From d7aee3aa432c498a8738ea35880bf2fa4f2e31c0 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 10:20:42 -0700
Subject: [PATCH 01/23] testing visual output of readme

---
 data/README.md | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 data/README.md

diff --git a/data/README.md b/data/README.md
new file mode 100644
index 0000000..2356caf
--- /dev/null
+++ b/data/README.md
@@ -0,0 +1,6 @@
+## Description of calibratable parameters
+
+
+| Parameter name | Units |  Physical limits  | Range tested for stability | Applies to individual soil layers or entire model domain | Description |
+| -------- | -------- | ------ | ----- | ---- | ------- | ----------- |
+| theta_r | - | 0<theta_r<1, theta_r<theta_e | 0.01<theta_e<0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. |

From f391c147a0a82738d14ef322245fa201564dc003 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 10:23:46 -0700
Subject: [PATCH 02/23] testing visual output of readme

---
 data/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data/README.md b/data/README.md
index 2356caf..5bc5b56 100644
--- a/data/README.md
+++ b/data/README.md
@@ -3,4 +3,4 @@
 
 | Parameter name | Units |  Physical limits  | Range tested for stability | Applies to individual soil layers or entire model domain | Description |
 | -------- | -------- | ------ | ----- | ---- | ------- | ----------- |
-| theta_r | - | 0<theta_r<1, theta_r<theta_e | 0.01<theta_e<0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. |
+| theta_r | - | 0\<\theta_r<1, theta_r<\theta_e | 0.01<\theta_e<0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. |

From ca4528a31538886d6b87b35ef4c2ec2677ca4315 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 10:26:22 -0700
Subject: [PATCH 03/23] testing visual output of readme

---
 data/README.md | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/data/README.md b/data/README.md
index 5bc5b56..1dd05dc 100644
--- a/data/README.md
+++ b/data/README.md
@@ -1,6 +1,7 @@
 ## Description of calibratable parameters
 
+A detailed description of the calibratable parameters is given below. 
 
 | Parameter name | Units |  Physical limits  | Range tested for stability | Applies to individual soil layers or entire model domain | Description |
-| -------- | -------- | ------ | ----- | ---- | ------- | ----------- |
-| theta_r | - | 0\<\theta_r<1, theta_r<\theta_e | 0.01<\theta_e<0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. |
+| -------- | -------- | ------ | ----- | ---- | ----------- |
+| theta_r | - | 0<theta_r<1, theta_r<theta_e | 0.01<theta_e<0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. |

From e68a2880f54b3cd36d38d2030b053a32d0ec10c1 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 10:35:05 -0700
Subject: [PATCH 04/23] testing visual output of readme

---
 data/README.md | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/data/README.md b/data/README.md
index 1dd05dc..f28a243 100644
--- a/data/README.md
+++ b/data/README.md
@@ -5,3 +5,10 @@ A detailed description of the calibratable parameters is given below.
 | Parameter name | Units |  Physical limits  | Range tested for stability | Applies to individual soil layers or entire model domain | Description |
 | -------- | -------- | ------ | ----- | ---- | ----------- |
 | theta_r | - | 0<theta_r<1, theta_r<theta_e | 0.01<theta_e<0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. |
+| theta_e | - | 0<theta_e<1, theta_r<theta_e | 0.3<theta_e<0.8 | Soil layer | theta_e is the maximum volumetric water content that a soil layer can naturally attain. Note that theta_e must be greater than theta_r. |
+| alpha | 1/cm | alpha>0 | 0.001<alpha<0.3 | Soil layer | alpha is the van Genuchten parameter related to the inverse of air entry pressure. Note that in nature, expected values of alpha are distributed logarithmically, so calibrating on the log of alpha rather than alpha directly is likely a better choice for most calibration algorithms. |
+| n | - | n>1 | 1.01<n<3 | Soil layer | n is the van Genuchten parameter related to pore size distribution. Note that another commonly reported van Genuchten parameter, m, is related to n via m = 1 - 1/n. We recommend that n>1.01. Values larger than 3 are acceptable. |
+| Ks | cm/h | Ks>0 | 0.001<K_s<100 | Soil layer | K_s is the saturated hydraulic conductivity of a soil. Note that in nature, expected values of K_s are distributed logarithmically, so calibrating on the log of K_s rather than K_s directly is likely a better choice for most calibration algorithms. |
+| ponded_head_max | cm | ponded_head_max>=0 | 0<=ponded_head_max<=5 | Entire model domain | This is the maximum amount of ponded water that is allowed to accumulate on the soil surface. While stability tests have only included a maximum value of 5 cm, any value greater than or equal to 0 should be acceptable. A common choice will be 0. This parameter can be set in the config file.  |
+| field_capacity_psi | cm | 0<field_capacity_cm, field_capacity_cm<wilting_point_psi | 10.3<field_capacity_cm<516.6 | Entire model domain | This is the wilting point of the model domain, expressed as a capillary head. Together with wilting_point_psi, the field capacity is used to determine the intensity of the reduction of PET to become AET. The numbers 10.3 cm and 516.6 cm correspond to pressures of 1/100 atm and 1/2 atm of water. Note that the model generally uses absolute values of capillary head; in this case, these limits are absolute values of negative numbers and physically represent unsaturated soil. While field capacity will vary per soil type, we use a single value for the entire model domain, following the method for PET->AET correction used by HYDRUS. This parameter can be set in the config file. |
+

From 0188aed176215b7aeeb3d15903d43d500acb4f01 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 10:38:00 -0700
Subject: [PATCH 05/23] updating data directory with readme for calibratable
 params

