Messages

[GadGeo - Edit Domain]

Hello Mark,

you can fill the hollow objects with a solid material using GadGeo - Edit Domain before losing the GAD-information as described in the GadGeo User Guide under Distinguish between background and hollow parts. After your other steps are done, you can reassign this ID again with ProcessGeo - Reassign Material ID.

Best regards,
Janine

Hello Mark,

if the structure is generated with one of the GeoDict structure generators, the GAD (GeoDict Analytical Data) information of the fibers should be in memory. Then, GeoDict knows, that no binder should be placed into the interior of hollow fibers and it should just work.

Did you maybe discard the GAD-objects or change the structure in a way, that the GAD-information got lost?
Did you get your structure in another way?

Best regards,
Janine

Hello Finn and Caroline,

GeoDict 2024 does not directly support the handling of solid electrolytes. It can work however, if you follow the steps outlined in the video tutorial How to model an All Solid State Battery.

Did you set the transference number of the electrolyte to 0.99?
For the LIR solver you can use 1, but for the BEST solvers you need to use 0.99 in GeoDict 2024.

Did you try to disable the porosity of the separator or to reassign the separator to solid electrolyte?

Did this problem also occur when doing a fully resolved simulation using the LIR solver?

Since GeoDict 2025, solid electrolytes are directly supported in the material database and in BatteryDict as described here:
https://geodict-userguide.math2market.de/2026/batterydict_chargebattery_allsolidstatebatteries.html

Thus, we would highly recommend to upgrade to GeoDict 2026 if you are researching solid state batteries.

Best regards,

Janine

[Material Database User Guide]

Hello Shunsuke,

this is explained in the Material Database User Guide.

Additionally for GeoDict 2022 I created a YouTube tutorial (how to add a new material to the database starts at about 6:25) for this. Although there were some changes between GeoDict 2022 and 2026 the concept stays the same.

For a short summary what to do:

• Open the material database (Settings -> Open & Edit Material Database)
• Either enter a name for Add Material and click Add or choose a material already similar to your new custom material and click Copy.
• On the right find the parameters you want to change. Under the General tab decide if it is a solid material and which property groups you want to define.
• The density can then be entered under the Solid (or Fluid) tab, the electrical conductivity can be entered under the Electrical Conductivity tab
• After all parameters are set as needed click Save Database at the bottom of the dialog.
• Now you can choose this new material under the Constituent Materials tab in the solver options dialogs or in the Constituent Materials dialog.

Best regards,
Janine

[FiberGeo]

Hello Shunsuke,

the structure generators FiberGeo and GrainGeo offer a large amount of possibilities to generate the desired structure.

Have a view at the different available object types in FiberGeo and GrainGeo.
       
There, you can define size distributions for each object type as described here.
   
There is no direct input for the loading in the structure generators. You can define a volume percentage, object number, density or grammage as described here.
   
There is a GeoApp called Bimodal Electrode, where you can define a loading. However, it only generates a cathode or anode structure with spherical, elliptical or polyhedral particles and binder.

Regarding the connection of particles to a fiber shape, there are several possibilities:
    1. If you don't need the individual particles resolved, you can simply generate fibers using FiberGeo.
    2. In GrainGeo you have a particle type called sphere agglomerate. If your particles have spherical shape, maybe this is a good object type for you?
    3. You can first create a fiber structure with FiberGeo and then afterwards use GrainGeo with the option Create in Current, and for the Center Distribution of the object choose On Current Objects. Then, the grains will only be placed where the fibers have been.

Best regards,
Janine

Hi,

do you have a structure model where you want to add surface roughness? That can be done with GrainGeo - Roughen Surface (https://geodict-userguide.math2market.de/2025/graingeo_roughensurface.html).
Or do you have a segmented scan where the solid surface is rough and you want to somehow calculate the roughness? Is this to create a statistical digital twin? There is no direct solution for this, but using Python scripting you can optimize the structure according to the desired properties, e.g. pore size distribution or permeability. 

