nested-fit 5.6.6.dev120__tar.gz → 5.6.7.dev122__tar.gz

{nested_fit-5.6.6.dev120 → nested_fit-5.6.7.dev122}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nested_fit
-Version: 5.6.6.dev120
+Version: 5.6.7.dev122
 Summary: The nested_fit package.
 Author: Martino Trassinelli, Lune Maillard, César Godinho
 Project-URL: Homepage, https://github.com/martinit18/nested_fit
@@ -444,7 +444,7 @@ Examples of use of a legacy function can be found in `examples/data_analysis/aaa
 
 ## Present version and history of the past versions
 
-The present version is 5.6.4\
+The present version is 5.6.6\
 New features:
 - New function to visualizing the capacty heat for POTENTIAL calculations
 - Latex input support for compound variable names (i.e. x_{sub})
@@ -453,6 +453,7 @@ New features:
 - Optional management of memory of dead points (in RAM or file)
 - Optional writing of dead points information
 - Optional writing of parameter statistics (mean, standard deviation, etc.)
+- Persistent option commands cache
 
 
 Previous versions are:

{nested_fit-5.6.6.dev120 → nested_fit-5.6.7.dev122}/README.md

@@ -419,7 +419,7 @@ Examples of use of a legacy function can be found in `examples/data_analysis/aaa
 
 ## Present version and history of the past versions
 
-The present version is 5.6.4\
+The present version is 5.6.6\
 New features:
 - New function to visualizing the capacty heat for POTENTIAL calculations
 - Latex input support for compound variable names (i.e. x_{sub})
@@ -428,6 +428,7 @@ New features:
 - Optional management of memory of dead points (in RAM or file)
 - Optional writing of dead points information
 - Optional writing of parameter statistics (mean, standard deviation, etc.)
+- Persistent option commands cache
 
 
 Previous versions are:

{nested_fit-5.6.6.dev120 → nested_fit-5.6.7.dev122}/nested_fit.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nested_fit
-Version: 5.6.6.dev120
+Version: 5.6.7.dev122
 Summary: The nested_fit package.
 Author: Martino Trassinelli, Lune Maillard, César Godinho
 Project-URL: Homepage, https://github.com/martinit18/nested_fit
@@ -444,7 +444,7 @@ Examples of use of a legacy function can be found in `examples/data_analysis/aaa
 
 ## Present version and history of the past versions
 
-The present version is 5.6.4\
+The present version is 5.6.6\
 New features:
 - New function to visualizing the capacty heat for POTENTIAL calculations
 - Latex input support for compound variable names (i.e. x_{sub})
@@ -453,6 +453,7 @@ New features:
 - Optional management of memory of dead points (in RAM or file)
 - Optional writing of dead points information
 - Optional writing of parameter statistics (mean, standard deviation, etc.)
+- Persistent option commands cache
 
 
 Previous versions are:

{nested_fit-5.6.6.dev120 → nested_fit-5.6.7.dev122}/nested_fit.egg-info/SOURCES.txt

@@ -218,5 +218,4 @@ test/CMakeLists.txt
 test/README.md
 test/str.f90
 test/test.f90
-tmp/.nf_input.yaml.~6ff749be
-tmp/nf_input.yaml
+tmp/.nf_input.yaml.~6ff749be

{nested_fit-5.6.6.dev120 → nested_fit-5.6.7.dev122}/pynested_fit/nested_res.py

@@ -123,7 +123,8 @@ class Analysis(object):
                 sep=r"\s+",
                 engine='python',
                 header=0,
-                names=["density","energy"]
+                names=["density","energy"],
+                usecols=[0, 1] # (Damià) if Q_POTENTIAL file also has columns V, Q, T
             )
             print(self.df_e.columns)
             print('Available parameters:', list(self.df_e.columns))
@@ -250,7 +251,7 @@ class Analysis(object):
         # Max parameter set
         output_data['max'] = [float(lines[11+index].split()[1]) for index in range(npar)]
         
-        if input_data['writing']['statistics'] and ((not input_data['search']['hard_writing']) or input_data['writing']['all_parameters']):
+        if (not 'writing' in input_data or input_data['writing']['statistics']) or (('writing' in input_data and not input_data['search']['hard_writing']) and ('writing' in input_data and input_data['writing']['all_parameters'])):
             # Average and standard deviation of parameters
             #output_data['mean']= [[float(lines[10+npar+index].split()[1]),float(lines[10+npar+index].split()[3])] for index in range(npar)]
             output_data['mean'] = [float(lines[13+npar+index].split()[1]) for index in range(npar)]
@@ -1311,8 +1312,8 @@ class Analysis(object):
 