---
 data/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data/README.md b/data/README.md
index f28a243..eb78798 100644
--- a/data/README.md
+++ b/data/README.md
@@ -8,7 +8,7 @@ A detailed description of the calibratable parameters is given below.
 | theta_e | - | 0<theta_e<1, theta_r<theta_e | 0.3<theta_e<0.8 | Soil layer | theta_e is the maximum volumetric water content that a soil layer can naturally attain. Note that theta_e must be greater than theta_r. |
 | alpha | 1/cm | alpha>0 | 0.001<alpha<0.3 | Soil layer | alpha is the van Genuchten parameter related to the inverse of air entry pressure. Note that in nature, expected values of alpha are distributed logarithmically, so calibrating on the log of alpha rather than alpha directly is likely a better choice for most calibration algorithms. |
 | n | - | n>1 | 1.01<n<3 | Soil layer | n is the van Genuchten parameter related to pore size distribution. Note that another commonly reported van Genuchten parameter, m, is related to n via m = 1 - 1/n. We recommend that n>1.01. Values larger than 3 are acceptable. |
-| Ks | cm/h | Ks>0 | 0.001<K_s<100 | Soil layer | K_s is the saturated hydraulic conductivity of a soil. Note that in nature, expected values of K_s are distributed logarithmically, so calibrating on the log of K_s rather than K_s directly is likely a better choice for most calibration algorithms. |
+| Ks | cm/h | Ks>0 | 0.001<K_s<100 | Soil layer | Ks is the saturated hydraulic conductivity of a soil. Note that in nature, expected values of Ks are distributed logarithmically, so calibrating on the log of Ks rather than Ks directly is likely a better choice for most calibration algorithms. |
 | ponded_head_max | cm | ponded_head_max>=0 | 0<=ponded_head_max<=5 | Entire model domain | This is the maximum amount of ponded water that is allowed to accumulate on the soil surface. While stability tests have only included a maximum value of 5 cm, any value greater than or equal to 0 should be acceptable. A common choice will be 0. This parameter can be set in the config file.  |
 | field_capacity_psi | cm | 0<field_capacity_cm, field_capacity_cm<wilting_point_psi | 10.3<field_capacity_cm<516.6 | Entire model domain | This is the wilting point of the model domain, expressed as a capillary head. Together with wilting_point_psi, the field capacity is used to determine the intensity of the reduction of PET to become AET. The numbers 10.3 cm and 516.6 cm correspond to pressures of 1/100 atm and 1/2 atm of water. Note that the model generally uses absolute values of capillary head; in this case, these limits are absolute values of negative numbers and physically represent unsaturated soil. While field capacity will vary per soil type, we use a single value for the entire model domain, following the method for PET->AET correction used by HYDRUS. This parameter can be set in the config file. |
 

From 0fe9589e9b008291a4009476de9bad5b7042b85f Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 10:42:37 -0700
Subject: [PATCH 06/23] adjusting formatting of new table

---
 data/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data/README.md b/data/README.md
index eb78798..f00c90e 100644
--- a/data/README.md
+++ b/data/README.md
@@ -2,7 +2,7 @@
 
 A detailed description of the calibratable parameters is given below. 
 
-| Parameter name | Units |  Physical limits  | Range tested for stability | Applies to individual soil layers or entire model domain | Description |
+| Parameter name | Units |  Physical limits  | Range tested for stability | Applies to individual soil layers or entire model domain | Description &nbsp &nbsp &nbsp &nbsp |
 | -------- | -------- | ------ | ----- | ---- | ----------- |
 | theta_r | - | 0<theta_r<1, theta_r<theta_e | 0.01<theta_e<0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. |
 | theta_e | - | 0<theta_e<1, theta_r<theta_e | 0.3<theta_e<0.8 | Soil layer | theta_e is the maximum volumetric water content that a soil layer can naturally attain. Note that theta_e must be greater than theta_r. |

From 2b53d69c532d7e1b12767c33869fe56d1ab1191c Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 10:46:38 -0700
Subject: [PATCH 07/23] adjusting formatting of new table

---
 data/README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/data/README.md b/data/README.md
index f00c90e..6250466 100644
--- a/data/README.md
+++ b/data/README.md
@@ -2,8 +2,8 @@
 
 A detailed description of the calibratable parameters is given below. 
 
-| Parameter name | Units |  Physical limits  | Range tested for stability | Applies to individual soil layers or entire model domain | Description &nbsp &nbsp &nbsp &nbsp |
-| -------- | -------- | ------ | ----- | ---- | ----------- |
+| Parameter name | Units |  Physical limits  | Range tested for stability | Applies to individual soil layers or entire model domain | Description |
+| --- | --- | --- | --- | --- | --------------- |
 | theta_r | - | 0<theta_r<1, theta_r<theta_e | 0.01<theta_e<0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. |
 | theta_e | - | 0<theta_e<1, theta_r<theta_e | 0.3<theta_e<0.8 | Soil layer | theta_e is the maximum volumetric water content that a soil layer can naturally attain. Note that theta_e must be greater than theta_r. |
 | alpha | 1/cm | alpha>0 | 0.001<alpha<0.3 | Soil layer | alpha is the van Genuchten parameter related to the inverse of air entry pressure. Note that in nature, expected values of alpha are distributed logarithmically, so calibrating on the log of alpha rather than alpha directly is likely a better choice for most calibration algorithms. |

From 3b22fd044997cdfd3acc9e952dae1bc9935fcd50 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 10:47:34 -0700
Subject: [PATCH 08/23] adjusting formatting of new table

---
 data/README.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/data/README.md b/data/README.md
index 6250466..4977c42 100644
--- a/data/README.md
+++ b/data/README.md
@@ -4,7 +4,8 @@ A detailed description of the calibratable parameters is given below.
 
 | Parameter name | Units |  Physical limits  | Range tested for stability | Applies to individual soil layers or entire model domain | Description |
 | --- | --- | --- | --- | --- | --------------- |
-| theta_r | - | 0<theta_r<1, theta_r<theta_e | 0.01<theta_e<0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. |
+| theta_r | - | 0<theta_r<1
+ theta_r<theta_e | 0.01<theta_e<0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. |
 | theta_e | - | 0<theta_e<1, theta_r<theta_e | 0.3<theta_e<0.8 | Soil layer | theta_e is the maximum volumetric water content that a soil layer can naturally attain. Note that theta_e must be greater than theta_r. |
 | alpha | 1/cm | alpha>0 | 0.001<alpha<0.3 | Soil layer | alpha is the van Genuchten parameter related to the inverse of air entry pressure. Note that in nature, expected values of alpha are distributed logarithmically, so calibrating on the log of alpha rather than alpha directly is likely a better choice for most calibration algorithms. |
 | n | - | n>1 | 1.01<n<3 | Soil layer | n is the van Genuchten parameter related to pore size distribution. Note that another commonly reported van Genuchten parameter, m, is related to n via m = 1 - 1/n. We recommend that n>1.01. Values larger than 3 are acceptable. |

From ef78e59d5aa3b46cc22c3ba12ae8e551e029109d Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 10:49:16 -0700
Subject: [PATCH 09/23] adjusting formatting of new table

---
 data/README.md | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/data/README.md b/data/README.md
index 4977c42..9e21c1f 100644
--- a/data/README.md
+++ b/data/README.md
@@ -4,8 +4,7 @@ A detailed description of the calibratable parameters is given below.
 
