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Hi All,
I am trying to wannierize a wave function for Black Phosporene generated using quantum espresso as stated in :
This is my wannier input file
num_wann = 4
num_bands = 65
dis_num_iter = 400
num_iter = 100
guiding_centres =.true.
dis_win_min =0
dis_win_max =21
!dis_froz_min =0
dis_froz_max =8
begin atoms_frac
P 0.000000 1.999871 1.256290
P 0.499999 1.999871 0.811825
P 0.000000 1.364018 0.122453
P 0.499999 1.364018 0.566918
end atoms_frac
begin projections
P:sp3
end projections
begin unit_cell_cart
bohr
03.29549 00.00000 00.00000
00.00000 10.93010 00.00000
00.00000 00.00000 04.54364
end_unit_cell_cart
bands_plot = .true.
begin kpoint_path
G 0.000000 0.00000 0.00000 X 0.500000 0.00000 0.00000
X 0.500000 0.00000 0.00000 Y 0.000000 0.50000 0.00000
Y 0.000000 0.50000 0.00000 Z 0.000000 0.00000 0.50000
Z 0.000000 0.00000 0.50000 G 0.000000 0.00000 0.00000
end kpoint_path
mp_grid : 8 8 1
search_shells = 65
begin kpoints
0.000000000000000 0.000000000000000 0.000000000000000 0.0156250000
0.000000000000000 0.125000000000000 0.000000000000000 0.0156250000
0.000000000000000 0.249999999999999 0.000000000000000 0.0156250000
0.000000000000000 0.374999999999999 0.000000000000000 0.0156250000
0.000000000000000 -0.499999999999999 0.000000000000000 0.0156250000
-0.000000000000000 -0.374999999999999 -0.000000000000000 0.0156250000
-0.000000000000000 -0.249999999999999 -0.000000000000000 0.0156250000
-0.000000000000000 -0.125000000000000 -0.000000000000000 0.0156250000
0.125000000000000 0.000000000000000 0.000000000000000 0.0156250000
0.125000000000000 0.125000000000000 0.000000000000000 0.0156250000
0.125000000000000 0.249999999999999 0.000000000000000 0.0156250000
0.125000000000000 0.374999999999999 0.000000000000000 0.0156250000
0.125000000000000 -0.499999999999999 0.000000000000000 0.0156250000
0.125000000000000 -0.374999999999999 0.000000000000000 0.0156250000
0.125000000000000 -0.249999999999999 0.000000000000000 0.0156250000
0.125000000000000 -0.125000000000000 0.000000000000000 0.0156250000
0.249999999999999 0.000000000000000 0.000000000000000 0.0156250000
0.249999999999999 0.125000000000000 0.000000000000000 0.0156250000
0.249999999999999 0.249999999999999 0.000000000000000 0.0156250000
0.249999999999999 0.374999999999999 0.000000000000000 0.0156250000
0.249999999999999 -0.499999999999999 0.000000000000000 0.0156250000
0.249999999999999 -0.374999999999999 0.000000000000000 0.0156250000
0.249999999999999 -0.249999999999999 0.000000000000000 0.0156250000
0.249999999999999 -0.125000000000000 0.000000000000000 0.0156250000
0.374999999999999 0.000000000000000 0.000000000000000 0.0156250000
0.374999999999999 0.125000000000000 0.000000000000000 0.0156250000
0.374999999999999 0.249999999999999 0.000000000000000 0.0156250000
0.374999999999999 0.374999999999999 0.000000000000000 0.0156250000
0.374999999999999 -0.499999999999999 0.000000000000000 0.0156250000
0.374999999999999 -0.374999999999999 0.000000000000000 0.0156250000
0.374999999999999 -0.249999999999999 0.000000000000000 0.0156250000
0.374999999999999 -0.125000000000000 0.000000000000000 0.0156250000
-0.499999999999998 0.000000000000000 0.000000000000000 0.0156250000
-0.499999999999998 0.125000000000000 0.000000000000000 0.0156250000
-0.499999999999998 0.249999999999999 0.000000000000000 0.0156250000
-0.499999999999998 0.374999999999999 0.000000000000000 0.0156250000
-0.499999999999998 -0.499999999999999 0.000000000000000 0.0156250000
0.499999999999998 -0.374999999999999 0.000000000000000 0.0156250000
0.499999999999998 -0.249999999999999 0.000000000000000 0.0156250000
0.499999999999998 -0.125000000000000 0.000000000000000 0.0156250000
