fmu-pem 0.0.2__tar.gz → 0.0.4__tar.gz

{fmu_pem-0.0.2 → fmu_pem-0.0.4}/.gitignore

@@ -1,4 +1,6 @@
 /.venv/
+/venv/
+/venv_external/
 /.vscode/
 # Local debug scripts etc
 Notebooks_and_scripts/
@@ -9,6 +11,9 @@ Notebooks/
 /dist/
 /src/fmu_pem.egg-info/
 **/__pycache__/
+**/*_cache/
+/.idea/
+/.vscode/
 src/fmu/pem/version.py
 
 # npm and node relevant build files
@@ -19,3 +24,9 @@ dist
 fmu-pem-schema.json
 **/.vitepress/dist
 **/.vitepress/cache
+/ERT/storage/
+/ERT/logs/
+/ERT/.runpath_list
+/logs/
+/tests/data/sim2seis/input/pem/venv_ext/
+scripts/debug_lines.py

{fmu_pem-0.0.2 → fmu_pem-0.0.4}/ERT/run_pem.ert

@@ -7,7 +7,8 @@
 
 DEFINE <USER> $USER
 DEFINE <SCRATCH> /scratch/fmu
-DEFINE <CONFIG_PATH> /private/hfle/drogon_hfle/dev/rms/model
+DEFINE <CONFIG_PATH> /private/hfle/drogon_hfle/dev/sim2seis/model
+DEFINE <MODEL_PATH> /private/hfle/drogon_hfle/dev/sim2seis/model
 
 NUM_REALIZATIONS 1
 RUNPATH     <SCRATCH>/<USER>/fmu_sim2seis_pem/realization-<IENS>/iter-<ITER>
@@ -15,11 +16,9 @@ RUNPATH     <SCRATCH>/<USER>/fmu_sim2seis_pem/realization-<IENS>/iter-<ITER>
 -- Copy required input files for the PEM, directories are automatically created by COPY_FILE
 FORWARD_MODEL COPY_FILE(<FROM>=<CONFIG_PATH>/../../fmuconfig/output/global_variables.yml,      <TO>=<RUNPATH>/fmuconfig/output/global_variables.yml)
 FORWARD_MODEL COPY_FILE(<FROM>=<CONFIG_PATH>/../../fmuconfig/output/global_variables_pred.yml, <TO>=<RUNPATH>/fmuconfig/output/global_variables_pred.yml)
-FORWARD_MODEL COPY_FILE(<FROM>=<CONFIG_PATH>/../../sim2seis/input/pem/ECLIPSE.EGRID,           <TO>=<RUNPATH>/sim2seis/input/pem/ECLIPSE.EGRID)
-FORWARD_MODEL COPY_FILE(<FROM>=<CONFIG_PATH>/../../sim2seis/input/pem/ECLIPSE.INIT,            <TO>=<RUNPATH>/sim2seis/input/pem/ECLIPSE.INIT)
-FORWARD_MODEL COPY_FILE(<FROM>=<CONFIG_PATH>/../../sim2seis/input/pem/ECLIPSE.UNRST,           <TO>=<RUNPATH>/sim2seis/input/pem/ECLIPSE.UNRST)
-FORWARD_MODEL COPY_FILE(<FROM>=<CONFIG_PATH>/../../sim2seis/input/pem/export_grid.roff,      <TO>=<RUNPATH>/sim2seis/input/pem/export_grid.roff)
-FORWARD_MODEL COPY_FILE(<FROM>=<CONFIG_PATH>/../../sim2seis/input/pem/export_prop.roff,      <TO>=<RUNPATH>/sim2seis/input/pem/export_prop.roff)
+
+-- Copy the input file directory, it can vary which volume fraction files that are included in the PEM run
+FORWARD_MODEL COPY_DIRECTORY(<FROM>=<CONFIG_PATH>/../../sim2seis/input/pem, <TO>=<RUNPATH>/sim2seis/input)
 