 | Parameter name | Units |  Physical limits  | Range tested for stability | Applies to individual soil layers or entire model domain | Description |
 | --- | --- | --- | --- | --- | --------------- |
-| theta_r | - | 0<theta_r<1
- theta_r<theta_e | 0.01<theta_e<0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. |
+| theta_r | - | 0<theta_r<1 <br> theta_r<theta_e | 0.01<theta_e<0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. |
 | theta_e | - | 0<theta_e<1, theta_r<theta_e | 0.3<theta_e<0.8 | Soil layer | theta_e is the maximum volumetric water content that a soil layer can naturally attain. Note that theta_e must be greater than theta_r. |
 | alpha | 1/cm | alpha>0 | 0.001<alpha<0.3 | Soil layer | alpha is the van Genuchten parameter related to the inverse of air entry pressure. Note that in nature, expected values of alpha are distributed logarithmically, so calibrating on the log of alpha rather than alpha directly is likely a better choice for most calibration algorithms. |
 | n | - | n>1 | 1.01<n<3 | Soil layer | n is the van Genuchten parameter related to pore size distribution. Note that another commonly reported van Genuchten parameter, m, is related to n via m = 1 - 1/n. We recommend that n>1.01. Values larger than 3 are acceptable. |

From 3486be738a3cced245952bd5984c16efc44f1b0e Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 10:50:20 -0700
Subject: [PATCH 10/23] adjusting formatting of new table

---
 data/README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/data/README.md b/data/README.md
index 9e21c1f..16699ef 100644
--- a/data/README.md
+++ b/data/README.md
@@ -4,11 +4,11 @@ A detailed description of the calibratable parameters is given below.
 
 | Parameter name | Units |  Physical limits  | Range tested for stability | Applies to individual soil layers or entire model domain | Description |
 | --- | --- | --- | --- | --- | --------------- |
-| theta_r | - | 0<theta_r<1 <br> theta_r<theta_e | 0.01<theta_e<0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. |
-| theta_e | - | 0<theta_e<1, theta_r<theta_e | 0.3<theta_e<0.8 | Soil layer | theta_e is the maximum volumetric water content that a soil layer can naturally attain. Note that theta_e must be greater than theta_r. |
+| theta_r | - | 0<theta_r<1, <br> theta_r<theta_e | 0.01<theta_e<0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. |
+| theta_e | - | 0<theta_e<1, <br> theta_r<theta_e | 0.3<theta_e<0.8 | Soil layer | theta_e is the maximum volumetric water content that a soil layer can naturally attain. Note that theta_e must be greater than theta_r. |
 | alpha | 1/cm | alpha>0 | 0.001<alpha<0.3 | Soil layer | alpha is the van Genuchten parameter related to the inverse of air entry pressure. Note that in nature, expected values of alpha are distributed logarithmically, so calibrating on the log of alpha rather than alpha directly is likely a better choice for most calibration algorithms. |
 | n | - | n>1 | 1.01<n<3 | Soil layer | n is the van Genuchten parameter related to pore size distribution. Note that another commonly reported van Genuchten parameter, m, is related to n via m = 1 - 1/n. We recommend that n>1.01. Values larger than 3 are acceptable. |
 | Ks | cm/h | Ks>0 | 0.001<K_s<100 | Soil layer | Ks is the saturated hydraulic conductivity of a soil. Note that in nature, expected values of Ks are distributed logarithmically, so calibrating on the log of Ks rather than Ks directly is likely a better choice for most calibration algorithms. |
 | ponded_head_max | cm | ponded_head_max>=0 | 0<=ponded_head_max<=5 | Entire model domain | This is the maximum amount of ponded water that is allowed to accumulate on the soil surface. While stability tests have only included a maximum value of 5 cm, any value greater than or equal to 0 should be acceptable. A common choice will be 0. This parameter can be set in the config file.  |
-| field_capacity_psi | cm | 0<field_capacity_cm, field_capacity_cm<wilting_point_psi | 10.3<field_capacity_cm<516.6 | Entire model domain | This is the wilting point of the model domain, expressed as a capillary head. Together with wilting_point_psi, the field capacity is used to determine the intensity of the reduction of PET to become AET. The numbers 10.3 cm and 516.6 cm correspond to pressures of 1/100 atm and 1/2 atm of water. Note that the model generally uses absolute values of capillary head; in this case, these limits are absolute values of negative numbers and physically represent unsaturated soil. While field capacity will vary per soil type, we use a single value for the entire model domain, following the method for PET->AET correction used by HYDRUS. This parameter can be set in the config file. |
+| field_capacity_psi | cm | 0<field_capacity_cm, <br> field_capacity_cm<wilting_point_psi | 10.3<field_capacity_cm<516.6 | Entire model domain | This is the wilting point of the model domain, expressed as a capillary head. Together with wilting_point_psi, the field capacity is used to determine the intensity of the reduction of PET to become AET. The numbers 10.3 cm and 516.6 cm correspond to pressures of 1/100 atm and 1/2 atm of water. Note that the model generally uses absolute values of capillary head; in this case, these limits are absolute values of negative numbers and physically represent unsaturated soil. While field capacity will vary per soil type, we use a single value for the entire model domain, following the method for PET->AET correction used by HYDRUS. This parameter can be set in the config file. |
 

From bb4f971eda0fbee4987afdf7c871a241542189a9 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 10:51:58 -0700
Subject: [PATCH 11/23] adjusting formatting of new table

---
 data/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data/README.md b/data/README.md
index 16699ef..f7a36a2 100644
--- a/data/README.md
+++ b/data/README.md
@@ -10,5 +10,5 @@ A detailed description of the calibratable parameters is given below.
 | n | - | n>1 | 1.01<n<3 | Soil layer | n is the van Genuchten parameter related to pore size distribution. Note that another commonly reported van Genuchten parameter, m, is related to n via m = 1 - 1/n. We recommend that n>1.01. Values larger than 3 are acceptable. |
 | Ks | cm/h | Ks>0 | 0.001<K_s<100 | Soil layer | Ks is the saturated hydraulic conductivity of a soil. Note that in nature, expected values of Ks are distributed logarithmically, so calibrating on the log of Ks rather than Ks directly is likely a better choice for most calibration algorithms. |
 | ponded_head_max | cm | ponded_head_max>=0 | 0<=ponded_head_max<=5 | Entire model domain | This is the maximum amount of ponded water that is allowed to accumulate on the soil surface. While stability tests have only included a maximum value of 5 cm, any value greater than or equal to 0 should be acceptable. A common choice will be 0. This parameter can be set in the config file.  |
-| field_capacity_psi | cm | 0<field_capacity_cm, <br> field_capacity_cm<wilting_point_psi | 10.3<field_capacity_cm<516.6 | Entire model domain | This is the wilting point of the model domain, expressed as a capillary head. Together with wilting_point_psi, the field capacity is used to determine the intensity of the reduction of PET to become AET. The numbers 10.3 cm and 516.6 cm correspond to pressures of 1/100 atm and 1/2 atm of water. Note that the model generally uses absolute values of capillary head; in this case, these limits are absolute values of negative numbers and physically represent unsaturated soil. While field capacity will vary per soil type, we use a single value for the entire model domain, following the method for PET->AET correction used by HYDRUS. This parameter can be set in the config file. |
+| field_capacity_psi | cm | 0<field_capacity_cm, <br> field_capacity_cm<<br>wilting_point_psi | 10.3<field_capacity_cm<<br>516.6 | Entire model domain | This is the wilting point of the model domain, expressed as a capillary head. Together with wilting_point_psi, the field capacity is used to determine the intensity of the reduction of PET to become AET. The numbers 10.3 cm and 516.6 cm correspond to pressures of 1/100 atm and 1/2 atm of water. Note that the model generally uses absolute values of capillary head; in this case, these limits are absolute values of negative numbers and physically represent unsaturated soil. While field capacity will vary per soil type, we use a single value for the entire model domain, following the method for PET->AET correction used by HYDRUS. This parameter can be set in the config file. |
 