-0.374999999999999 -0.000000000000000 -0.000000000000000 0.0156250000
-0.374999999999999 0.125000000000000 0.000000000000000 0.0156250000
-0.374999999999999 0.249999999999999 0.000000000000000 0.0156250000
-0.374999999999999 0.374999999999999 0.000000000000000 0.0156250000
-0.374999999999999 0.499999999999999 0.000000000000000 0.0156250000
-0.374999999999999 -0.374999999999999 -0.000000000000000 0.0156250000
-0.374999999999999 -0.249999999999999 -0.000000000000000 0.0156250000
-0.374999999999999 -0.125000000000000 -0.000000000000000 0.0156250000
-0.249999999999999 -0.000000000000000 -0.000000000000000 0.0156250000
-0.249999999999999 0.125000000000000 0.000000000000000 0.0156250000
-0.249999999999999 0.249999999999999 0.000000000000000 0.0156250000
-0.249999999999999 0.374999999999999 0.000000000000000 0.0156250000
-0.249999999999999 0.499999999999999 0.000000000000000 0.0156250000
-0.249999999999999 -0.374999999999999 -0.000000000000000 0.0156250000
-0.249999999999999 -0.249999999999999 -0.000000000000000 0.0156250000
-0.249999999999999 -0.125000000000000 -0.000000000000000 0.0156250000
-0.125000000000000 -0.000000000000000 -0.000000000000000 0.0156250000
-0.125000000000000 0.125000000000000 0.000000000000000 0.0156250000
-0.125000000000000 0.249999999999999 0.000000000000000 0.0156250000
-0.125000000000000 0.374999999999999 0.000000000000000 0.0156250000
-0.125000000000000 0.499999999999999 0.000000000000000 0.0156250000
-0.125000000000000 -0.374999999999999 -0.000000000000000 0.0156250000
-0.125000000000000 -0.249999999999999 -0.000000000000000 0.0156250000
-0.125000000000000 -0.125000000000000 -0.000000000000000 0.0156250000
end kpoints
But I am getting following error when executing wannier90.x -pp pwscf:
Running in serial (with serial executable)
------
SYSTEM
------
Lattice Vectors (Ang)
a_1 1.743898 0.000000 0.000000
a_2 0.000000 5.783960 0.000000
a_3 0.000000 0.000000 2.404391
Unit Cell Volume: 24.25222 (Ang^3)
Reciprocal-Space Vectors (Ang^-1)
b_1 3.602954 0.000000 0.000000
b_2 0.000000 1.086312 0.000000
b_3 0.000000 0.000000 2.613213
*----------------------------------------------------------------------------*
| Site Fractional Coordinate Cartesian Coordinate (Ang) |
+----------------------------------------------------------------------------+
| P 1 0.00000 1.99987 1.25629 | 0.00000 11.56717 3.02061 |
| P 2 0.50000 1.99987 0.81183 | 0.87195 11.56717 1.95194 |
| P 3 0.00000 1.36402 0.12245 | 0.00000 7.88943 0.29442 |
| P 4 0.50000 1.36402 0.56692 | 0.87195 7.88943 1.36309 |
*----------------------------------------------------------------------------*
------------
K-POINT GRID
------------
Grid size = 8 x 8 x 1 Total points = 64
*---------------------------------- MAIN ------------------------------------*
| Number of Wannier Functions : 4 |
| Number of Objective Wannier Functions : 4 |
| Number of input Bloch states : 65 |
| Output verbosity (1=low, 5=high) : 1 |
| Timing Level (1=low, 5=high) : 1 |
| Optimisation (0=memory, 3=speed) : 3 |
| Length Unit : Ang |
| Post-processing setup (write *.nnkp) : T |
| Using Gamma-only branch of algorithms : F |
*----------------------------------------------------------------------------*
*------------------------------- WANNIERISE ---------------------------------*
| Total number of iterations : 100 |
| Number of CG steps before reset : 5 |
| Trial step length for line search : 2.000 |
| Convergence tolerence : 0.100E-09 |
| Convergence window : -1 |
| Iterations between writing output : 1 |
| Iterations between backing up to disk : 100 |
| Write r^2_nm to file : F |
| Write xyz WF centres to file : F |
| Write on-site energies <0n|H|0n> to file : F |
| Use guiding centre to control phases : T |
| Use phases for initial projections : F |
