First pass, add a PDF class

.gitignore

@@ -1,4 +1,7 @@
 # To ignore
 *.*~
 **/*.*~
-git_push.sh
+git_push.sh
+__pycache__
+outputs/
+tmp_lhapdf

README

@@ -1,21 +1,25 @@
 Readme (under construction) for fixpar_nnpdf code
 
-Requires NNPDF code from https://docs.nnpdf.science via conda installation. Tested for:
+Requires NNPDF code from https://docs.nnpdf.science either from source or conda
 
-conda install nnpdf python=3.9
-
-(I think python version may be needed for lhapdf to run though need to double check that)
+```
+    conda install nnpdf -c https://packages.nnpdf.science/conda -c conda-forge
+```
 
 To run simply execute:
 
 python fixpar_nnpdf.py --config=configs/**.yaml
 
-for the corresponding .yaml file. Some explanation of the various flags is provided in the example .yaml files but clearly this needs better documentation + some specific example cases to be provided.
+for the corresponding .yaml file. Some explanation of the various flags is provided in the example .yaml files but clearly this needs better documentation + some specific example cases to be provided. Adding to this, to run:
+
+- A fixed chi^2 output. Set fixpar to False. 
+- A fit. Set fixpar to True. The second column of 0/1's in the input file (in input/) specify whether a given parmeter is free (1) or fixed (0). If all are fixed this will be as if fixpar is set to True. The parameters for the best fit will be output to outputs/pars/$label.dat and the covariance matrix to outputs/cov/$label.dat.
+- An eigenvector scan. Set readcov to True, with the 'cov input file' given by the output of a previous fit. Then specify if dynamic tolerance is used (dynamic_tol) and if not the size of the fixed tolerance (t2_err).
 
 The outputs are in the outputs/ folder:
 
 /evgrids  : the output pdf grids which can then be evolved using the NNPDF evolution (to be tided/documented)
 /buffer : outputs from running code
 /cov : covariance matrix (used for error calculation)
 /evscans: outputs if eigenvector scan is done
-/pars : the PDF parameters
+/pars : the PDF parameters

configs/fit_example.yaml

@@ -0,0 +1,68 @@
+# input files
+inputs:
+  # PDF parameter inputs:  
+  input file: inputdef_2parfree.dat 
+  # input covariance matrix file (if used)
+  cov input file: newmin_final_remin_out.dat
+  # if true then read in covariance matrix and evaluate PDF errors
+  readcov: False
+
+#  output files
+outputs:
+  # label for output files
+  label: fitout_jcm
+
+basis pars:
+  # If true then two term gluon parameterisation uesd
+  g_second_term: True
+  # if true and g_second_term=False then includes 7th Chebyshev for gluon
+  g_cheb7: False
+  # If true then delta_S+ set to that of sea
+  asp_fix: True
+  # If true thedelta_d=delta_u for d_V and u_V (need to set delta_d fixed or will crash!)
+  dvd_eq_uvd: False
+
+pdf pars:
+  # use external LHAPDF grid as input 
+  lhin: False
+  # if true then use lhapdf grids for theory evaluation 
+  # (for PDF pd fits can use parameterisation directly instead, otherwise has to be true)
+  uselha: True
+  # if lhin=true, name of set input
+  PDFlabel_lhin: NNPDF40_nnlo_pch_as_01180
+
+pdf closure:
+  # if true then scatters when doing direct PDF pd fit
+  pdfscat: False
+  # label of pseudodata used
+  pdlabel: 'NNPDF40pch_gl_l0'
+  #  if true then do direct fit to PDF pseudodata
+  pdpdf: False
+
+pseudodata flags:
+  # if true then write pseudodata out to file
+  pdout: False
+  # if true then write pseudodata out to file
+  pdin: False
+
+fit pars:
+  # Only use t0 for chi2i and chi2o in levmar (i.e. no derivative at all)
+  t0_noderivin: True
+  # run with fixed input parameters (override input card flags)
+  fixpar: False
+  # NNPDF theory id (211 = NNLO pch)
+  theoryidi: 40001000
+  # impose NNPDF positivity in fit
+  nnpdf_pos: False
+  # if true then impose 4.0 positivity constraint, if pos_const=True
+  pos_40: True
+  # if true impose weight to prefer delta_d > 0.25
+  deld_const: False
+  # if true then generates a replica from baseline dataset with seed irep
+  pseud: False
+  # irep number - also used when generating error grids
+  irep: 0
+  # NMC PD data - set covariance matrix to be diagonal
+  nmcpd_diag: False
+  # dataset flag - global, HERAonly, noHERA, noLHC
+  dset_type: 'global_new'