From 84e47eb6a3ab86470914b8d2f0e165d3560c3564 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 10:53:47 -0700
Subject: [PATCH 12/23] adjusting formatting of new table

---
 data/README.md | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/data/README.md b/data/README.md
index f7a36a2..a0d1849 100644
--- a/data/README.md
+++ b/data/README.md
@@ -4,11 +4,11 @@ A detailed description of the calibratable parameters is given below.
 
 | Parameter name | Units |  Physical limits  | Range tested for stability | Applies to individual soil layers or entire model domain | Description |
 | --- | --- | --- | --- | --- | --------------- |
-| theta_r | - | 0<theta_r<1, <br> theta_r<theta_e | 0.01<theta_e<0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. |
-| theta_e | - | 0<theta_e<1, <br> theta_r<theta_e | 0.3<theta_e<0.8 | Soil layer | theta_e is the maximum volumetric water content that a soil layer can naturally attain. Note that theta_e must be greater than theta_r. |
-| alpha | 1/cm | alpha>0 | 0.001<alpha<0.3 | Soil layer | alpha is the van Genuchten parameter related to the inverse of air entry pressure. Note that in nature, expected values of alpha are distributed logarithmically, so calibrating on the log of alpha rather than alpha directly is likely a better choice for most calibration algorithms. |
-| n | - | n>1 | 1.01<n<3 | Soil layer | n is the van Genuchten parameter related to pore size distribution. Note that another commonly reported van Genuchten parameter, m, is related to n via m = 1 - 1/n. We recommend that n>1.01. Values larger than 3 are acceptable. |
-| Ks | cm/h | Ks>0 | 0.001<K_s<100 | Soil layer | Ks is the saturated hydraulic conductivity of a soil. Note that in nature, expected values of Ks are distributed logarithmically, so calibrating on the log of Ks rather than Ks directly is likely a better choice for most calibration algorithms. |
-| ponded_head_max | cm | ponded_head_max>=0 | 0<=ponded_head_max<=5 | Entire model domain | This is the maximum amount of ponded water that is allowed to accumulate on the soil surface. While stability tests have only included a maximum value of 5 cm, any value greater than or equal to 0 should be acceptable. A common choice will be 0. This parameter can be set in the config file.  |
-| field_capacity_psi | cm | 0<field_capacity_cm, <br> field_capacity_cm<<br>wilting_point_psi | 10.3<field_capacity_cm<<br>516.6 | Entire model domain | This is the wilting point of the model domain, expressed as a capillary head. Together with wilting_point_psi, the field capacity is used to determine the intensity of the reduction of PET to become AET. The numbers 10.3 cm and 516.6 cm correspond to pressures of 1/100 atm and 1/2 atm of water. Note that the model generally uses absolute values of capillary head; in this case, these limits are absolute values of negative numbers and physically represent unsaturated soil. While field capacity will vary per soil type, we use a single value for the entire model domain, following the method for PET->AET correction used by HYDRUS. This parameter can be set in the config file. |
+| theta_r | - | 0< theta_r <1, <br> theta_r < theta_e | 0.01 < theta_e < 0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. |
+| theta_e | - | 0 < theta_e < 1, <br> theta_r < theta_e | 0.3 < theta_e < 0.8 | Soil layer | theta_e is the maximum volumetric water content that a soil layer can naturally attain. Note that theta_e must be greater than theta_r. |
+| alpha | 1/cm | alpha > 0 | 0.001 < alpha < 0.3 | Soil layer | alpha is the van Genuchten parameter related to the inverse of air entry pressure. Note that in nature, expected values of alpha are distributed logarithmically, so calibrating on the log of alpha rather than alpha directly is likely a better choice for most calibration algorithms. |
+| n | - | n > 1 | 1.01 < n <3 | Soil layer | n is the van Genuchten parameter related to pore size distribution. Note that another commonly reported van Genuchten parameter, m, is related to n via m = 1 - 1/n. We recommend that n > 1.01. Values larger than 3 are acceptable. |
+| Ks | cm/h | Ks > 0 | 0.001 < K_s < 100 | Soil layer | Ks is the saturated hydraulic conductivity of a soil. Note that in nature, expected values of Ks are distributed logarithmically, so calibrating on the log of Ks rather than Ks directly is likely a better choice for most calibration algorithms. |
+| ponded_head_max | cm | ponded_head_max >= 0 | 0 <= ponded_head_max <= 5 | Entire model domain | This is the maximum amount of ponded water that is allowed to accumulate on the soil surface. While stability tests have only included a maximum value of 5 cm, any value greater than or equal to 0 should be acceptable. A common choice will be 0. This parameter can be set in the config file.  |
+| field_capacity_psi | cm | 0 < field_capacity_cm, <br> field_capacity_cm < <br> wilting_point_psi | 10.3 < field_capacity_cm< <br> 516.6 | Entire model domain | This is the wilting point of the model domain, expressed as a capillary head. Together with wilting_point_psi, the field capacity is used to determine the intensity of the reduction of PET to become AET. The numbers 10.3 cm and 516.6 cm correspond to pressures of 1/100 atm and 1/2 atm of water. Note that the model generally uses absolute values of capillary head; in this case, these limits are absolute values of negative numbers and physically represent unsaturated soil. While field capacity will vary per soil type, we use a single value for the entire model domain, following the method for PET->AET correction used by HYDRUS. This parameter can be set in the config file. |
 

From 5644708004f48987d31201b5dee04fd4aeea4216 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 10:54:56 -0700
Subject: [PATCH 13/23] adjusting formatting of new table

