
<param name="hdf5Filename" type="char*" ctype="std::string"/>
+ <param name="rpcmIsReduced" type="int"/>
</method>
<method name="readRPCM">
<param name="cov" type="CovarianceData"/>
diff --git a/sammy/src/io/interface/cpp/Hdf5IOInterface.cpp b/sammy/src/io/interface/cpp/Hdf5IOInterface.cpp
index 419d9310b..83d6fb957 100644
--- a/sammy/src/io/interface/cpp/Hdf5IOInterface.cpp
+++ b/sammy/src/io/interface/cpp/Hdf5IOInterface.cpp
@@ -2,16 +2,16 @@
* This file has been dynamically generated by Class Interface Xml (CIX)
* DO NOT MODIFY THIS FILE -- CHANGES WILL BE OVERWRITTEN UPON REGENERATION
* If changes need to occur, modify the appropriate CIX xml file
-* Date Generated: Wed Jan 26 13:57:17 EST 2022
+* Date Generated: Sat Apr 02 11:08:38 EDT 2022
* If any issues are experiences with this generated file that cannot be fixed
* with adjustment of the CIX xml file, please contact Robert A. Lefebvre, raq@ornl.gov
*/
#include <string.h>
#include "Hdf5IOInterface.h"
using namespace sammy;
-void Hdf5IO_writeRPCM(void * Hdf5IO_ptr,CovarianceData * cov,char* hdf5Filename)
+void Hdf5IO_writeRPCM(void * Hdf5IO_ptr,CovarianceData * cov,SammyRMatrixParameters * resParData,char* hdf5Filename,int * rpcmIsReduced)
{
- ((Hdf5IO*)Hdf5IO_ptr)->writeRPCM(*cov,std::string(hdf5Filename));
+ ((Hdf5IO*)Hdf5IO_ptr)->writeRPCM(*cov,*resParData,std::string(hdf5Filename),*rpcmIsReduced);
}
void Hdf5IO_readRPCM(void * Hdf5IO_ptr,CovarianceData * cov,char* hdf5Filename)
diff --git a/sammy/src/io/interface/cpp/Hdf5IOInterface.h b/sammy/src/io/interface/cpp/Hdf5IOInterface.h
index b2ea36368..5e436ef2d 100644
--- a/sammy/src/io/interface/cpp/Hdf5IOInterface.h
+++ b/sammy/src/io/interface/cpp/Hdf5IOInterface.h
@@ -2,7 +2,7 @@
* This file has been dynamically generated by Class Interface Xml (CIX)
* DO NOT MODIFY THIS FILE -- CHANGES WILL BE OVERWRITTEN UPON REGENERATION
* If changes need to occur, modify the appropriate CIX xml file
-* Date Generated: Wed Jan 26 13:57:17 EST 2022
+* Date Generated: Sat Apr 02 11:08:38 EDT 2022
* If any issues are experiences with this generated file that cannot be fixed
* with adjustment of the CIX xml file, please contact Robert A. Lefebvre, raq@ornl.gov
*/
@@ -13,7 +13,7 @@ using namespace sammy;
#ifdef __cplusplus
extern "C" {
#endif
-void Hdf5IO_writeRPCM(void * Hdf5IO_ptr,CovarianceData * cov,char* hdf5Filename);
+void Hdf5IO_writeRPCM(void * Hdf5IO_ptr,CovarianceData * cov,SammyRMatrixParameters * resParData,char* hdf5Filename,int * rpcmIsReduced);
void Hdf5IO_readRPCM(void * Hdf5IO_ptr,CovarianceData * cov,char* hdf5Filename);
void* Hdf5IO_initialize();
void Hdf5IO_destroy(void * Hdf5IO_ptr);
diff --git a/sammy/src/io/interface/fortran/Hdf5IO_I.f90 b/sammy/src/io/interface/fortran/Hdf5IO_I.f90
index f9f92f7f4..ace498dff 100644
--- a/sammy/src/io/interface/fortran/Hdf5IO_I.f90
+++ b/sammy/src/io/interface/fortran/Hdf5IO_I.f90
@@ -2,19 +2,21 @@
!! This file has been dynamically generated by Class Interface Xml (CIX)