         # Plot interpolation
         if clear: plt.clf()
-        plt.xlabel('Value of parameter ' + title1)
-        plt.ylabel('Value of parameter ' + title2)
+        plt.xlabel('Value of parameter ' + title1) # (Damià) title1 and title2 not defined in this function.
+        plt.ylabel('Value of parameter ' + title2) # I guess they should be par_name1 and par_name2. Please check.
         # Plot the 2D interpolation
         plt.axis([xmin, xmax, ymin, ymax])
         if levels:

{nested_fit-5.6.6.dev120 → nested_fit-5.6.7.dev122}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "nested_fit"
-version = "5.6.6.dev120"
+version = "5.6.7.dev122"
 description = "The nested_fit package."
 readme = "README.md"
 
@@ -65,7 +65,7 @@ archs = ["x86_64", "arm64"]
 archs = ["x86_64"]
 
 [tool.setuptools_scm]
-fallback_version = "5.6.6.dev120"
+fallback_version = "5.6.7.dev122"
 
 [options]
 python_requires = ">=3.8"

{nested_fit-5.6.6.dev120 → nested_fit-5.6.7.dev122}/src/Mod_input_parse.f90

@@ -418,11 +418,11 @@ MODULE MOD_INPUTPARSE
         END DO
     END SUBROUTINE
 
-    ! Max subkeys = 1024
+    ! Max subkeys = 1024*4 ! (Damià) *4 to allow for more params in nf_input.yaml
     SUBROUTINE INPUTDATA_MAP_SUBKEYSOF(map, key, output, count)
         CLASS(InputDataMap_t)   , INTENT(INOUT), TARGET :: map
         CHARACTER(*)            , INTENT(IN)            :: key
-        CHARACTER(128)          , INTENT(OUT)           :: output(1024)
+        CHARACTER(128)          , INTENT(OUT)           :: output(1024*4) ! (Damià) *4 to allow for more params in nf_input.yaml
         INTEGER                 , INTENT(OUT)           :: count
         INTEGER                                         :: i
         TYPE(InputDataMapPair_t), POINTER               :: next

nested_fit-5.6.7.dev122/src/Mod_options.f90

@@ -0,0 +1,47 @@
+! Brief  : Manages a small cache file that handles option saving
+! Author : César Godinho
+! Date   : Modified - 21/07/2026
+
+MODULE MOD_OPTIONS
+    ! Module for cli options
+
+    ! Module for metadata
+    USE MOD_METADATA
+  
+    IMPLICIT NONE
+    LOGICAL :: opt_compact_output = .FALSE.
+    LOGICAL :: opt_lib_output = .FALSE.
+    CHARACTER(LEN=128) :: opt_input_file = 'nf_input.yaml'
+    LOGICAL :: opt_suppress_output = .FALSE.
+    LOGICAL :: opt_file_has_header = .FALSE.
+    
+    CHARACTER(LEN=512) :: opt_cpp_comp_cmd = 'g++ -c -shared -O3 -w -fPIC'
+    CHARACTER(LEN=512) :: opt_f90_comp_cmd = 'gfortran -cpp -c -shared -O3 -w -fPIC -ffree-line-length-0'
+    CHARACTER(LEN=512) :: opt_lnk_cmd      = 'gcc -shared -fPIC -lgfortran'
+
+    CONTAINS
+    SUBROUTINE OPT_LOAD_CACHE()
+        IMPLICIT NONE
+        INTEGER :: ios
+
+        OPEN(747, FILE=TRIM(nf_cache_folder)//'cache.opt', ACTION='read', STATUS='old', IOSTAT=ios)
+        IF(ios.EQ.0) THEN
+            READ(747, '(A)') opt_cpp_comp_cmd
+            READ(747, '(A)') opt_f90_comp_cmd
+            READ(747, '(A)') opt_lnk_cmd
+        ENDIF
+        CLOSE(747)
+    END SUBROUTINE
+
+    SUBROUTINE OPT_SAVE_CACHE()
+        IMPLICIT NONE
+
+        WRITE(*, *) 'Saving cache...'
+
+        OPEN(747, FILE=TRIM(nf_cache_folder)//'cache.opt', ACTION='write', STATUS='replace')
+        WRITE(747, *) TRIM(opt_cpp_comp_cmd)
+        WRITE(747, *) TRIM(opt_f90_comp_cmd)
+        WRITE(747, *) TRIM(opt_lnk_cmd)
+        CLOSE(747)
+    END SUBROUTINE
+END MODULE MOD_OPTIONS