---
 data/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data/README.md b/data/README.md
index a0d1849..27434ac 100644
--- a/data/README.md
+++ b/data/README.md
@@ -10,5 +10,5 @@ A detailed description of the calibratable parameters is given below.
 | n | - | n > 1 | 1.01 < n <3 | Soil layer | n is the van Genuchten parameter related to pore size distribution. Note that another commonly reported van Genuchten parameter, m, is related to n via m = 1 - 1/n. We recommend that n > 1.01. Values larger than 3 are acceptable. |
 | Ks | cm/h | Ks > 0 | 0.001 < K_s < 100 | Soil layer | Ks is the saturated hydraulic conductivity of a soil. Note that in nature, expected values of Ks are distributed logarithmically, so calibrating on the log of Ks rather than Ks directly is likely a better choice for most calibration algorithms. |
 | ponded_head_max | cm | ponded_head_max >= 0 | 0 <= ponded_head_max <= 5 | Entire model domain | This is the maximum amount of ponded water that is allowed to accumulate on the soil surface. While stability tests have only included a maximum value of 5 cm, any value greater than or equal to 0 should be acceptable. A common choice will be 0. This parameter can be set in the config file.  |
-| field_capacity_psi | cm | 0 < field_capacity_cm, <br> field_capacity_cm < <br> wilting_point_psi | 10.3 < field_capacity_cm< <br> 516.6 | Entire model domain | This is the wilting point of the model domain, expressed as a capillary head. Together with wilting_point_psi, the field capacity is used to determine the intensity of the reduction of PET to become AET. The numbers 10.3 cm and 516.6 cm correspond to pressures of 1/100 atm and 1/2 atm of water. Note that the model generally uses absolute values of capillary head; in this case, these limits are absolute values of negative numbers and physically represent unsaturated soil. While field capacity will vary per soil type, we use a single value for the entire model domain, following the method for PET->AET correction used by HYDRUS. This parameter can be set in the config file. |
+| field_capacity_psi | cm | 0 < field_capacity_cm, <br> field_capacity_cm < wilting_point_psi | 10.3 < field_capacity_cm < <br> 516.6 | Entire model domain | This is the wilting point of the model domain, expressed as a capillary head. Together with wilting_point_psi, the field capacity is used to determine the intensity of the reduction of PET to become AET. The numbers 10.3 cm and 516.6 cm correspond to pressures of 1/100 atm and 1/2 atm of water. Note that the model generally uses absolute values of capillary head; in this case, these limits are absolute values of negative numbers and physically represent unsaturated soil. While field capacity will vary per soil type, we use a single value for the entire model domain, following the method for PET->AET correction used by HYDRUS. This parameter can be set in the config file. |
 

From 7d555a2bf677c691ca2bb52c91cfe2fe8af7786c Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 10:56:06 -0700
Subject: [PATCH 14/23] adjusting formatting of new table

---
 data/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data/README.md b/data/README.md
index 27434ac..ea8748c 100644
--- a/data/README.md
+++ b/data/README.md
@@ -10,5 +10,5 @@ A detailed description of the calibratable parameters is given below.
 | n | - | n > 1 | 1.01 < n <3 | Soil layer | n is the van Genuchten parameter related to pore size distribution. Note that another commonly reported van Genuchten parameter, m, is related to n via m = 1 - 1/n. We recommend that n > 1.01. Values larger than 3 are acceptable. |
 | Ks | cm/h | Ks > 0 | 0.001 < K_s < 100 | Soil layer | Ks is the saturated hydraulic conductivity of a soil. Note that in nature, expected values of Ks are distributed logarithmically, so calibrating on the log of Ks rather than Ks directly is likely a better choice for most calibration algorithms. |
 | ponded_head_max | cm | ponded_head_max >= 0 | 0 <= ponded_head_max <= 5 | Entire model domain | This is the maximum amount of ponded water that is allowed to accumulate on the soil surface. While stability tests have only included a maximum value of 5 cm, any value greater than or equal to 0 should be acceptable. A common choice will be 0. This parameter can be set in the config file.  |
-| field_capacity_psi | cm | 0 < field_capacity_cm, <br> field_capacity_cm < wilting_point_psi | 10.3 < field_capacity_cm < <br> 516.6 | Entire model domain | This is the wilting point of the model domain, expressed as a capillary head. Together with wilting_point_psi, the field capacity is used to determine the intensity of the reduction of PET to become AET. The numbers 10.3 cm and 516.6 cm correspond to pressures of 1/100 atm and 1/2 atm of water. Note that the model generally uses absolute values of capillary head; in this case, these limits are absolute values of negative numbers and physically represent unsaturated soil. While field capacity will vary per soil type, we use a single value for the entire model domain, following the method for PET->AET correction used by HYDRUS. This parameter can be set in the config file. |
+| field_capacity_psi | cm | 0 < field_capacity_psi, <br>field_capacity_psi < wilting_point_psi | 10.3 < field_capacity_psi < 516.6 | Entire model domain | This is the wilting point of the model domain, expressed as a capillary head. Together with wilting_point_psi, the field capacity is used to determine the intensity of the reduction of PET to become AET. The numbers 10.3 cm and 516.6 cm correspond to pressures of 1/100 atm and 1/2 atm of water. Note that the model generally uses absolute values of capillary head; in this case, these limits are absolute values of negative numbers and physically represent unsaturated soil. While field capacity will vary per soil type, we use a single value for the entire model domain, following the method for PET->AET correction used by HYDRUS. This parameter can be set in the config file. |
 

From a574d5f045ca75a74157ae13b66cc8a6e4065f92 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 11:05:54 -0700
Subject: [PATCH 15/23] adding table containing example soil parameters

---
 data/README.md | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/data/README.md b/data/README.md
index ea8748c..cc7a64a 100644
--- a/data/README.md
+++ b/data/README.md
@@ -12,3 +12,20 @@ A detailed description of the calibratable parameters is given below.
 | ponded_head_max | cm | ponded_head_max >= 0 | 0 <= ponded_head_max <= 5 | Entire model domain | This is the maximum amount of ponded water that is allowed to accumulate on the soil surface. While stability tests have only included a maximum value of 5 cm, any value greater than or equal to 0 should be acceptable. A common choice will be 0. This parameter can be set in the config file.  |
 | field_capacity_psi | cm | 0 < field_capacity_psi, <br>field_capacity_psi < wilting_point_psi | 10.3 < field_capacity_psi < 516.6 | Entire model domain | This is the wilting point of the model domain, expressed as a capillary head. Together with wilting_point_psi, the field capacity is used to determine the intensity of the reduction of PET to become AET. The numbers 10.3 cm and 516.6 cm correspond to pressures of 1/100 atm and 1/2 atm of water. Note that the model generally uses absolute values of capillary head; in this case, these limits are absolute values of negative numbers and physically represent unsaturated soil. While field capacity will vary per soil type, we use a single value for the entire model domain, following the method for PET->AET correction used by HYDRUS. This parameter can be set in the config file. |
 