| Iterations before starting guiding centres: 0 |
| Iterations between using guiding centres : 1 |
*----------------------------------------------------------------------------*
*------------------------------- DISENTANGLE --------------------------------*
| Using band disentanglement : T |
| Total number of iterations : 400 |
| Mixing ratio : 0.500 |
| Convergence tolerence : 1.000E-10 |
| Convergence window : 3 |
*----------------------------------------------------------------------------*
*-------------------------------- PLOTTING ----------------------------------*
| Plotting interpolated bandstructure : T |
| Number of K-path sections : 4 |
| Divisions along first K-path section : 100 |
| Output format : gnuplot |
| Output mode : s-k |
*----------------------------------------------------------------------------*
| K-space path sections: |
| From: G 0.000 0.000 0.000 To: X 0.500 0.000 0.000 |
| From: X 0.500 0.000 0.000 To: Y 0.000 0.500 0.000 |
| From: Y 0.000 0.500 0.000 To: Z 0.000 0.000 0.500 |
| From: Z 0.000 0.000 0.500 To: G 0.000 0.000 0.000 |
*----------------------------------------------------------------------------*
Time to read parameters 0.011 (sec)
*---------------------------------- K-MESH ----------------------------------*
+----------------------------------------------------------------------------+
| Distance to Nearest-Neighbour Shells |
| ------------------------------------ |
| Shell Distance (Ang^-1) Multiplicity |
| ----- ----------------- ------------ |
| 1 0.135789 2 |
| 2 0.271578 2 |
| 3 0.407367 2 |
| 4 0.450369 2 |
| 5 0.470395 4 |
| 6 0.525915 4 |
| 7 0.543156 2 |
| 8 0.607273 4 |
| 9 0.678945 2 |
| 10 0.705586 4 |
| 11 0.814734 2 |
| 12 0.814739 4 |
| 13 0.900739 2 |
| 14 0.910916 4 |
| 15 0.930926 4 |
| 16 0.940789 4 |
| 17 0.950523 2 |
| 18 0.988574 4 |
| 19 1.051821 4 |
| 20 1.051831 4 |
| 21 1.086312 2 |
| 22 1.127961 4 |
| 23 1.175970 4 |
| 24 1.214546 4 |
| 25 1.222101 2 |
| 26 1.302445 4 |
| 27 1.309513 4 |
| 28 1.351108 2 |
| 29 1.357890 2 |
| 30 1.357914 4 |
| 31 1.378132 4 |
| 32 1.411171 4 |
| 33 1.411184 4 |
| 34 1.430629 4 |
| 35 1.456197 4 |
| 36 1.493679 2 |
| 37 1.512104 4 |
| 38 1.518177 4 |
| 39 1.560099 4 |
| 40 1.577746 4 |
| 41 1.629468 2 |
| 42 1.629477 4 |
| 43 1.651964 4 |
| 44 1.690562 4 |
| 45 1.733657 4 |
| 46 1.744250 4 |
| 47 1.765257 2 |
| 48 1.801477 2 |
| 49 1.806587 4 |
| 50 1.821803 4 |
| 51 1.821819 4 |
| 52 1.821833 4 |
| 53 1.846962 4 |
| 54 1.861853 4 |
| 55 1.881579 4 |
| 56 1.901046 2 |
| 57 1.915557 4 |
| 58 1.925172 4 |
| 59 1.953665 4 |
| 60 1.977147 4 |
| 61 1.981783 4 |
| 62 2.014093 4 |
| 63 2.036835 2 |
| 64 2.036864 4 |
| 65 2.086032 4 |
+----------------------------------------------------------------------------+
| The b-vectors are chosen automatically |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
| SVD found small singular value, Rejecting this shell and trying the next |
Unable to satisfy B1 with any of the first 65 shells
Your cell might be very long, or you may have an irregular MP grid
Try increasing the parameter search_shells in the win file (default=12)
Exiting.......
kmesh_get_automatic
Can anyone help in this regard.
With Thanks,
Shreevathsa N S
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I found this error Error at k-point 33 ndimwin 30 num_wann 32.
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I have two monthly rasters (LST landsat 8) for the months July and August. I want to create another raster for the month June.
How should I proceed? I was thinking to take the mean but it doesn't make so much sense because June is the first month of my analysis and the LST should be lower compared to July and August.