!! DO NOT MODIFY THIS FILE -- CHANGES WILL BE OVERWRITTEN UPON REGENERATION
!! If changes need to occur, modify the appropriate CIX xml file
-!! Date Generated: Wed Jan 26 13:57:17 EST 2022
+!! Date Generated: Sat Apr 02 11:08:38 EDT 2022
!! If any issues are experiences with this generated file that cannot be fixed
!! with adjustment of the CIX xml file, please contact Robert A. Lefebvre, raq@ornl.gov
!!/
module Hdf5IO_I
use, intrinsic :: ISO_C_BINDING
interface
-subroutine f_Hdf5IO_writeRPCM(Hdf5IO_ptr, cov,hdf5Filename ) BIND(C,name="Hdf5IO_writeRPCM")
+subroutine f_Hdf5IO_writeRPCM(Hdf5IO_ptr, cov,resParData,hdf5Filename,rpcmIsReduced ) BIND(C,name="Hdf5IO_writeRPCM")
use,intrinsic :: ISO_C_BINDING
implicit none
type(C_PTR), value :: Hdf5IO_ptr;
type(C_PTR), value :: cov;
+ type(C_PTR), value :: resParData;
character(C_CHAR) :: hdf5Filename;
+ integer(C_INT) :: rpcmIsReduced;
end subroutine
subroutine f_Hdf5IO_readRPCM(Hdf5IO_ptr, cov,hdf5Filename ) BIND(C,name="Hdf5IO_readRPCM")
use,intrinsic :: ISO_C_BINDING
diff --git a/sammy/src/io/interface/fortran/Hdf5IO_M.f90 b/sammy/src/io/interface/fortran/Hdf5IO_M.f90
index c6c492573..ad4efc070 100644
--- a/sammy/src/io/interface/fortran/Hdf5IO_M.f90
+++ b/sammy/src/io/interface/fortran/Hdf5IO_M.f90
@@ -2,7 +2,7 @@
!! This file has been dynamically generated by Class Interface Xml (CIX)
!! DO NOT MODIFY THIS FILE -- CHANGES WILL BE OVERWRITTEN UPON REGENERATION
!! If changes need to occur, modify the appropriate CIX xml file
-!! Date Generated: Wed Jan 26 13:57:17 EST 2022
+!! Date Generated: Sat Apr 02 11:08:38 EDT 2022
!! If any issues are experiences with this generated file that cannot be fixed
!! with adjustment of the CIX xml file, please contact Robert A. Lefebvre, raq@ornl.gov
!!/
@@ -10,6 +10,7 @@ module Hdf5IO_M
use, intrinsic :: ISO_C_BINDING
use Hdf5IO_I
use CovarianceData_M
+use SammyRMatrixParameters_M
type Hdf5IO
type(C_PTR) :: instance_ptr=C_NULL_PTR
contains
@@ -19,12 +20,14 @@ type Hdf5IO
procedure, pass(this) :: destroy => Hdf5IO_destroy
end type Hdf5IO
contains
-subroutine Hdf5IO_writeRPCM(this, cov, hdf5Filename)
+subroutine Hdf5IO_writeRPCM(this, cov, resParData, hdf5Filename, rpcmIsReduced)
implicit none
class(Hdf5IO)::this
class(CovarianceData)::cov
+ class(SammyRMatrixParameters)::resParData
character(len=*)::hdf5Filename
- call f_Hdf5IO_writeRPCM(this%instance_ptr, cov%instance_ptr,hdf5Filename//C_NULL_CHAR)
+ integer(C_INT)::rpcmIsReduced
+ call f_Hdf5IO_writeRPCM(this%instance_ptr, cov%instance_ptr,resParData%instance_ptr,hdf5Filename//C_NULL_CHAR,rpcmIsReduced)
end subroutine
subroutine Hdf5IO_readRPCM(this, cov, hdf5Filename)
implicit none
diff --git a/sammy/src/io/tests/Hdf5IOTest.cpp b/sammy/src/io/tests/Hdf5IOTest.cpp
index 53fb088ac..4a2b85100 100644
--- a/sammy/src/io/tests/Hdf5IOTest.cpp
+++ b/sammy/src/io/tests/Hdf5IOTest.cpp
@@ -9,8 +9,10 @@ TEST(Hdf5IO,readWriteRPCM)
{
sammy::CovarianceData covData;