+Below is a table that contains parameters for 12 soil classes, taken from the HYDRUS-1D soils catalog, which in turn are based on the paper: Carsel, R.F., and Parrish, R. S., Developing joint probability distributions of soil water retention characteristics, Water Resour. Res, 24, 755-769, 1988.
+
+| Textural Class      | θr    | θs  | α     | n    | Ks          |
+|---------------------|-------|-----|-------|------|-------------|
+| Sand                | 0.045 | 0.43 | 0.145 | 2.68 | 29.7        |
+| Loamy Sand          | 0.057 | 0.41 | 0.124 | 2.28 | 14.59166667 |
+| Sandy Loam          | 0.065 | 0.41 | 0.075 | 1.89 | 4.420833333 |
+| Loam                | 0.078 | 0.43 | 0.036 | 1.56 | 1.04        |
+| Silt                | 0.034 | 0.46 | 0.016 | 1.37 | 0.25        |
+| Silty Loam          | 0.067 | 0.45 | 0.02  | 1.41 | 0.45        |
+| Sandy Clay Loam     | 0.1   | 0.39 | 0.059 | 1.48 | 1.31        |
+| Clay Loam           | 0.095 | 0.41 | 0.019 | 1.31 | 0.26        |
+| Silty Clay Loam     | 0.089 | 0.43 | 0.01  | 1.23 | 0.07        |
+| Sandy Clay          | 0.1   | 0.38 | 0.027 | 1.23 | 0.12        |
+| Silty Clay          | 0.07  | 0.36 | 0.005 | 1.09 | 0.02        |
+| Clay                | 0.068 | 0.38 | 0.008 | 1.09 | 0.2         |
+

From fb4630237a03d4553f0d03ae31624bfc42202a72 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 11:06:55 -0700
Subject: [PATCH 16/23] adjusting descrption of new table

---
 data/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data/README.md b/data/README.md
index cc7a64a..2af583b 100644
--- a/data/README.md
+++ b/data/README.md
@@ -12,7 +12,7 @@ A detailed description of the calibratable parameters is given below.
 | ponded_head_max | cm | ponded_head_max >= 0 | 0 <= ponded_head_max <= 5 | Entire model domain | This is the maximum amount of ponded water that is allowed to accumulate on the soil surface. While stability tests have only included a maximum value of 5 cm, any value greater than or equal to 0 should be acceptable. A common choice will be 0. This parameter can be set in the config file.  |
 | field_capacity_psi | cm | 0 < field_capacity_psi, <br>field_capacity_psi < wilting_point_psi | 10.3 < field_capacity_psi < 516.6 | Entire model domain | This is the wilting point of the model domain, expressed as a capillary head. Together with wilting_point_psi, the field capacity is used to determine the intensity of the reduction of PET to become AET. The numbers 10.3 cm and 516.6 cm correspond to pressures of 1/100 atm and 1/2 atm of water. Note that the model generally uses absolute values of capillary head; in this case, these limits are absolute values of negative numbers and physically represent unsaturated soil. While field capacity will vary per soil type, we use a single value for the entire model domain, following the method for PET->AET correction used by HYDRUS. This parameter can be set in the config file. |
 
-Below is a table that contains parameters for 12 soil classes, taken from the HYDRUS-1D soils catalog, which in turn are based on the paper: Carsel, R.F., and Parrish, R. S., Developing joint probability distributions of soil water retention characteristics, Water Resour. Res, 24, 755-769, 1988.
+Below is a table that contains example parameters for 12 soil classes, taken from the HYDRUS-1D soils catalog, which in turn are based on the paper: Carsel, R.F., and Parrish, R. S., Developing joint probability distributions of soil water retention characteristics, Water Resour. Res, 24, 755-769, 1988.
 
 | Textural Class      | θr    | θs  | α     | n    | Ks          |
 |---------------------|-------|-----|-------|------|-------------|

From fa0440aabed9c19ad0e20b21bbfde2c88f68cf12 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 11:10:49 -0700
Subject: [PATCH 17/23] updating readme with link to calib params explanation

---
 README.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/README.md b/README.md
index 6197d16..32c4abb 100644
--- a/README.md
+++ b/README.md
@@ -13,6 +13,9 @@ Detailed instructions on how to build and run LASAM can be found here [INSTALL](
 ## Model Configuration File
 A detailed description of the parameters for model configuration is provided [here](https://github.com/NOAA-OWP/LGAR-C/tree/master/configs/README.md).
 
+## Calibratable parameters
+A detailed description of calibratable parameters is provided [here](https://github.com/NOAA-OWP/LGAR-C/tree/master/data/README.md).
+
 ## Nextgen Realization Files
 Realization files for running LASAM (coupled/uncoupled modes) in the nextgen framework are provided [here](https://github.com/NOAA-OWP/LGAR-C/tree/master/realizations/README.md).
   

From db68e87ab718922fa2f4daa8dd059984c6aaf3b7 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 11:23:36 -0700
Subject: [PATCH 18/23] adding units description to second table in data readme

---
 data/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data/README.md b/data/README.md
index 2af583b..acd478a 100644
--- a/data/README.md
+++ b/data/README.md
@@ -12,7 +12,7 @@ A detailed description of the calibratable parameters is given below.
 | ponded_head_max | cm | ponded_head_max >= 0 | 0 <= ponded_head_max <= 5 | Entire model domain | This is the maximum amount of ponded water that is allowed to accumulate on the soil surface. While stability tests have only included a maximum value of 5 cm, any value greater than or equal to 0 should be acceptable. A common choice will be 0. This parameter can be set in the config file.  |
 | field_capacity_psi | cm | 0 < field_capacity_psi, <br>field_capacity_psi < wilting_point_psi | 10.3 < field_capacity_psi < 516.6 | Entire model domain | This is the wilting point of the model domain, expressed as a capillary head. Together with wilting_point_psi, the field capacity is used to determine the intensity of the reduction of PET to become AET. The numbers 10.3 cm and 516.6 cm correspond to pressures of 1/100 atm and 1/2 atm of water. Note that the model generally uses absolute values of capillary head; in this case, these limits are absolute values of negative numbers and physically represent unsaturated soil. While field capacity will vary per soil type, we use a single value for the entire model domain, following the method for PET->AET correction used by HYDRUS. This parameter can be set in the config file. |
 
-Below is a table that contains example parameters for 12 soil classes, taken from the HYDRUS-1D soils catalog, which in turn are based on the paper: Carsel, R.F., and Parrish, R. S., Developing joint probability distributions of soil water retention characteristics, Water Resour. Res, 24, 755-769, 1988.
+Below is a table that contains example parameters for 12 soil classes, taken from the HYDRUS-1D soils catalog, which in turn are based on the paper: Carsel, R.F., and Parrish, R. S., Developing joint probability distributions of soil water retention characteristics, Water Resour. Res, 24, 755-769, 1988. θr, θs, and n are unitless, α has units of 1/cm, and Ks has units of cm/h.
 
 | Textural Class      | θr    | θs  | α     | n    | Ks          |
 |---------------------|-------|-----|-------|------|-------------|

From e060c3d77165eecf99c8aa69702b0c156d222d77 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 12:33:24 -0700
Subject: [PATCH 19/23] added text describing why LASAM should be applied in
 arid or semi arid areas

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index 32c4abb..2d1a796 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,8 @@
 # Lumped Arid/Semi-arid Model (LASAM) for infiltration and surface runoff
 The LASAM simulates infiltration and runoff based on Layered Green & Ampt with redistribution (LGAR) model. LGAR is a model which partitions precipitation into infiltration and runoff, and is designed for use in arid or semi-arid climates. LGAR closely mimics precipitation partitioning results simulated by the famous Richards/Richardson equation (RRE), without the inherent reliability and stability challenges the RRE poses. Therefore, this model is useful when accurate, stable precipitation partitioning simulations are desired in arid or semi-arid areas. LGAR in Python (no longer supported) is available [here](https://github.com/NOAA-OWP/LGAR-Py).
 