R 4.4.1, RStudio , Windows 11.
Please no ChatGPT answers without knowing if its response is correct or not.
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I'm not sure I can download a ready made monthly LST from Landsat 8 (or 9). At least I'm not aware of such data.
What if I scale down the July's raster by let's say 0.9 and produce the June's LST? Dies this make sense?
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The paper in question is "Interpolation of Nitrogen Fertilizer Use in Canada from Fertilizer Use Surveys". This paper was very recently published by Agronomy (MDPI). Agronomy has, in the last day or so, uploaded a new file for this paper that has several critical typos corrected. But the ResearchGate link still has the uncorrected version of this file. The agronomy doi link to this corrected copy is
Thank you - James Dyer, Senior Author
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First you remove the old version then upload new version, on line you can edit only title, once you upload you cannot edit.
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I used two standards (one came with the ELISA kit and the other I made myself, by preparing a series of known concentrations of the target analyte) on the same plate in my ELISA run. Why are the interpolated concentrations for my unknown samples different between the two standards?
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Dear Alaleh
If you are sure of the 100% purity of your homemade standard sample and the absence of interfering impurity in it, and the dilution is also done with the special buffer of the kit, please show the linear equation of the two standard graphs. Is the difference between the two graphs only in the y-intercept or are the slope of the lines also different?
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I have a question that I would like to share to get some feedback.
In spectral methods, increasing the degree of a polynomial for a fixed element results in obtaining more points (for example, with a shape function of degree 2, we can accurately determine 3 points, and by increasing the degree, we can determine even more points, such as 20). However, we cannot infer information about the space between two points directly because, in Euclidean space, only a single straight line passes between two points. To gain information between points, we need to increase the number of elements or the degree of the shape function.
My question is: why don't we solve this problem in Riemannian space? Unlike Euclidean space, Riemannian space allows for curvature, meaning we do not have to rely on straight lines between two points. With this idea, we can obtain information between two points using lower-degree polynomials derived from Riemannian space.
My hypothesis is that the basis function created from Riemannian space inherently provides this feature, just as the basis function in Euclidean space inherently provides information between two points.
This is an idea that has come to my mind, and I would like to know your thoughts on how valid this idea might be.
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Your question is strictly related to the Nyquist theorem. Any wavenumber greater than pi/h cannot be resolved. Increasing the accuracy dose not solve the matter, you have to reduce h.
Any reconstruction between two nodes is arbitrary, this is the boundary of the discrete world of computation.
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I am working with temperature, precipitation data (0.1 degree from CDS store) and population density data (2.5 min from SEDAC) and often have to change the resolution of either data to achieve a common resolution. I do this using cdo but often get confused on which interpolation method would be more appropriate or give accurate results for a particular variable. And does the choice of method also depends on whether we are interpolating from coarser to finer grid or vice-versa? What method should be used for population data? Can you guide me on this or provide some good references?
cdo remapbil,target_file_name temp.nc outfile.nc cdo remapcon,target_file_name prec.nc outfile.nc
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You can uses remapdis o remapbil for regular grids. The interpolation for both methods are very same. You can analized performance compared reanalysis with local meteorological data. The metrics are used common RSME, Bias, Taylor Diagram.
Best regards Axel
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I am interested to calculate the peierls barrier for the movement of screw dislocation in BCC iron between two peierls vally. For this I am using nudged elastic band (NEB) method in LAMMPS.
We developed initial and final replicas using ATOMSK. However we have to create intermediate replicas having Kinks (between initial and final position) using linear interpolation.
Is there any mathematical relation for generating such replicas or any software that can be used for the same purpose.
Please leave your comments.
Thanks
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LAMMPS will be able to give you the intermediate configurations from the NEB calculations.
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Hi, I have attached a sample file. It is the rainfall gridded data from India Meteorological Department (IMD). As you can see that there is missing data between the data (color) and the white line (which is the borderline/shoreline adjoining the sea and land). One of my study areas fall onto this missing area but no data.
Does anyone of you know how to interpolate it using the nearest 4 neighbors to generate the data over that missing area using CDO or GrADS?
Would appreciate your help and advice !!
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I've attached a PNG version of your file 'paradeep-imd.eps 99.61 KB' - 'EPS', ( Encapsulated PostScript ) is not a very common image format. I haven't sseen one for a long time, they were prevalent back in the 80s, and 90s ( https://www.adobe.com/creativecloud/file-types/image/vector/eps-file.html#history-of-the-eps-file ).