sammy::CovarianceData covDataR;
+ sammy::SammyRMatrixParameters resParData; //dummy
sammy::Hdf5IO h5;
sammy::Hdf5IO h5R;
+ int wantUparam = 1;
// ----- set up the resonance covariance ---------------
covData.makeNewUCovariance();
@@ -19,7 +21,7 @@ TEST(Hdf5IO,readWriteRPCM)
cov->setCovariance(0,0,2.0); cov->setCovariance(0,1,1.0);
cov->setCovariance(1,0,1.0); cov->setCovariance(1,1,4.0);
- h5.writeRPCM(covData, "testreadwrite.h5");
+ h5.writeRPCM(covData,resParData, "testreadwrite.h5",wantUparam);
h5R.readRPCM(covDataR,"testreadwrite.h5");
endf::ResonanceCovariance * covR = covDataR.getUCovariance();
diff --git a/sammy/src/salmon/CovToolBox.cpp b/sammy/src/salmon/CovToolBox.cpp
index 9fb033497..0b2c7284e 100644
--- a/sammy/src/salmon/CovToolBox.cpp
+++ b/sammy/src/salmon/CovToolBox.cpp
@@ -48,4 +48,35 @@ namespace sammy{
}
}
}
+
+ std::vector<double> CovToolBox::getPhysParam(SammyRMatrixParameters & resParData){
+
+ // --------------- grab all the *varied* pars --------------------------
+ int nr = resParData.getNumResonances();
+ std::vector<double> physParam;
+ for(int iRes =0;iRes<nr;++iRes){ // loop over resonances
+ sammy::SammyResonanceInfo *resInfo = resParData.getResonanceInfo(iRes);
+ int iGrp = resInfo->getSpinGroupIndex();
+ endf::RMatResonance *resonance = resParData.getResonance(resInfo);
+ sammy::SammySpinGroupInfo *spinInfo = resParData.getSpinGroupInfo(iGrp);
+
+ int parPerRes = spinInfo->getNumResPar();
+ for(int par=0;par<parPerRes;++par){ // loop over par's for each res
+ int covInd = 0; // >0 means varied or PUP'd
+ if(par==0){
+ covInd = resInfo->getEnergyFitOption();
+ if( covInd>0 && covInd!=3 ){
+ physParam.push_back(resonance->getEres());
+ }
+ }
+ else{
+ covInd = resInfo->getChannelFitOption(par-1);
+ if( covInd>0 && covInd!=3 ){
+ physParam.push_back(resonance->getWidth(par-1));
+ }
+ }
+ }
+ }
+ return physParam;
+ }
}
\ No newline at end of file
diff --git a/sammy/src/salmon/CovToolBox.h b/sammy/src/salmon/CovToolBox.h
index 7a17de76f..b6a9df3a8 100644
--- a/sammy/src/salmon/CovToolBox.h
+++ b/sammy/src/salmon/CovToolBox.h
@@ -5,6 +5,9 @@
#include "ScaleData/Core/io/CoverxFile.h"
#include "ScaleUtils/EndfLib/CrossSectionCovariance.h"
+#include "endf/SammyRMatrixParameters.h"
+#include "endf/SammyResonanceInfo.h"
+#include "endf/CovarianceData.h"
#include <iostream>
#include <algorithm>
@@ -29,6 +32,15 @@ namespace sammy {
void fillCrossCovFromCoverx(coverx::CoverxFile & cf,
endf::CrossCovList & cc);
+ /***********************************************************************
+ * Find varied parameters fill a vector with them and return the
+ * physical parameters in the rigid "SAMMY order" in a vector of doubles
+ *
+ * @param resParData the full r-matrix parameters object
+ * @return physParam vector of varied physical parameters
+ **********************************************************************/
+ std::vector<double> getPhysParam(SammyRMatrixParameters & resParData);
+
private:
};
--
GitLab