Best regards,
Janine

[Settings > Edit Expert Settings]

Hi Jack Davis,

Good news: using the following expert settings (Settings > Edit Expert Settings) and a threshold of 0.7 we could improve the result significantly:


   
Short explanation for the chosen expert settings :
   

• Reconnection Threshold: we strongly relaxed it because the fibers are very isolated and it does not connect through the pore space.
• Max Distance: this parameter is important because otherwise only the local fiber radius is considered.
• Remove Crossing Radius: this removes crossing artefacts at crossings, preventing branched fibers
• Cleanse Centerlines: this cleans the result improving the centerlines. This is needed because the fibers have such a rough surface. For this reason also a higher threshold is needed. It is easier to connect through gaps, than to resolve crossings.

 

Another thing that improves the result a little bit more is to apply a "morphological closing" before using FiberFind. For this, use ProcessGeo > Morphological Operations > Dilate.
First reassign the non-fiber material to pore material (ProcessGeo - Reassign Materials & Material IDs).
Then, dilate the fiber material with the same ID.
Afterwards dilate the pore material with pore material.
Then, the fibers are little bit smoothed without losing to much of their shape.
This helps FiberFind to identify the fibers afterwards. 

Best regards,
Janine

[FiberGeo > Create]

Dear Jack Davis,

I'm sorry for the late reply. I think it would be great if you could send the structure file. If you don't want to share it here, send it to support@math2market.de. Then, we can have a look at it.

In case the current networks cannot handle this structure, it could help if you train your own custom network using GeoDict-AI specialized on your structures.
https://geodict-userguide.math2market.de/2025/geodictai.html

There is also a tutorial for training a neural network for identifying binder. I will send you the password for unzipping the tutorial via e-mail.
https://www.gddownload.de/Tutorials/Training-Neural-Network-for-binder-identification-in-NMC-cathodes-with-GeoDictAI.zip

If you want to train your own network, I think the training data generation macro should then (at least) contain the following steps:
  * use FiberGeo > Create to create the fibers https://geodict-userguide.math2market.de/2025/fibergeo_create.html
    * create the fibers as close as possible to the original regarding fiber curvature, diameters, etc.
  * save the structure as *.gad file (File > Save Structure as)
  * use GrainGeo > Roughen Surface to roughen the surface https://geodict-userguide.math2market.de/2025/graingeo_roughensurface.html
  * use GadGeo > Add & Import > Add GAD Objects from File to add the previously saved gad file to the current structure to have the gad data and the roughened data in memory at the same time https://geodict-userguide.math2market.de/2025/gadgeo_addgadfile.html

Best regards,
Janine

Hi,

your code worked more or less for me. In your plot it seems, as if no solid material ID was found. Did you load the segmented structure file with material ID 1 and 2?

By the way, it would be great if you would copy paste your code here instead of using screenshots. Then, it would be easier for me to reproduce the problem Use the "#" symbol above the editor to enter the code beginning and ending markers

However I did not understand, why you want to divide the X-values by 2? Then the histogram gets moved to the left. I assume, that you wanted to account for the problem of the different lengths of the arrays count and bin_edges. For that I think it would be better to just remove the last entry of bin_edges. Even better would be to use matplotlib instead to plot the histogram. You can find an example for a very basic plot below. Matplotlib offers many options to change the plotting style as desired.

Another improvement you find in my code example below is to get the gray values with numpy.where instead of a for loop. This is much faster for large gray value images.

Code Select Expand


import numpy as np
import matplotlib.pyplot as plt

VolumeInfo  = gd.getVolumeFieldsInfo() # get list of dictionaries of loaded Volume Fields and assign it to variable VolumeInfo
nx, ny, nz  = gd.getVolDimensions()    # get the number of voxels in X-, Y- and Z-direction and assign the numbers to variables
Structure   = gd.getStructure()        # assign 3D numpy array describing the loaded structure to the variable Structure