 -- Copy all model files in ../../sim2seis/model for flexibility. The PEM .yml file (new_pem_config.yml) is
 -- always required, .pkl model files are required if tmatrix model is used in the PEM
@@ -30,12 +29,14 @@ FORWARD_MODEL MAKE_DIRECTORY(<DIRECTORY> = <RUNPATH>/sim2seis/output/pem)
 FORWARD_MODEL MAKE_DIRECTORY(<DIRECTORY> = <RUNPATH>/share/results/grids)
 
 -- Create start directory
-FORWARD_MODEL MAKE_DIRECTORY(<DIRECTORY> = <RUNPATH>/rms/model)
+FORWARD_MODEL MAKE_DIRECTORY(<DIRECTORY> = <RUNPATH>/sim2seis/model)
 
 -- PEM parameter setting
-DEFINE <PEM_STARTDIR> <RUNPATH>/rms/model
-DEFINE <RELPATH_PEM> <RUNPATH>/sim2seis/model
+DEFINE <PEM_CONFIGDIR> <RUNPATH>/sim2seis/model
 DEFINE <PEM_CONFIG_FILE_NAME> new_pem_config.yml
+DEFINE <GLOBAL_PATH> ../../fmuconfig/output
+DEFINE <GLOBAL_CONFIG_FILE> global_variables.yml
+DEFINE <MOD_PREFIX> HIST
 
 -- Run the PEM
-FORWARD_MODEL PEM(<START_DIR>=<PEM_STARTDIR>, <CONFIG_DIR>=<RELPATH_PEM>, <CONFIG_FILE>=<PEM_CONFIG_FILE_NAME>)
+FORWARD_MODEL PEM(<CONFIG_DIR>=<PEM_CONFIGDIR>, <CONFIG_FILE>=<PEM_CONFIG_FILE_NAME>, <GLOBAL_DIR>=<GLOBAL_PATH>, <GLOBAL_FILE>=<GLOBAL_CONFIG_FILE>, <MODEL_DIR>=<MODEL_PATH>, <MOD_DATE_PREFIX>=<MOD_PREFIX>)

{fmu_pem-0.0.2 → fmu_pem-0.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fmu-pem
-Version: 0.0.2
+Version: 0.0.4
 Summary: pem
 License:                     GNU GENERAL PUBLIC LICENSE
                                Version 3, 29 June 2007
@@ -695,7 +695,8 @@ Requires-Dist: xtgeo>=4.7.1
 Requires-Dist: fmu-tools
 Requires-Dist: fmu-config
 Requires-Dist: fmu-dataio
-Requires-Dist: rock-physics-open>=0.1.2
+Requires-Dist: fmu-datamodels
+Requires-Dist: rock-physics-open>=0.3.3
 Requires-Dist: PyYAML>=6.0.1
 Requires-Dist: pydantic
 Requires-Dist: ert>=14.1.10
@@ -716,7 +717,8 @@ Requires-Dist: sphinx_rtd_theme; extra == "docs"
 Dynamic: license-file
 
 > [!WARNING]
-> `fmu-pem` is not yet qualified technology, and as of today only applicable for selected pilot test fields.
+> `fmu-pem` is not yet qualified technology, and as of today only applicable for
+    selected pilot test fields.
 
 **[📚 User documentation](https://equinor.github.io/fmu-pem/)**
 
@@ -731,25 +733,28 @@ based on the [rock-physics-open](https://github.com/equinor/rock-physics-open) l
 
 To install `fmu-pem`, first activate a virtual environment, then type:
 