{nested_fit-5.6.6.dev120 → nested_fit-5.6.7.dev122}/src/Mod_potentials.f90

@@ -640,11 +640,12 @@ CONTAINS
     REAL(8), DIMENSION(:), INTENT(IN) :: par
     REAL(8), DIMENSION(4) :: Q_ENERGY_LJ_2D_LP_PRIOR
     REAL(8), PARAMETER :: pi=3.141592653589793d0
+    INTEGER(4), PARAMETER :: first_coord = 7
     REAL(8) ::  eps=1.
-    REAL(8), DIMENSION(SIZE(par)-5) :: x
-    REAL(8), DIMENSION(SIZE(par)-5+2*INT(par(1))) :: y
+    REAL(8), DIMENSION(SIZE(par)-(first_coord-1)) :: x
+    REAL(8), DIMENSION(SIZE(par)-(first_coord-1)+2*INT(par(1))) :: y
     !REAL(8), DIMENSION(3*INT(par(1))) :: x_c     
-    INTEGER(4) :: N, i, j, P, k, ind_xi, ind_xj, first_coord
+    INTEGER(4) :: N, i, j, P, k, ind_xi, ind_xj
     REAL(8) :: rij, ener, r0, tau, nu, m, rharm, lambda_P2, dx, dy, box_x, box_y, V, harm
     
     N = INT(par(1))
@@ -658,7 +659,7 @@ CONTAINS
     !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
     m = par(4)
     r0 = par(5)
-    first_coord = 7 ! npar of 1st coordinate
+    ! first_coord = 7 ! npar of 1st coordinate
     lambda_P2 = 1./(m*P*tau**2)
     y(:(2*N*(P-1))) = par((first_coord+2*N):) ! First P-1 beads
     DO i=1,2*N
@@ -705,4 +706,4 @@ CONTAINS
   
 
 
-END MODULE MOD_POTENTIALS
+END MODULE MOD_POTENTIALS

{nested_fit-5.6.6.dev120 → nested_fit-5.6.7.dev122}/src/nested_fit.f90

@@ -7,6 +7,7 @@ PROGRAM NESTED_FIT
   !      Add PyPI binary distribution for multiple linux systems
   !      Add PyPI source distribution as a default for other systems
   !      Rename CLI command to `nested_fit` to use the latest installed version via pip
+  !      Add persistent option commands cache
   ! 5.4  Merge of executable for data analysis and function exploration
   !      New outout with max of clusters in a file
   !      New RANDOM_WALK with detailed balance respected
@@ -315,10 +316,16 @@ PROGRAM NESTED_FIT
     "Change the number of threads OpenMP runs on. Setting to 0 will use all the available.",&
     B_SET_OMP_THREADS&
   ))
+
+  ! Load argument / options cache
+  CALL OPT_LOAD_CACHE()
   
   ! Parse executable arguments
   CALL PARSE_ARGUMENTS()
 
+  ! Save argument / options cache
+  CALL OPT_SAVE_CACHE()
+
   !!!!!!!! Initiate random generator with the same seed each time !!!!!!!!!!!
 #ifdef NORNG_ON  
   CALL LOG_WARNING_HEADER()
@@ -1137,8 +1144,8 @@ PROGRAM NESTED_FIT
    INTEGER                        :: numparams
    INTEGER                        :: i
    LOGICAL                        :: fix_logical = .FALSE.
-   CHARACTER(128)                 :: legacy_param_keys(1024)
-   CHARACTER(128)                 :: legacy_param_names(1024)
+   CHARACTER(128)                 :: legacy_param_keys(1024*4) ! (Damià) *4 to allow for more params in nf_input.yaml
+   CHARACTER(128)                 :: legacy_param_names(1024*4) ! (Damià) *4 to allow for more params in nf_input.yaml
    INTEGER                        :: legacy_param_count
    CHARACTER(128)                 :: splitarr(16)
    INTEGER                        :: splitarr_count