Name        = VolumeInfo[0]['name']    # assign the name of the volume field to the variable Name.
VolumeField = gd.getVolumeField(Name)  # assign the numpy array describing the volume field to the variable VolumeField
Statistic   = []                       # Create empty list to store the statistical values

grayvalues = np.empty((nx,ny,nz),dtype=np.float32) # create 3D numpy array with the same shape as the gray value image
material_ID = np.where(Structure[:,:,:]==1)        # find out where the structure has ID 1
grayvalues[material_ID]=VolumeField[material_ID]   # take the gray values where the structure has ID 1 and save them in the new field

flat      = grayvalues.flatten()

# ---------- plot with graph dialog GeoPy API ------------------
gDlg      = gd.makeGraphDialog()                   
graph     = gDlg.addGraph('Histogram', Name, "Voxel Count")
bin_count = 256
counts, bin_edges = np.histogram(flat,bins = bin_count, range=(0,255))

x_values = bin_edges[1:-1]   # crop the first value, because the number of zeros is not interesting, crop the last value to match the number of entries in counts
y_values = counts[1:]        # crop the first entry, because the number of zeros is not interesting
x_list   = x_values.tolist()
y_list   = y_values.tolist()

graph.addData(x_list,y_list, Name)     
gDlg.run()                                   

# ---------- plot with matplotlib ------------------
plt.hist(flat, bins=bin_edges)
plt.title('Histogram')
plt.xlabel('Gray Values')
plt.ylabel('Voxel Count')
plt.savefig('HistogramPlot.png')


Hi TP,

following the topic in the User Guide I mentioned earlier, you can just record the execution of several macros into one. Just start Macro Recording and then in the Macro Execution Control select one macro after the other and click Record Only for each of them in the order you want to run them. Afterwards, end macro recording. Finally, you can run the new macro which then executes all the other macros automatically.

If you just want to run the same permeability simulation on different structures, it would be more elegant to just use one macro and the Python code shown in the tutorial I linked you in my earlier post. There, different structures are saved in one folder and the goal is to analyze Open and Closed Porosity on each of them automatically. You only have to replace the command for the open and closed porosity by the corresponding permeability simulation command.

Best regards,
Janine

Hello,

yes, the job queue server is not included in your license. For a job queue server you would need a floating license to access GeoDict from different machines in your internal network. Then you and your colleagues could send jobs to a defined job queue server. With a node-locked license you only have access to GeoDict from one machine. Thus, you don't have a job server machine.

However, if you know the macros to run beforehand, you can create a macro, that runs the other macros one after the other. The macro execution can be recorded in a macro the same way as all other commands. Find an example in the User Guide:
https://geodict-userguide.math2market.de/2025/automation_varymacrofromgeopymacro.html

Also, if you want to run the same commands with varying parameters on different structures, you only need one macro. Learn how to create a parameter macro here:
https://geodict-userguide.math2market.de/2025/automation_createparametermacro.html

If you model the structures with the GeoDict structure generators, this can just be part of the macro. If you have a stack of structures, you can automatically run the study on all structure files in one folder as described in the tutorial "Automating the handling of multiple datasets with GeoPy". Download the tutorial from our website and request the password via e-mail.
https://www.math2market.com/service-support/learning-opportunities/tutorials.html

Does this help you?

Best regards,
Janine

[Color By]

Hi,

I assume, your gray value image does not have index 1. If only one image is loaded it has always index 0. If more images are loaded, have a look at the Color By combo-box in the Volume Field tab. Counting starts with 0. The fields have the order in which they are loaded to GeoDict.
[attachimg=1]

Another thing I noted in your code example, is that the indentation does not seem to make sense within the loop. In the example in the User Guide it was meant like the following. I marked the significant differences to your code with "!!!".