-```
+```shell
 pip install fmu-pem
 ```
 
 The PEM is controlled by parameter settings in a *yaml-file*, given as part of the
-command line arguments, or by the workflow parameter if it is run as an ERT forward model.
+command line arguments, or by the workflow parameter if it is run as an ERT forward
+model.
 
 ### Calibration of rock physics models
 
 Calibration of the rock physics models is normally carried out in
 [RokDoc](https://www.ikonscience.com/rokdoc-geoprediction-software-platform/)
-prior to running the PEM. Fluid and mineral properties can be found in the RokDoc project, or
-from LFP logs, if they are available.
+prior to running the PEM. Fluid and mineral properties can be found in the RokDoc
+project, or from LFP logs, if they are available.
 
-> [!NOTE]  
-> The fluid models contained in this module may not cover all possible cases. Gas condensate, very heavy oil, 
-> or reservoir pressure under hydrocarbon bubble point will need additional proprietary code to run.
+> [!NOTE]
+> The fluid models contained in this module may not cover all possible cases. Gas
+condensate, very heavy oil, > or reservoir pressure under hydrocarbon bubble point will
+need additional proprietary code to run.
 >
 > Equinor users can install additional proprietary models using
+
 > ```bash
 > pip install "git+ssh://git@github.com/equinor/rock-physics"`
 > ```
@@ -757,10 +762,13 @@ from LFP logs, if they are available.
 ## How to develop fmu-pem?
 
 Developing the user interface can be done by:
+
 ```bash
 cd ./documentation
 npm ci  # Install dependencies
 npm run create-json-schema  # Extract JSON schema from Python code
 npm run docs:dev  # Start local development server
 ```
-The JSON schema itself (type, title, description etc.) comes from the corresponding Pydantic models in the Python code.
+
+The JSON schema itself (type, title, description etc.) comes from the corresponding
+Pydantic models in the Python code.

{fmu_pem-0.0.2 → fmu_pem-0.0.4}/README.md

@@ -1,5 +1,6 @@
 > [!WARNING]
-> `fmu-pem` is not yet qualified technology, and as of today only applicable for selected pilot test fields.
+> `fmu-pem` is not yet qualified technology, and as of today only applicable for
+    selected pilot test fields.
 
 **[📚 User documentation](https://equinor.github.io/fmu-pem/)**
 
@@ -14,25 +15,28 @@ based on the [rock-physics-open](https://github.com/equinor/rock-physics-open) l
 
 To install `fmu-pem`, first activate a virtual environment, then type:
 
-```
+```shell
 pip install fmu-pem
 ```
 
 The PEM is controlled by parameter settings in a *yaml-file*, given as part of the
-command line arguments, or by the workflow parameter if it is run as an ERT forward model.
+command line arguments, or by the workflow parameter if it is run as an ERT forward
+model.
 
 ### Calibration of rock physics models
 
 Calibration of the rock physics models is normally carried out in
 [RokDoc](https://www.ikonscience.com/rokdoc-geoprediction-software-platform/)
-prior to running the PEM. Fluid and mineral properties can be found in the RokDoc project, or
-from LFP logs, if they are available.
+prior to running the PEM. Fluid and mineral properties can be found in the RokDoc
+project, or from LFP logs, if they are available.
 
-> [!NOTE]  
-> The fluid models contained in this module may not cover all possible cases. Gas condensate, very heavy oil, 
-> or reservoir pressure under hydrocarbon bubble point will need additional proprietary code to run.
+> [!NOTE]
+> The fluid models contained in this module may not cover all possible cases. Gas
+condensate, very heavy oil, > or reservoir pressure under hydrocarbon bubble point will
+need additional proprietary code to run.
 >
 > Equinor users can install additional proprietary models using
+
 > ```bash
 > pip install "git+ssh://git@github.com/equinor/rock-physics"`
 > ```
@@ -40,10 +44,13 @@ from LFP logs, if they are available.
 ## How to develop fmu-pem?
 
 Developing the user interface can be done by:
+
 ```bash
 cd ./documentation
 npm ci  # Install dependencies
 npm run create-json-schema  # Extract JSON schema from Python code
 npm run docs:dev  # Start local development server
 ```
-The JSON schema itself (type, title, description etc.) comes from the corresponding Pydantic models in the Python code.
+
+The JSON schema itself (type, title, description etc.) comes from the corresponding
+Pydantic models in the Python code.

{fmu_pem-0.0.2 → fmu_pem-0.0.4}/SECURITY.md

@@ -2,10 +2,10 @@ If you discover a security vulnerability in this project, please follow the step
 
 ### For "non-critical" issues
 
-- **Alternative A:**  
+- **Alternative A:**
 Create a GitHub issue for the vulnerability. Avoid putting sensitive information in the issue.
 
-- **Alternative B:**  
+- **Alternative B:**
 Send an email to the projects maintainer describing the issue.
 