nested_fit-5.6.6.dev120/src/Mod_options.f90

@@ -1,17 +0,0 @@
-MODULE MOD_OPTIONS
-    ! Module for cli options
-  
-    IMPLICIT NONE
-    LOGICAL :: opt_compact_output = .FALSE.
-    LOGICAL :: opt_lib_output = .FALSE.
-    CHARACTER(LEN=128) :: opt_input_file = 'nf_input.yaml'
-    LOGICAL :: opt_suppress_output = .FALSE.
-    LOGICAL :: opt_file_has_header = .FALSE.
-    
-    ! TODO(César): This should be in a config file.
-    ! TODO(César): Also add this to the nf cache to load on next runs.
-    CHARACTER(LEN=512) :: opt_cpp_comp_cmd = 'g++ -c -shared -O3 -w -fPIC'
-    CHARACTER(LEN=512) :: opt_f90_comp_cmd = 'gfortran -cpp -c -shared -O3 -w -fPIC -ffree-line-length-0'
-    CHARACTER(LEN=512) :: opt_lnk_cmd      = 'gcc -shared -fPIC -lgfortran'
-    
-END MODULE MOD_OPTIONS

nested_fit-5.6.6.dev120/tmp/nf_input.yaml

@@ -1,59 +0,0 @@
-calculation_mode: Q_POTENTIAL
-clustering:
-  enabled: false
-  method: k
-  # parameter1: 0.5
-  # parameter2: 0.2
-convergence:
-  accuracy: -10
-  method: ENERGY_MAX
-  parameter: 0.01
-datafiles: []
-function:
-  expression: Q_ENERGY_LJ_2D_PBC
-  params:
-    # --- Constants ---
-    N:    { fixed: true, value:   2, step: -1, min: -5.0, max: 5.0, npar: 1 }
-    P:    { fixed: true, value:   3, step: -1, min: -5.0, max: 5.0, npar: 2 }
-    tau:  { fixed: true, value: 0.5, step: -1, min: -5.0, max: 5.0, npar: 3 }
-    m:    { fixed: true, value: 1.0, step: -1, min: -5.0, max: 5.0, npar: 4 }
-    r0:   { fixed: true, value: 0.5, step: -1, min: -5.0, max: 5.0, npar: 5 }
-    
-    # --- Coordinates (Bead 1, Atom 1) ---
-    x_11: { value:  0.0, step: -1, min: -5.0, max: 5.0, npar: 6 }
-    y_11: { value:  0.0, step: -1, min: -5.0, max: 5.0, npar: 7 }
-    
-    # --- Coordinates (Bead 1, Atom 2) ---
-    x_12: { value:  0.0, step: -1, min: -5.0, max: 5.0, npar: 8 }
-    y_12: { value:  0.0, step: -1, min: -5.0, max: 5.0, npar: 9 }
-    
-    # --- Coordinates (Bead 2, Atom 1) ---
-    x_21: { value:  0.1, step: -1, min: -5.0, max: 5.0, npar: 10 }
-    y_21: { value:  0.1, step: -1, min: -5.0, max: 5.0, npar: 11 }
-    
-    # --- Coordinates (Bead 2, Atom 2) ---
-    x_22: { value:  0.1, step: -1, min: -5.0, max: 5.0, npar: 12 }
-    y_22: { value:  0.1, step: -1, min: -5.0, max: 5.0, npar: 13 }
-    
-    # --- Coordinates (Bead 3, Atom 1) ---
-    x_31: { value: -0.1, step: -1, min: -5.0, max: 5.0, npar: 14 }
-    y_31: { value: -0.1, step: -1, min: -5.0, max: 5.0, npar: 15 }
-    
-    # --- Coordinates (Bead 3, Atom 2) ---
-    x_32: { value: -0.1, step: -1, min: -5.0, max: 5.0, npar: 16 }
-    y_32: { value: -0.1, step: -1, min: -5.0, max: 5.0, npar: 17 }
-likelihood: GAUSSIAN
-search:
-  hard_writing: true
-  livepoints: 1000
-  max_steps: 100000
-  max_tries: 1000
-  method: SLICE_SAMPLING
-  num_tries: 1
-  param1: 0.5
-  param2: 3
-  tries_mult: 100
-version: 5.6
-writing:
-  all_parameters: true
-  statistics: true