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I have found some methods like clipping and interpolation or hampel filter ...
Is there any other efficient or better methods?
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Dear all,
I am going to derive the precipitation data from NETCDF files of CMIP5 GCMs in order to  forecast precipitation after doing Bias Correction with Quantile Mapping as a downscaling method. In the literature that some of the bests are attached, the nearest neighborhood and Inverse Distance Method are highly recommended.
The nearest neighbour give the average value of the grid to each point located in the grid as a simple method. According to the attached paper (drought-assessment-based-on-m...) the author claimed that the NN method is better than other methods such as IDM because:
"The major reason is that we intended to preserve the
original climate signal of the GCMs even though the large grid spacing.
Involving more GCM grid cell data on the interpolation procedure
(as in Inverse Distance Weighting–IDW) may result to significant
information dilution, or signal cancellation between two or more grid
cell data from GCM outputs."
But in my opinion maybe the IDM is a better choice because I think as the estimates of subgrid-scale values are generally not provided and the other attached paper (1-s2.0-S00221...) is a good instance for its efficiency.
I would appreciate if someone can answer this question with an evidence. Which interpolation method do you recommend for interpolation of GCM cmip5 outputs?
Thank you in advance.
Yours,
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Differents authors, such as Torma et al., 2015 recommended used fir reggriding of precipitation inverse of distance weithing (idw). If you use Climate Data Operator (CDO) you can use its command:
cdo remapdis,gridfile infile.nc outfile.nc
Please, you read CDO User Manual.
Best regards,
Axel
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Hi,
I’m using udf to define a praticle surface reaction. The dpm_scalar_update marco is used to get the data of species mass fraction of the praticle surface reaction. No errors occur while loading the udfs. However, this error called (Variable (sv: 742, pick: species, dim: 14) cannot be interpolated. Not allocated) occurs when the dpm iterate. And the iteration stil goes on...
If anyone tell me what cause this error, it would be much appreciated.
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please be sure that the physical model you defined particularly at tht interface of the boundaries are correct.
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GIS tools are great for interpolating small-scale data, but when you want to interpolate data for the entire surface of a planet, it's problematic. The problem arises because the interpolation is done in -/+ 180 longitude and -/+ 90 latitude in terms of planar coordinates, even though the data are adjacent at the extremities. A further problem is that the distance between data points in this case can only be calculated using spherical geometry, which is not usually implemented in interpolation algorithms. In such a case, one has to write code, but I wonder what other people's experience is? Is there a program that handles this problem natively?
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Gáspár Albert INRE:"idea', if you found it useful, 'recommend' the answer so that others down the line can discover it.
What follows has a huge caveat, the specifics of your work is way over my head, but my work does have an aspect of dealing efficiently with all sorts of coordinate systems and data representations, so the following are more for possibly sparking trains of thought which someone far more capable than me might find useful - somewhat inspired by the false dichotomy between vector and raster formats in a GIS.
The 'spherical' issue is as old as geography itself, and up until now has been addressed piecemeal mostly by projecting geographic coordinate systems, and the performance limitations of computational infrastructure available. Relatively recently, the notion of DDGs (Discrete Global Grids) is undergoing an explosion of refinement as a 'sphere' ( ... and 'sphere-ish) as a recursive n-dimensional data representation (cursory, rough overview at https://spatialparalysis.xyz/blog/dggs-eli5/ but a quick Google Scholar finds more detailed descriptions: https://scholar.google.com/scholar?lookup=0&q=A+Review+of+the+Research+on+Discrete+Global+Grid+Systems+in+Digital+Earth ). Although on first appearance it would seem complex to calculate through these fields, there are now methods which mitigate this. These are already making their way into weather modeling ( https://www.abccolumbia.com/2019/01/11/ibm-to-deliver-worlds-highest-resolution-weather-model/ ).
From my naive reading of your project, it seemed to be analogous to a sort of 'weather' model, except with 'rock' instead of 'gas'.
The other vauge 'hunch' is how modern GPUs use quaternion representations and maths to short circuit the need for Cartesian calculations and transformations (quaternion interpolation) - and not just the 'spatial' sorts of computation, but for physics engines ( collision detection, etc. like when there are two spinning irregular objects with different rotational axes).