 ### For "critical" and time sensitive issues

fmu_pem-0.0.4/documentation/docs/.vitepress/config.mts

@@ -0,0 +1,59 @@
+import {readFileSync} from "fs"
+import {defineConfig} from 'vitepress'
+
+// Copied from https://github.com/equinor/vscode-lang-ert/blob/master/syntaxes/ert.tmLanguage.json
+const ertLanguageGrammar = JSON.parse(readFileSync("./docs/ert.tmLanguage.json"))
+
+// https://vitepress.dev/reference/site-config
+export default defineConfig({
+    title: "FMU PEM",
+    description: "User documentation for using fmu-pem",
+    head: [
+        ["link", {rel: "stylesheet", href: "https://unpkg.com/tailwindcss@^2/dist/tailwind.min.css"}]
+    ],
+    markdown: {
+        math: true,
+        languages: [ertLanguageGrammar]
+    },
+    themeConfig: {
+        // https://vitepress.dev/reference/default-theme-config
+        nav: [
+            {text: 'Home', link: '/'},
+        ],
+        logo: {light: "/fmu_logo_light_mode.svg", dark: "/fmu_logo_dark_mode.svg"},
+        sidebar: [
+            {
+                text: 'Setup',
+                items: [
+                    {
+                        text: "fmu-PEM manual", link: "/use-cases", items: [
+                            {text: 'Read and validate YAML file', link: '/yaml-validation'},
+                            {text: 'Import reservoir simulator results', link: '/import-sim-results'},
+                            {text: 'Estimate effective mineral properties', link: '/effective-mineral-properties'},
+                            {text: 'Estimate effective fluid properties', link: '/fluid-properties'},
+                            {text: 'Estimate effective pressure', link: '/effective-pressure'},
+                            {text: 'Estimate saturated rock properties', link: '/saturated-rock'},
+                            {text: '(Optional) estimate difference properties', link: '/difference-properties'},
+                            {text: 'Save intermediate (optional) and final estimates', link: '/save-results'},
+                            {text: 'Model file formats', link: '/model-file-formats'},
+                        ]
+                    },
+                    {text: 'ERT configuration', link: '/ert-configuration'},
+                    {text: 'PEM configuration', link: '/pem-configuration'}
+                ]
+            },
+            {
+                text: 'Developer Documentation',
+                items: [
+                    {text: 'Zone-Aware Fluid Properties', link: '/zone-aware-fluids'},
+                    {text: 'Zone-Based Saturated Rock Properties', link: '/zone-based-saturated-rock'},
+                    {text: 'Zone Implementation Roadmap', link: '/zone-implementation-roadmap'}
+                ]
+            }
+        ],
+        socialLinks: [
+            {icon: 'github', link: 'https://github.com/equinor/fmu-pem'}
+        ]
+    },
+    ignoreDeadLinks: true
+})

fmu_pem-0.0.4/documentation/docs/difference-properties.md

@@ -0,0 +1,28 @@
+# Calculate difference properties
+
+`fmu-pem` is normally used for estimating 4D seismic response, and difference between simulator model time steps
+can be more important than absolute values. In `fmu-sim2seis` workflow, the difference is calculated from absolute
+values in a set of `Vp`, `Vs` and `Rho` parameters, ref. [Save results](./save-results.md). Additional difference
+parameters can be generated in `fmu-pem` for QC or calibration purposes.
+
+A section in the YAML configuration file specifies which parameters are selected for difference calculation, and
+what kind of difference attributes should be estimated:
+
+```yaml
+# For 4D parameters: settings for which difference parameters to calculate
+diff_calculation:
+  AI: [diffpercent, ratio]
+  SI: [diffpercent, ratio]
+  VPVS: [ratio]
+  TWTPP: [diff]
+  DENS: [diffpercent]
+  VP: [diffpercent]
+  VS: [diffpercent]
+  SWAT: [diff]
+  SGAS: [diff]
+```
+
+For convenience, it is possible to calculate differences of input parameter, as well, as in the example above for
+`SWAT` and `SGAS`. The three difference attributes that can be selected, are `diff`, `diffpercent` and `ratio`.
+
+In the FMU directory structure, the difference estimates are stored in `share/results/grids`.