Code Select Expand


VolumeInfo  = gd.getVolumeFieldsInfo() # get list of dictionaries of loaded Volume Fields and assign it to variable VolumeInfo
nx, ny, nz  = gd.getVolDimensions()    # get the number of voxels in X-, Y- and Z-direction and assign the numbers to variables
Structure   = gd.getStructure()        # assign 3D numpy array describing the loaded structure to the variable Structure

# !!! In the following command ensure to have the right index for your gray value field !!!
Name        = VolumeInfo[0]['name']    # assign the name of the volume field to the variable Name.
VolumeField = gd.getVolumeField(Name)  # assign the numpy array describing the volume field to the variable VolumeField
Statistic   = []                       # Create empty list to store the statistical values

for k in range(nz): # loop over all Z-layers
value_sum   = 0    # creating variable value_sum to sum up the result values
value_count = 0    # creating variable value_count to count the summands

for j in range(ny):  # loop over all Y-layers

  for i in range(nx): # loop over all X-layers

    if Structure[i][j][k] == 0:                       # condition: if the kth Z-value in the jth Y-column of the ith X-layeris pore space (ID 0), the following indented section is executed
       value_sum   = value_sum + VolumeField[i][j][k] # add all pore space result values of the kth Z-layer to the sum value_sum
       value_count = value_count + 1                  # count the summands of value_sum

# !!! The following section should have the right indentation according to what should be plotted. Since we want to have one value for each Z-layer it belongs to the outer loop (for k in range nz) and thus needs to have the same indentation level as the head of the second loop, here 1 space. !!!
meanVal = value_sum / value_count # compute mean value of all pore space result values in the kth Z-layer and assign it to the variable meanVal
Statistic.append(meanVal)         # append the mean value of the Z-layer to the Statistic list

# !!! The following section needs to be outside of the loop to plot all data in one plot !!!
gDlg  = gd.makeGraphDialog()                  # create a graph dialog object
graph = gDlg.addGraph(Name, "Z layers", Name) # add a graph object with the name of the volume field as title and Y-axis legend and Z-layers as X-axis legend 
Z_layers = list(range(1, nz + 1))             # writes the Z-layer numbers 1, 2, ..., nz-1, nz into a list named Z-layers
graph.addData(Z_layers, Statistic, Name)      # add a single dataset with the Z-layers as X-values, the mean result values as Y-values and the name of the volume field as legend to this graph
gDlg.run()                                    # show graph dialog


This will output something like this:
[attachimg=2]

Hello Caroline,

you can reduce the number of data points in the Electrolyte Model Parameters. Then, less computations are done for the meso parameters.

We have a tutorial for creating the txt files. This tutorial also has txt files for many of the database materials including NMC622. You can download it here: https://www.gddownload.de/Tutorials/Create-txt-file-for-concentration-dependent-parameters-in-active-material-expert-settings.zip
The password can be requested here: https://www.math2market.com/service-support/technical-support.html
But I will just send you the password via e-mail.

Best regards,
Janine

Hello Caroline,

do you run a homogenized simulation? For the homogenized simulation currently the meso parameters are computed for each data point from the concentration dependent parameter tables, which takes much time. With the upcoming Service Pack 3 for GeoDict 2025 it is possible to reduce this time. For this, set the Separator and  Binder & Carbon Black model parameters to porous and the input mode of the effective values to Tortuosity Factors. Then, the meso parameter can be computed from the tortuosity, which is much faster.

For the active material you can use concentration dependent parameters by using an expert setting as described in this YouTube tutorial: https://www.youtube.com/watch?v=wEhk8YZtQSI

Best regards,
Janine

Hello Jack,

there are many options to analyze volume fields with the Compute Metrics command, as described here: https://geodict-userguide.math2market.de/2025/geodict_computemetrics.html

For example, you can compute the mean value and standard deviation for a specific material with it. However, the option to compute the histogram for only one material is not included yet.

But if needed, you can use Python to create your own custom histogram GeoApp.

For example, you get a 3D numpy array of your structure using the command gd.getStructure() as described here:
https://geodict-userguide.math2market.de/2025/automation_api_structure.html?anchor=getstructure

and for your volume field using gd.getVolumefield(volume field index), as described here:
https://geodict-userguide.math2market.de/2025/automation_api-results.html?anchor=getvolumefield

Then, you can for example use numpy methods to get a histogram for only one material ID.
https://numpy.org/doc/stable/index.html

Best regards,
Janine