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Explore the influence of interpolation techniques on animation smoothness and realism in computer graphics. Seeking insights from experts in the field.
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Another factor for a smooth visualisation of an interpolated result, is the data used for the interpolation.
If the data used are "poor", i.e. unable to give high quality interpolation result, it is almost for sure to get an expected poor visualisation result as well.
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I need your helpe PLEASE!
For my research paper, and In order to develop my dataset, i fielded the missing observation with interpolation/extrapolation method. And I need to ensure the quality and behavior of data before starting my analysis. Could you kindly provide more details on the specific steps and methodologies to be employed to ensure the meaningfulness and verifiability of the results, I am particularly interested in understanding:
- The quality assurance measures taken before and after applying interpolation/extrapolation techniques.
-Is there a trend approach to be adopted to reflect developments within the periods for the missing data?
- and if there are any diagnostic tests to be conducted to validate the reliability of the fielded data.
Thank you in advance for your time and consideration.
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BEFORE
1. Data verification:
2. Data preprocessing:
3. Model selection:
4. Validation and cross-validation:
5. Sensitivity analysis:
6. Error estimation:
After applying interpolation or extrapolation techniques, additional quality assurance measures can be taken:
1. Result validation
2. Sensitivity analysis
3. Result visualization:
By following these quality assurance measures, the accuracy and reliability of the interpolation or extrapolation results can be improved, ensuring that the derived values are as valid and useful as possible.
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In B-spline interpolation, how control points and knot vector influences on trajectory optimization for robot path planning?
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That is a vast topic (especially since the term 'robot' has thousands of variations), all with lots of dependencies. What references have you read, as a starting point?
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Hello everyone, I encountered a problem when using SBDART to calculate the thermal radiation effect of dust aerosol of different heights. If use the aerosol.dat to input the aerosol profile. Do you have a sample file of the file and how to calculate the pmom and moma? If you do not enter a custom file, you can set zbaer and dbaer, but it will automatically interpolate. The trend is always down. How did you enter the real aerosol profile? Thank you
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Do you have a sample aerosol.data file? I don't known how to customize this file,thanks a lot
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hello
I wane to interpolate temperature in an alpine region (valle d aosta ) , i want to know how i can obtain better results ?i have data of 87 meteorological stations that distributed in an area of about 3000 km2 and also 8 statins in a smaller area in this region , as the region has a complex topography, I chose to do kriging with external drift to consider elevation as a co-variable , in this case which are should be used?the smaller about 500 km2 with 8 stations or the whole area ?(87 stations and 3000km2)
thanks
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There is a point outside your study area (located in the northern part), you should consider either removing it or correct its location. I believe you will have a better luck using the 87 stations.
As for the Kriging with External Drift (KED), it suffers from expensive computational cost, as it computes Kriging weights locally. As you can understand, the bigger the study area, the higher the computational time required for the interpolation. Compared with KED, area-to-point regression Kriging (ATPRK) is more efficient and you can incorporate multiple covariates. This is something you need to consider.
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Dear all, I am pretty new to Quantum Espresso and Wannier90. After finding out the bandstructure of my system using QE, I am trying to find out the wannier interpolated band structure, but these two band structures show a significant discrepancy. I have tried changing the projection and disentanglement window, but I am not getting a better result. The input files and bandstructure plots can be found here https://drive.google.com/drive/folders/1kxI7TZ4UD4x3TlCX8vT-J2WVLzm0nBTX?usp=sharing . It might be a minor solution for the experts. Hoping to get a positive response. Thank You.
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the criterion is the dispersion less than 4A2
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Dear Scholars,
Assume a mobile air pollution monitoring strategy using a network of sensors that move around the city, specifically a network of sensors that quantify PM2.5 at a height of 1.5 meters that lasts about 20 minutes. Clearly, using this strategy we would lose temporal resolution to gain spatial resolution.
If we would like to perform spatial interpolation to "fill" the empty spaces, what would you recommend? What do you think about it? What would be your approximations?
Regards
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El método de INTERPOLACION de Krigin resulta más apropiado por su capacidad espacial.
