🧹 Cleaned up 4TT models and parameters

glotaran · Feb 27, 2023 · f93712f · f93712f
1 parent 621113c
commit f93712f
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diff --git a/4TT/models/refined6osc.yml b/4TT/models/refined6osc.yml
@@ -32,9 +32,6 @@ megacomplex:
   decay:
     type: decay
     k_matrix: [k1]
-  #  baseline:
-  #    type: baseline
-  #    dimension: time
   artifact:
     type: coherent-artifact
     order: 3

diff --git a/4TT/models/sequential.yml b/4TT/models/sequential.yml
@@ -1,17 +1,12 @@
 initial_concentration:
   j1:
-    # compartments: [S2, S1, T1, S2rel, T1hot]
-    # parameters: [j.1, j.0, j.0, j.0, j.0]
     compartments: [S2, S1, T1, T1hot]
     parameters: [j.1, j.0, j.0, j.0]
 
 k_matrix:
   k1:
     matrix:
-      # "(S2rel, S2)": kinetic.to_S2rel_from_S2
       "(S1, S2)": kinetic.to_S1_from_S2
-      # "(S1, S2rel)": kinetic.to_S1_from_S2rel
-      # "(T1hot, S2rel)": kinetic.to_T1hot_from_S2rel
       "(T1hot, S1)": kinetic.to_T1hot_from_S1
       "(T1, T1hot)": kinetic.to_T1_from_T1hot
       "(T1, T1)": kinetic.from_T1
@@ -25,9 +20,6 @@ megacomplex:
   decay:
     type: decay
     k_matrix: [k1]
-  #  baseline:
-  #    type: baseline
-  #    dimension: time
   artifact:
     type: coherent-artifact
     order: 3

diff --git a/4TT/models/sequential5osc.yml b/4TT/models/sequential5osc.yml
@@ -1,17 +1,12 @@
 initial_concentration:
   j1:
-    # compartments: [S2, S1, T1, S2rel, T1hot]
-    # parameters: [j.1, j.0, j.0, j.0, j.0]
     compartments: [S2, S1, T1, T1hot]
     parameters: [j.1, j.0, j.0, j.0]
 
 k_matrix:
   k1:
     matrix:
-      # "(S2rel, S2)": kinetic.to_S2rel_from_S2
       "(S1, S2)": kinetic.to_S1_from_S2
-      # "(S1, S2rel)": kinetic.to_S1_from_S2rel
-      # "(T1hot, S2rel)": kinetic.to_T1hot_from_S2rel
       "(T1hot, S1)": kinetic.to_T1hot_from_S1
       "(T1, T1hot)": kinetic.to_T1_from_T1hot
       "(T1, T1)": kinetic.from_T1
@@ -25,9 +20,6 @@ megacomplex:
   decay:
     type: decay
     k_matrix: [k1]
-  #  baseline:
-  #    type: baseline
-  #    dimension: time
   artifact:
     type: coherent-artifact
     order: 3

diff --git a/4TT/models/sequential6osc.yml b/4TT/models/sequential6osc.yml
@@ -1,17 +1,12 @@
 initial_concentration:
   j1:
-    # compartments: [S2, S1, T1, S2rel, T1hot]
-    # parameters: [j.1, j.0, j.0, j.0, j.0]
     compartments: [S2, S1, T1, T1hot]
     parameters: [j.1, j.0, j.0, j.0]
 
 k_matrix:
   k1:
     matrix:
-      # "(S2rel, S2)": kinetic.to_S2rel_from_S2
       "(S1, S2)": kinetic.to_S1_from_S2
-      # "(S1, S2rel)": kinetic.to_S1_from_S2rel
-      # "(T1hot, S2rel)": kinetic.to_T1hot_from_S2rel
       "(T1hot, S1)": kinetic.to_T1hot_from_S1
       "(T1, T1hot)": kinetic.to_T1_from_T1hot
       "(T1, T1)": kinetic.from_T1
@@ -34,9 +29,6 @@ megacomplex:
   decay:
     type: decay
     k_matrix: [k1]
-  #  baseline:
-  #    type: baseline
-  #    dimension: time
   artifact:
     type: coherent-artifact
     order: 3

