🧹 Cleaned up rc model and parameters

rc/models/target_rc.yml

@@ -5,7 +5,6 @@ dataset_groups:
     link_clp: True
 
 dataset:
-  # Kcr_rcra:
   rc:
     megacomplex: [artifact1, complex1]
     initial_concentration: input1
@@ -44,19 +43,16 @@ irf:
     # width: irf.rc.dcm.width
     width: irf.width1
     # scale: [irf.scale1,irf.scale4]
-    # dispersion_center: irf.common_disp_center
     dispersion_center: irf.common_dispcenter
     # center_dispersion_coefficients: [irf.rc.dcm.disp1, irf.rc.dcm.disp2]
     # center_dispersion_coefficients: [rc.dcm.irf.disp1, rc.dcm.irf.disp2]
     center_dispersion_coefficients: [irf.data1_disp1, irf.data1_disp2]
     model_dispersion_with_wavenumber: true
 
 weights:
-  # - datasets: [Kcr_rcra]
   - datasets: [dataset1]
     global_interval: [520, 535]
     value: 0.4
-  # - datasets: [Kcr_rcra]
   - datasets: [dataset1]
     global_interval: [1, 420]
     value: 0.2

rc/parameters/target_rc.yml

@@ -1,95 +1,23 @@
 inputs1:
   - ["s1", 1, { vary: False }]
   - ["0", 0, { vary: False }]
-  - ["s5", 0.12, { vary: False }]
-  - ["s5gcrcg", 1, { "expr": "$inputs1.s5*2" }]
-  - ["s5rcgcr", 1, { "expr": "$inputs1.s5*0.5" }]
-
-ratesrgr:
-  - ["k55", 0.521E-03, { "vary": False }]
-ratesgcrcg:
-  - ["k55", 1.06102962E-03, { "vary": False }]
-  - ["k52", 1, { "expr": "$ratesgcrcg.k51" }]
-  - ["k51", 0.635131359, { "vary": False }]
-  - ["k54", 1, { "expr": "$ratesgcrcg.k53" }]
-  - ["k53", 0.975641429, { "vary": False }]
-  - ["k62", 1, { "expr": "$ratesgcrcg.k61" }]
-  - ["k61", 1, { "expr": "$rates.k61*2" }]
 
 rates:
-  - ["k11", 1.e-9, { "vary": False }]
   - ["k21", 7.72667789, { "vary": False }]
   - ["k32", 1.57667196, { "vary": False }]
   - ["k43", 0.150893405, { "vary": False }]
   - ["k44", 5.71769197E-04, { "vary": False }]
-  - ["k55", 3.31293675E-04, { "vary": False }]
-  - ["k52", 1, { "expr": "$rates.k51" }]
-  - ["k51", 0.318180293, { "vary": False }]
-  - ["k54", 1, { "expr": "$rates.k53" }]
-  - ["k53", 0.458410978, { "vary": False }]
-  - ["k62", 1, { "expr": "$rates.k61" }]
-  - ["k61", 0.147264779, { "vary": False }]
-  - ["k66", 9.56490561E-02, { "vary": False }]
-
-# rates:
-#   rc:
-#     dcm:
-#       - ["to_r2_from_r1", 7.72667789, {"vary": False}]
-#       - ["to_r3_from_r2", 1.57667196, {"vary": False}]
-#       - ["to_r4_from_r3", 0.150893405, {"vary": False}]
-#       - ["from_r4", 5.71769197E-04, {"vary": False}]
-
-area:
-  - ["1", 1, { "vary": False }]
 
 rel:
   - ["r1", 1, { "vary": False }]
   - ["r2", 1.1, { "vary": False }]
 
 scale:
   - ["1", 1, { "vary": False }]
-  # - ["2", 1.4788, {"vary": True}]
-  # - ["3", 1157.5, {"vary": True}]
-  # - ["4", 1, {"expr": "$scale.3"}]
-  # - ["5", 1, {"expr": "$scale.3"}]
-  # - ["6", 1, {"expr": "$scale.3"}]
-  # - ["7", 0.6036, {"vary": True}]
-  # - ["6", 0.761856318, {"vary": True}]
-
-# scalem:
-#   - ["1", 1, {"vary": False}]
-#   - ["2", 0.481, {"vary": False}]
-#   - ["3", 0.4956, {"vary": False}]
-#   - ["4", 0.599, {"vary": False}]
-#   - ["5", 0.459, {"vary": False}]
-#   - ["6", 1., {"vary": False}]
-#   - ["7", 0.08188, {"vary": False}]
-#   - ["8", 0.1148, {"vary": False}]
-#   - ["9", 0.0917, {"vary": False}]
-#   - ["10", 0.07, {"vary": False}]
 
 irf:
   - ["common_dispcenter", 550, { "vary": False }]
   - ["data1_disp1", -0.840490937, { "vary": False }]
   - ["data1_disp2", -0.354524136, { "vary": False }]
   - ["center1", 1.21, { "vary": True }]
-  - ["center2", 1.03445363, { "vary": False }]
-  - ["center7", 1.0418, { "vary": False }]
-  # - ["center3",57.6, {"vary": False}]
-  # - ["center4",57.1045876, {"vary": False}]
   - ["width1", 5.053E-02, { "vary": False }]
-  - ["width2", 5.19465879E-02, { "vary": False }]
-  - ["width7", 7.2146E-02, { "vary": False }]
-  # - ["width4",6.47719383, {"vary": False}]
-  # - ["scale1",1, {"vary": False}]
-  # - ["scale2",1.54392803, {"vary": True}]
-  # - ["scale3",11870.8076, {"vary": True}]
-  # - ["scale4", 1, {"expr": "$irf.scale3"}]
-  # - ["scale5", 1, {"expr": "$irf.scale3"}]
-  # - ["scale6", 1, {"expr": "$irf.scale3"}]
-# For instance:
-# group1:
-#   sub_group1:
-#     - ["value1"]
-#
-# this translates to group1.sub_group1.value1 in your model file