configs/fit_mshtfit_publication_longmin.yaml

@@ -0,0 +1,72 @@
+# input files
+inputs:
+  # PDF parameter inputs:  
+  input file: input_mshtfit_publication_longmin.dat
+  # input covariance matrix file (if used)
+  cov input file: newmin_final_remin_out.dat
+  # if true then read in covariance matrix and evaluate PDF errors
+  readcov: False
+
+#  output files
+outputs:
+  # label for output files
+  label: mshtfit_publication_longmin_out
+
+basis pars:
+  # If true then two term gluon parameterisation uesd
+  g_second_term: True
+  # if true and g_second_term=False then includes 7th Chebyshev for gluon
+  g_cheb7: False
+  # If true then delta_S+ set to that of sea
+  asp_fix: True
+  # If true thedelta_d=delta_u for d_V and u_V (need to set delta_d fixed or will crash!)
+  dvd_eq_uvd: False
+
+pdf pars:
+  # use external LHAPDF grid as input 
+  lhin: False
+  # if true then use lhapdf grids for theory evaluation 
+  # (for PDF pd fits can use parameterisation directly instead, otherwise has to be true)
+  uselha: True
+  # if lhin=true, name of set input
+  PDFlabel_lhin: NNPDF40_nnlo_pch_as_01180
+
+pdf closure:
+  # if true then scatters when doing direct PDF pd fit
+  pdfscat: False
+  # label of pseudodata used
+  pdlabel: 'NNPDF40pch_gl_l0'
+  #  if true then do direct fit to PDF pseudodata
+  pdpdf: False
+
+pseudodata flags:
+  # if true then write pseudodata out to file
+  pdout: False
+  # if true then write pseudodata out to file
+  pdin: False
+
+fit pars:
+  # Use dynamic tolerance in error calc
+  dynamic_tol: False
+  # T value for error calculation
+  t2_err: 1.
+  # Only use t0 for chi2i and chi2o in levmar (i.e. no derivative at all)
+  t0_noderivin: True
+  # run with fixed input parameters (override input card flags)
+  fixpar: False
+  # NNPDF theory id (211 = NNLO pch)
+  theoryidi: 40001000
+  # impose NNPDF positivity in fit
+  nnpdf_pos: False
+  # if true then impose 4.0 positivity constraint, if pos_const=True
+  pos_40: True
+  # if true impose weight to prefer delta_d > 0.25
+  deld_const: False
+  # if true then generates a replica from baseline dataset with seed irep
+  pseud: False
+  # irep number - also used when generating error grids
+  irep: 0
+  # NMC PD data - set covariance matrix to be diagonal
+  nmcpd_diag: False
+  # dataset flag - global, HERAonly, noHERA, noLHC
+  dset_type: 'global_new'

configs/fit_mshtfit_publication_shortmin.yaml

@@ -0,0 +1,72 @@
+# input files
+inputs:
+  # PDF parameter inputs:  
+  input file: input_mshtfit_publication_shortmin.dat
+  # input covariance matrix file (if used)
+  cov input file: newmin_final_remin_out.dat
+  # if true then read in covariance matrix and evaluate PDF errors
+  readcov: False
+
+#  output files
+outputs:
+  # label for output files
+  label: mshtfit_publication_shortmin_out
+
+basis pars:
+  # If true then two term gluon parameterisation uesd
+  g_second_term: True
+  # if true and g_second_term=False then includes 7th Chebyshev for gluon
+  g_cheb7: False
+  # If true then delta_S+ set to that of sea
+  asp_fix: True
+  # If true thedelta_d=delta_u for d_V and u_V (need to set delta_d fixed or will crash!)
+  dvd_eq_uvd: False
+
+pdf pars:
+  # use external LHAPDF grid as input 
+  lhin: False
+  # if true then use lhapdf grids for theory evaluation 
+  # (for PDF pd fits can use parameterisation directly instead, otherwise has to be true)
+  uselha: True
+  # if lhin=true, name of set input
+  PDFlabel_lhin: NNPDF40_nnlo_pch_as_01180
+
+pdf closure:
+  # if true then scatters when doing direct PDF pd fit
+  pdfscat: False
+  # label of pseudodata used
+  pdlabel: 'NNPDF40pch_gl_l0'
+  #  if true then do direct fit to PDF pseudodata
+  pdpdf: False
+
+pseudodata flags:
+  # if true then write pseudodata out to file
+  pdout: False
+  # if true then write pseudodata out to file
+  pdin: False
+
+fit pars:
+  # Use dynamic tolerance in error calc
+  dynamic_tol: False
+  # T value for error calculation
+  t2_err: 1.
+  # Only use t0 for chi2i and chi2o in levmar (i.e. no derivative at all)
+  t0_noderivin: True
+  # run with fixed input parameters (override input card flags)
+  fixpar: False
+  # NNPDF theory id (211 = NNLO pch)
+  theoryidi: 40001000
+  # impose NNPDF positivity in fit
+  nnpdf_pos: False
+  # if true then impose 4.0 positivity constraint, if pos_const=True
+  pos_40: True
+  # if true impose weight to prefer delta_d > 0.25
+  deld_const: False
+  # if true then generates a replica from baseline dataset with seed irep
+  pseud: False
+  # irep number - also used when generating error grids
+  irep: 0
+  # NMC PD data - set covariance matrix to be diagonal
+  nmcpd_diag: False
+  # dataset flag - global, HERAonly, noHERA, noLHC
+  dset_type: 'global_new'