+LASAM is designed for use in environments where cumulative potential evapotranspiration is greater than cumulative precipitation. Because the lower boundary condition of LASAM is effectively no-flow, the model assumes that water only leaves the vadose zone via AET. This is a reasonable assumption in arid and semi arid areas. If applied in humid areas, the model domain of LASAM will likely become completely saturated.
+
 **Published papers:** For details about the model please see our manuscript on LGAR ([weblink](https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2022WR033742)).
 
 ## Build and Run Instructions

From c75cb45eae530ece2f44c07e7f8fe193b90abeb1 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MacBook-Pro-2.local>
Date: Fri, 26 Apr 2024 12:59:26 -0700
Subject: [PATCH 20/23] updating data readme with more general comments

---
 data/README.md | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/data/README.md b/data/README.md
index acd478a..8c43cf5 100644
--- a/data/README.md
+++ b/data/README.md
@@ -12,7 +12,13 @@ A detailed description of the calibratable parameters is given below.
 | ponded_head_max | cm | ponded_head_max >= 0 | 0 <= ponded_head_max <= 5 | Entire model domain | This is the maximum amount of ponded water that is allowed to accumulate on the soil surface. While stability tests have only included a maximum value of 5 cm, any value greater than or equal to 0 should be acceptable. A common choice will be 0. This parameter can be set in the config file.  |
 | field_capacity_psi | cm | 0 < field_capacity_psi, <br>field_capacity_psi < wilting_point_psi | 10.3 < field_capacity_psi < 516.6 | Entire model domain | This is the wilting point of the model domain, expressed as a capillary head. Together with wilting_point_psi, the field capacity is used to determine the intensity of the reduction of PET to become AET. The numbers 10.3 cm and 516.6 cm correspond to pressures of 1/100 atm and 1/2 atm of water. Note that the model generally uses absolute values of capillary head; in this case, these limits are absolute values of negative numbers and physically represent unsaturated soil. While field capacity will vary per soil type, we use a single value for the entire model domain, following the method for PET->AET correction used by HYDRUS. This parameter can be set in the config file. |
 
-Below is a table that contains example parameters for 12 soil classes, taken from the HYDRUS-1D soils catalog, which in turn are based on the paper: Carsel, R.F., and Parrish, R. S., Developing joint probability distributions of soil water retention characteristics, Water Resour. Res, 24, 755-769, 1988. θr, θs, and n are unitless, α has units of 1/cm, and Ks has units of cm/h.
+Parameters that are specified per soil layer can either be scalar values with double precision (in the event the model is run with 1 layer) or vectors of doubles (in the event that the model is run with more than 1 layer), whereas parameters that are specified for the entire model domain are scalars with double precision. 
+
+Stability testing efforts have included varying initial conditions, where the initial condition throughout the soil moisture profile is set with a single value for capillary head, ranging from 3000 cm to 10 cm (again note that these are absolute values of negative numbers and indicate unsaturated soils). This value can be set in the config file. 
+
+We recommend that practical parameter values for calibration efforts of real soils use ranges that are for some parameters somewhat more restricted than the ones used in stability testing. For example, while it was desirable to test theta_e values up to 0.8, we do not expect to often see theta_e values of this magnitude in nature. Further, randomly sampling parameter values within even restricted ranges to build parameter sets could theoretically yield unrealistic soils (for example, a parameter set could have a K_s value of 0.01 cm/h, indicative of clay, and an n value of 2.5, indicative of sand). 
+
+Below is a table of parameters for soils from the HYDRUS soils catalog, which can give insights to likely parameter values per soil class. It contains example parameters for 12 soil classes, taken from the HYDRUS-1D soils catalog, which in turn are based on the paper: Carsel, R.F., and Parrish, R. S., Developing joint probability distributions of soil water retention characteristics, Water Resour. Res, 24, 755-769, 1988. θr, θs, and n are unitless, α has units of 1/cm, and Ks has units of cm/h.
 
 | Textural Class      | θr    | θs  | α     | n    | Ks          |
 |---------------------|-------|-----|-------|------|-------------|

From 10ced4161373a130726457f3ba2586db5e272711 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MBP-2.lan>
Date: Wed, 1 May 2024 10:28:09 -0700
Subject: [PATCH 21/23] Following feedback from Rachel, fixed a typo in the
 parameter range of theta_r, and updated descriptions of parameters that are
 specified per soil layer to indicate where these parameters can be set.

---
 data/README.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/data/README.md b/data/README.md
index 8c43cf5..455fd5d 100644
--- a/data/README.md
+++ b/data/README.md
@@ -4,11 +4,11 @@ A detailed description of the calibratable parameters is given below.
 