fmu_pem-0.0.4/documentation/docs/effective-mineral-properties.md

@@ -0,0 +1,48 @@
+# Effective mineral properties
+
+A volume of rock will generally consist of several minerals, each having its own elastic properties. To calculate
+the overall elastic properties of the volume, we need to know the elastic properties of each mineral, the volume
+fractions of the minerals, and we must have a model for how to mix the volume fractions.
+
+Default values for the elastic properties of the most common minerals are provided in `fmu-pem`, but they should
+be verified in each case. Shale is often given as the effective mineral properties of a combination of constituents,
+and it can range from a soft marine clay to a stiff, quartz-rich silt.
+
+
+| Mineral    | Density [kg/m^3] | Bulk modulus [GPa] | Shear modulus [GPa] |
+|------------|------------------|--------------------|---------------------|
+| Quartz     | 2650.0           | 36.8               | 44.0                |
+| Shale      | 2680.0           | 25.0               | 12.0                |
+| Calcite    | 2710.0           | 76.8               | 32.0                |
+| Dolomite   | 2870.0           | 94.9               | 45.0                |
+| Stevensite | 2490.0           | 32.5               | 45.0                |
+
+<span id="table-1-mineral-properties"><strong>Table 1:</strong> Default values of elastic properties for common minerals.</span>
+
+More mineral properties can be found in the **Rock Physics Handbook**.
+
+Mavko, G., Mukerji, T., & Dvorkin, J. (2020). *The Rock Physics Handbook* (3rd ed.). Cambridge University Press.
+
+## Volume fractions
+
+Please make sure that the section on [volume fractions](./import-sim-results.md) is understood, and that the `YAML` file
+contains information about all minerals that should be included in the PEM, and also if they are defined as volume
+fractions or mineral fractions.
+
+## Mix models for effective mineral properties
+
+Two models for mixing minerals are available in `fmu-pem`: **Hashin-Shtrikman** and **Voigt-Reuss-Hill** average. The
+difference between them is illustrated in [Figure 1](figure-1-bulk-modulus) and [Figure 2](figure-2-shear-modulus)
+below. In this example, quartz is mixed with a soft marine clay in different proportions. As shown, there is negligible
+difference in effective bulk modulus properties when selecting either Hashin-Shtrikman average or Voigt-Reuss-Hill average.
+The upper and lower bounds of both methods are also included in the plots. The bounds for Hashin-Shtrikman are notably
+narrower than for Voigt and Reuss bounds, with the latter representing the stiffest and softest theoretical combinations,
+respectively.
+
+<img src="./images/bulk_modulus_vs_quartz_fraction.png">
+<span id="figure-1-bulk-modulus"><strong>Figure 1:</strong> Bulk modulus for a mix of quartz and marine clay.</span>
+<br><br>
+
+<img src="./images/shear_modulus_vs_quartz_fraction.png">
+<span id="figure-2-shear-modulus"><strong>Figure 2:</strong> Shear modulus for a mix of quartz and marine clay.</span>
+<br><br>