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I am using a python script to run Agisoft Metashape on Jetson TX2. It takes a lot of time when there are more images involved in the creation of the model. I want to increase the speed of the operation by running those on CUDA. Can someone please help me with this?
import os import Metashape doc = Metashape.app.document print("Srcipt started") doc = Metashape.app.document chunk = doc.addChunk() chunk.label = "New Chunk" path_photos = Metashape.app.getExistingDirectory("main folder:") # image_list = os.listdir(path_photos) # photo_list = list() sub_folders = os.listdir(path_photos) for folder in sub_folders: folder = os.path.join(path_photos, folder) if not os.path.isdir(folder): continue image_list = os.listdir(folder) photo_list = list() new_group = chunk.addCameraGroup() new_group.label = os.path.basename(folder) for photo in image_list: if photo.rsplit(".", 1)[1].lower() in ["jpg", "jpeg", "tif", "tiff"]: # photo_list.append("/".join([path_photos, photo])) photo_list.append(os.path.join(folder, photo)) chunk.addPhotos(photo_list) for camera in chunk.cameras: if not camera.group: camera.group = new_group print("- Photos ajoutées") doc.chunk = chunk Metashape.app.update() # Processing: chunk.matchPhotos(downscale=1, generic_preselection=True, reference_preselection=False) chunk.alignCameras() chunk.buildDepthMaps(downscale=4) chunk.buildDenseCloud() chunk.buildModel(surface_type=Metashape.Arbitrary, interpolation=Metashape.EnabledInterpolation) chunk.buildUV() chunk.buildTexture(texture_size=4096) doc.save() # chunk.buildTexture(mapping = 'generic', blending = 'mosaic', size = 2048, count=1, frames = list(range(frames))) print("Script finished")
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Hi Shivani,
same here. It would be great to get Metashape running on a Jetson but as far as I can tell only the Mac version is also ARM compatible? Can you share some information on how you got it running?
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My sister is an architect and needs to use linear interpolation in the following situation:
The NCC states the maximum ramp length for a 1:14 ramp is 9 meters and a 1:20 ramp is 15 meters before you need a landing. The NCC states to calculate the maximum length of a ramp in between these gradients is to use linear interpolation.
She wants to specify a ramp of a 1:16.6 gradient and needs to calculate the maximum ramp length before needing a landing using the two values provided above. She is not confident her calculations are correct - she found the formula below but struggled to use it. So instead, she found this website - https://www.easycalculation.com/analytical/linear-interpolation.php. The solution that website provided was 11.6 meters. Can anyone confirm that this is correct and/or explain how to correctly calculate the linear interpolation for this example using the formula? Thanks in advance.
Linear interpolation = y1 + (x - x1)*(y2-y1)/(x2-x1)
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Let's calculate the maximum ramp length for a 1:16.6 gradient using linear interpolation based on the two values provided: 1:14 (9 meters) and 1:20 (15 meters) before needing a landing.
First, let's assign the values:
x1 = 14 (corresponding to 1:14 gradient)
y1 = 9 meters (maximum ramp length for 1:14 gradient)
x2 = 20 (corresponding to 1:20 gradient)
y2 = 15 meters (maximum ramp length for 1:20 gradient)
x = 16.6 (corresponding to 1:16.6 gradient)
Now, we can use the linear interpolation formula:
Linear interpolation = y1 + (x - x1)*(y2-y1)/(x2-x1)
Substitute the values:
Linear interpolation = 9 + (16.6 - 14)(15-9)/(20-14)
Linear interpolation = 9 + 2.66/6
Linear interpolation = 9 + 2.6
Linear interpolation = 11.6 meters
So, according to the formula, the maximum ramp length for a 1:16.6 gradient before needing a landing is 11.6 meters. The website you mentioned provided the correct result. Linear interpolation is a useful method for estimating values between two known data points, and it's commonly used in various fields, including architecture and engineering.
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Dear all,
I have land use shapefile (different classes) and PM 2.5 value (stored in station point shapefile). I would like to analyze the relationship between type of land use and PM 2.5 level. If I interpolate PM 2.5 level to raster file, Is there any tools in Arcmap that can run regression analysis between land use types and PM 2.5 level? Thank you
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In ArcMap, you can perform a regression analysis between land use types and PM 2.5 levels using the Geographically Weighted Regression (GWR) tool. GWR allows you to explore spatially varying relationships between variables, which is useful when analyzing how the relationship between land use and PM 2.5 levels changes across your study area.
Here's a step-by-step guide on how to conduct a GWR analysis in ArcMap:
  1. Load your land use shapefile and station point shapefile with PM 2.5 values into your ArcMap project.
  2. Convert your station point shapefile into a raster format using the Interpolate Shape tool. This will generate a raster layer representing the interpolated PM 2.5 values.