 | Parameter name | Units |  Physical limits  | Range tested for stability | Applies to individual soil layers or entire model domain | Description |
 | --- | --- | --- | --- | --- | --------------- |
-| theta_r | - | 0< theta_r <1, <br> theta_r < theta_e | 0.01 < theta_e < 0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. |
-| theta_e | - | 0 < theta_e < 1, <br> theta_r < theta_e | 0.3 < theta_e < 0.8 | Soil layer | theta_e is the maximum volumetric water content that a soil layer can naturally attain. Note that theta_e must be greater than theta_r. |
-| alpha | 1/cm | alpha > 0 | 0.001 < alpha < 0.3 | Soil layer | alpha is the van Genuchten parameter related to the inverse of air entry pressure. Note that in nature, expected values of alpha are distributed logarithmically, so calibrating on the log of alpha rather than alpha directly is likely a better choice for most calibration algorithms. |
-| n | - | n > 1 | 1.01 < n <3 | Soil layer | n is the van Genuchten parameter related to pore size distribution. Note that another commonly reported van Genuchten parameter, m, is related to n via m = 1 - 1/n. We recommend that n > 1.01. Values larger than 3 are acceptable. |
-| Ks | cm/h | Ks > 0 | 0.001 < K_s < 100 | Soil layer | Ks is the saturated hydraulic conductivity of a soil. Note that in nature, expected values of Ks are distributed logarithmically, so calibrating on the log of Ks rather than Ks directly is likely a better choice for most calibration algorithms. |
+| theta_r | - | 0< theta_r <1, <br> theta_r < theta_e | 0.01 < theta_r < 0.15 | Soil layer | theta_r is the residual water content, or the minimum volumetric water content that a soil layer can naturally attain. Note that theta_r must be less than than theta_e. This is set per soil layer, in the .dat file in the data directory.|
+| theta_e | - | 0 < theta_e < 1, <br> theta_r < theta_e | 0.3 < theta_e < 0.8 | Soil layer | theta_e is the maximum volumetric water content that a soil layer can naturally attain. Note that theta_e must be greater than theta_r. This is set per soil layer, in the .dat file in the data directory.|
+| alpha | 1/cm | alpha > 0 | 0.001 < alpha < 0.3 | Soil layer | alpha is the van Genuchten parameter related to the inverse of air entry pressure. Note that in nature, expected values of alpha are distributed logarithmically, so calibrating on the log of alpha rather than alpha directly is likely a better choice for most calibration algorithms. This is set per soil layer, in the .dat file in the data directory.|
+| n | - | n > 1 | 1.01 < n <3 | Soil layer | n is the van Genuchten parameter related to pore size distribution. Note that another commonly reported van Genuchten parameter, m, is related to n via m = 1 - 1/n. We recommend that n > 1.01. Values larger than 3 are acceptable. This is set per soil layer, in the .dat file in the data directory.|
+| Ks | cm/h | Ks > 0 | 0.001 < K_s < 100 | Soil layer | Ks is the saturated hydraulic conductivity of a soil. Note that in nature, expected values of Ks are distributed logarithmically, so calibrating on the log of Ks rather than Ks directly is likely a better choice for most calibration algorithms. This is set per soil layer, in the .dat file in the data directory.|
 | ponded_head_max | cm | ponded_head_max >= 0 | 0 <= ponded_head_max <= 5 | Entire model domain | This is the maximum amount of ponded water that is allowed to accumulate on the soil surface. While stability tests have only included a maximum value of 5 cm, any value greater than or equal to 0 should be acceptable. A common choice will be 0. This parameter can be set in the config file.  |
 | field_capacity_psi | cm | 0 < field_capacity_psi, <br>field_capacity_psi < wilting_point_psi | 10.3 < field_capacity_psi < 516.6 | Entire model domain | This is the wilting point of the model domain, expressed as a capillary head. Together with wilting_point_psi, the field capacity is used to determine the intensity of the reduction of PET to become AET. The numbers 10.3 cm and 516.6 cm correspond to pressures of 1/100 atm and 1/2 atm of water. Note that the model generally uses absolute values of capillary head; in this case, these limits are absolute values of negative numbers and physically represent unsaturated soil. While field capacity will vary per soil type, we use a single value for the entire model domain, following the method for PET->AET correction used by HYDRUS. This parameter can be set in the config file. |
 

From 035f9ea34e9b3e6a29594319ed757da00bf9a2d2 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MBP-2.lan>
Date: Wed, 1 May 2024 10:31:50 -0700
Subject: [PATCH 22/23] updating table that has HYDRUS soils examples to have
 units in header

---
 data/README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/data/README.md b/data/README.md
index 455fd5d..f406604 100644
--- a/data/README.md
+++ b/data/README.md
@@ -20,8 +20,8 @@ We recommend that practical parameter values for calibration efforts of real soi
 
 Below is a table of parameters for soils from the HYDRUS soils catalog, which can give insights to likely parameter values per soil class. It contains example parameters for 12 soil classes, taken from the HYDRUS-1D soils catalog, which in turn are based on the paper: Carsel, R.F., and Parrish, R. S., Developing joint probability distributions of soil water retention characteristics, Water Resour. Res, 24, 755-769, 1988. θr, θs, and n are unitless, α has units of 1/cm, and Ks has units of cm/h.
 
-| Textural Class      | θr    | θs  | α     | n    | Ks          |
-|---------------------|-------|-----|-------|------|-------------|
+| Textural Class      | θr [-] | θs [-] | α [1/cm] | n [-] | Ks [cm/h]   |
+|---------------------|--------|--------|----------|-------|-------------|
 | Sand                | 0.045 | 0.43 | 0.145 | 2.68 | 29.7        |
 | Loamy Sand          | 0.057 | 0.41 | 0.124 | 2.28 | 14.59166667 |
 | Sandy Loam          | 0.065 | 0.41 | 0.075 | 1.89 | 4.420833333 |

From 0476af1865d8b5d347e2a0566111328114b0ec23 Mon Sep 17 00:00:00 2001
From: Peter La Follette <peterlafollette@Peters-MBP-2.lan>
Date: Wed, 1 May 2024 10:33:47 -0700
Subject: [PATCH 23/23] removing units description from text because it is now
 in header

---
 data/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data/README.md b/data/README.md
index f406604..673bf4e 100644
--- a/data/README.md
+++ b/data/README.md
@@ -18,7 +18,7 @@ Stability testing efforts have included varying initial conditions, where the in
 
 We recommend that practical parameter values for calibration efforts of real soils use ranges that are for some parameters somewhat more restricted than the ones used in stability testing. For example, while it was desirable to test theta_e values up to 0.8, we do not expect to often see theta_e values of this magnitude in nature. Further, randomly sampling parameter values within even restricted ranges to build parameter sets could theoretically yield unrealistic soils (for example, a parameter set could have a K_s value of 0.01 cm/h, indicative of clay, and an n value of 2.5, indicative of sand). 
 
-Below is a table of parameters for soils from the HYDRUS soils catalog, which can give insights to likely parameter values per soil class. It contains example parameters for 12 soil classes, taken from the HYDRUS-1D soils catalog, which in turn are based on the paper: Carsel, R.F., and Parrish, R. S., Developing joint probability distributions of soil water retention characteristics, Water Resour. Res, 24, 755-769, 1988. θr, θs, and n are unitless, α has units of 1/cm, and Ks has units of cm/h.
+Below is a table of parameters for soils from the HYDRUS soils catalog, which can give insights to likely parameter values per soil class. It contains example parameters for 12 soil classes, taken from the HYDRUS-1D soils catalog, which in turn are based on the paper: Carsel, R.F., and Parrish, R. S., Developing joint probability distributions of soil water retention characteristics, Water Resour. Res, 24, 755-769, 1988.
 
 | Textural Class      | θr [-] | θs [-] | α [1/cm] | n [-] | Ks [cm/h]   |
 |---------------------|--------|--------|----------|-------|-------------|