fmu_pem-0.0.4/documentation/docs/effective-pressure.md

@@ -0,0 +1,38 @@
+# Effective pressure
+
+The matrix of porous rocks will be affected by the effective stress in terms of porosity, permeability and elastic
+moduli. In this context, we simplify it to regard elastic moduli to be stress sensitive, and to keep porosity
+constant. `fmu-pem` does not include any modelling of permeability.
+
+Although effective pressure is the commonly used term, it is somewhat inaccurate, and effective stress is more correct.
+In the `fmu-pem` case, we simplify the stress tensor to an isotropic pressure. To estimate effective pressure, we need to
+know the overburden pressure and the formation pressure at all grid cells. Formation pressure is provided by the
+reservoir simulator model, but overburden pressure is not available there. The best source for overburden pressure is
+provided by drilling or operational geology disciplines, and for most fields, it will be a single one-dimensional model,
+or in some cases one model per structure in the field. The relationship between overburden, formation and effective
+pressures is given as:
+
+$$P_{eff} = P_{ob} - \alpha \cdot P_f$$
+
+where $\alpha$ is the formation factor, also known as the Biot coefficient.
+
+## Variation with time
+
+As formation pressure is reduced by depletion, the effective pressure will vary with time. In `fmu-pem`, the effective
+pressure is estimated for each time step in the reservoir simulator **.UNRST** file.
+
+## Implementation in `fmu-pem`
+
+Two versions of estimation of effective pressure are included in `fmu-pem`: either a constant overburden pressure at
+top reservoir, or a linear depth trend. Formation factor is set to 1.0. These are the settings in the YAML config file:
+
+```yaml
+# Overburden pressure may be set to a constant, but the estimation is improved by using a depth trend
+# Unit is Pa
+pressure:
+  type: trend
+  intercept: 20.0e6
+  gradient: 9174.3
+#  type: constant
+#  value: 50000000.0
+```

fmu_pem-0.0.4/documentation/docs/ert-configuration.md

@@ -0,0 +1,18 @@
+# ERT configuration file
+
+You can include `fmu-pem` in your ERT setup by including the following snippet:
+
+````ert
+-- Define your variables:
+DEFINE <CONFIG_PATH> <RUNPATH>/sim2seis/model
+DEFINE <PEM_CONFIG_FILE_NAME> pem_config.yml
+DEFINE <GLOBAL_CONFIG_DIR> ../../fmuconfig/output
+DEFINE <GLOBAL_CONFIG_FILE> global_variables.yml
+DEFINE <MODEL_PATH> /my_fmu_structure/sim2seis/model
+DEFINE <MOD_PREFIX> HIST
+
+-- Run the pre-installed ERT forward model:
+FORWARD_MODEL PEM(<CONFIG_DIR>=<CONFIG_PATH>, <CONFIG_FILE>=<PEM_CONFIG_FILE_NAME>, <GLOBAL_DIR>=<GLOBAL_CONFIG_DIR>, <GLOBAL_FILE>=<GLOBAL_CONFIG_FILE>, <MODEL_DIR>=<MODEL_PATH>, <MOD_DATE_PREFIX>=<MOD_PREFIX>)
+````
+
+On the next page you will get help on setting up your `pem_config.yml`.

fmu_pem-0.0.4/documentation/docs/ert.tmLanguage.json

@@ -0,0 +1,155 @@
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+	"$schema": "https://raw.githubusercontent.com/martinring/tmlanguage/master/tmlanguage.json",
+	"name": "ert",
+	"patterns": [
+		{
+			"include": "#sections"
+		},
+		{
+			"include": "#comments"
+		},
+		{
+			"include": "#keywords"
+		},
+		{
+			"include": "#important"
+		},
+		{
+			"include": "#variables"
+		},
+		{
+			"include": "#parameters"
+		},
+		{
+			"include": "#strings"
+		},
+		{
+			"include": "#entities"
+		},
+		{
+			"include": "#endcomments"
+		},
+		{
+			"include": "#numbers"
+		},
+		{
+			"include": "#symbols"
+		}
+	],
+	"repository": {
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+			"patterns": [
+				{
+					"name": "keyword.ert",
+					"match": "^[A-Z][_A-Z0-9]*"
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+				{
+					"name": "variable.parameter.ert",
+					"match": "\\s[$A-Z][_A-Z0-9]*(?=\\s)"
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+		},
+		"important": {
+			"patterns": [
+				{
+					"name": "support.type.property-name.json",
+					"match": "<RUNPATH>|<CONFIG_PATH>"
+				}
+			]
+		},
+		"variables": {
+			"patterns": [
+				{
+					"name": "entity.name.type.ert",
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+						"6": {
+							"name": "meta.delimiter.decimal.period.ert"
+						}
+					}
+				}
+			]
+		},
+		"symbols": {
+			"patterns": [
+				{
+					"match": "=|\/|\\(|\\)|,",
+					"name": "storage.type.ert"
+				}
+			]
+		}
+	},
+	"scopeName": "source.ert"
+}