diff --git a/4TT/models/sequential6osc_S2rel.yml b/4TT/models/sequential6osc_S2rel.yml
@@ -23,9 +23,6 @@ megacomplex:
   decay:
     type: decay
     k_matrix: [k1]
-  #  baseline:
-  #    type: baseline
-  #    dimension: time
   artifact:
     type: coherent-artifact
     order: 3

diff --git a/4TT/parameters/sequential.yml b/4TT/parameters/sequential.yml
@@ -1,8 +1,5 @@
 osc:
   freq: [752.314148, 495.196503, 206.952820, 767.406006, { vary: True }]
-  # rates: [
-  #  3.04113483,    11.2777481,    8.30780029,   -9.46621990,  {vary: True}]
-  # 3.04113483,    11.2777481,    8.3078009,   {vary: True}]
   rates:
     - ["1", 3.04113483, { vary: True }]
     - ["2", 11.2777481, { vary: True }]
@@ -14,10 +11,7 @@ j:
   - ["0", 0.0, { non-negative: False, vary: False }]
 
 kinetic:
-  # - ['to_S2rel_from_S2',6.58372021, {non-negative: True, vary: False}]
   - ["to_S1_from_S2", 8.39700508, { non-negative: True, vary: True }]
-  # - ['to_S1_from_S2rel', 4.36121597, {non-negative: True, vary: False}]
-  # - ['to_T1hot_from_S2rel', 1.6, {non-negative: True, vary: False}]
   - ["to_T1hot_from_S1", 2.24768806, { non-negative: True, vary: True }]
   - ["to_T1_from_T1hot", 0.568519056, { non-negative: True, vary: False }]
   - ["from_T1", 1.00000005E-03, { non-negative: True, vary: False }]

diff --git a/4TT/parameters/sequential5osc.yml b/4TT/parameters/sequential5osc.yml
@@ -1,8 +1,5 @@
 osc:
   freq: [752.314148, 495.196503, 206.952820, 767.406006, { vary: True }]
-  # rates: [
-  #  3.04113483,    11.2777481,    8.30780029,   -9.46621990,  {vary: True}]
-  # 3.04113483,    11.2777481,    8.3078009,   {vary: True}]
   rates:
     - ["1", 3.04113483, { vary: True }]
     - ["2", 11.2777481, { vary: True }]
@@ -14,10 +11,7 @@ j:
   - ["0", 0.0, { non-negative: False, vary: False }]
 
 kinetic:
-  # - ['to_S2rel_from_S2',6.58372021, {non-negative: True, vary: False}]
   - ["to_S1_from_S2", 8.39700508, { non-negative: True, vary: True }]
-  # - ['to_S1_from_S2rel', 4.36121597, {non-negative: True, vary: False}]
-  # - ['to_T1hot_from_S2rel', 1.6, {non-negative: True, vary: False}]
   - ["to_T1hot_from_S1", 2.24768806, { non-negative: True, vary: True }]
   - ["to_T1_from_T1hot", 0.568519056, { non-negative: True, vary: True }]
   - ["from_T1", 1.00000005E-03, { non-negative: True, vary: False }]

diff --git a/4TT/parameters/sequential6osc_S2rel.yml b/4TT/parameters/sequential6osc_S2rel.yml
@@ -1,8 +1,5 @@
 osc:
   freq: [752.314148, 495.196503, 206.952820, 767.406006, { vary: True }]
-  # rates: [
-  #  3.04113483,    11.2777481,    8.30780029,   -9.46621990,  {vary: True}]
-  # 3.04113483,    11.2777481,    8.3078009,   {vary: True}]
   rates:
     - ["1", 3.04113483, { vary: True }]
     - ["2", 11.2777481, { vary: True }]