  3. Ensure that both your land use shapefile and the interpolated PM 2.5 raster have a common spatial extent and coordinate system.
  4. Open the Geographically Weighted Regression (GWR) tool by going to ArcToolbox > Spatial Statistics Tools > Geographically Weighted Regression.
  5. In the GWR tool dialog box, specify the following parameters:Input feature class: Select your land use shapefile. Dependent variable: Choose the interpolated PM 2.5 raster as the dependent variable. Independent variables: Select the relevant variables from your land use shapefile that you want to analyze in relation to PM 2.5 levels. Kernel type: Choose the appropriate kernel type based on the characteristics of your study area and data. Bandwidth: Specify the bandwidth value, which controls the extent of the neighborhood used in the analysis. Experiment with different bandwidth values to find an optimal fit for your data. Output GWR results: Specify the output location and name for the GWR results.
  6. Click OK to run the GWR analysis.
  7. Once the analysis is complete, you will obtain the GWR results, including the coefficients and significance values for each independent variable. These results will help you understand the relationship between land use types and PM 2.5 levels and how they vary spatially across your study area.
It's important to note that the GWR tool assumes that the relationships between variables vary smoothly across space. Additionally, it's recommended to consider any relevant data preprocessing steps, such as data normalization or transformation, before conducting the regression analysis.
Remember to consult the ArcMap documentation or seek further assistance from spatial analysis experts if you encounter any specific issues or require more advanced analysis techniques.
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Hi everyone,
I am trying to navigate the literature of how to process pupil data and have some questions about what to do with blinks. We are using SR Research EyeLink 1000 Plus with headrest. We are not utilizing any gaze positioning just looking at pupil size change during a cognitive task. We have a baseline of 250ms (-250ms to 0ms) and then stimulus presentation then 2000ms interest period (sampling at 1000Hz).
Since it is measured in arbitrary units we are doing a baseline correction to normalize the data to the baseline for each trial.
There seems to be mixed literature on interpolating blinks. Do it, not do it? Linear interpolation, cubic spline interpolation, etc.
I am a bit confused on:
1. Do we interpolate blinks during the baseline period?
2. How do we do time series data and normalize to baseline if there is fall out from blinks?
3. For the interpolation during each trial, which method is best?
When doing a cubic spline interpolation using R and it worked well for the dilation of the eye, but the same interpolation ran on the baseline of that trial did not look right.
No smoothing or filtering has yet been applied to this data
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Hi Danielle,
Because, as you say, there are so many inconsistencies in the literature as to how pupil preprocessing should go, I like to follow the pipeline suggested by Kret & Sjak-Shie:
They also published a code which you can use on your data.
Answering your questions briefly:
1. The blinks should be interpolated on continuos signal, not on a small window (like a baseline). However, if due to a blink you are missing too much data in the baseline, you may need to reject this trial, as you have no "real" signal to calculate the baseline from.
2. I'm not sure I understand what you mean "fall out form blinks" - is it maybe that due to the blink you have data loss in the time window of the baseline? If so, please see the point above.
3. This is a matter of discussion, of course, but again, I suggest you take a look at Kret & Sjak-Shie's paper. For a more elaborate discussion, take a look at (many) papers by Mathôt, maybe especially
About your last comment, I have a feeling that you run your preprocessing separately for the time windows of the stimuli and of the baselines - is that correct? Remember that you deal with a continuous signal, so things like interpolation should not be used on cut-out parts of that signal. If I misunderstood, sorry about it. Either way - the papers mentioned above should help a lot!
Good luck,
Lena
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That is, if I have data every hour, I need to obtain that same data but every 10 minutes.
In Rstudio, please.
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To interpolate geopositioning data on a smaller scale, you can use various spatial interpolation methods available in R.
One of the most commonly used methods is the inverse distance weighting (IDW) method.
Here is a sample code to interpolate the geopositioning data using IDW in RStudio:
First, load the necessary packages:
library(ggplot2) library(gstat)
Next, create a sample data frame with hourly data:
# create sample data frame with hourly data set.seed(123) df <- data.frame( x = runif(24, -180, 180), y = runif(24, -90, 90), value = rnorm(24, mean = 50, sd = 10), time = seq.POSIXt(as.POSIXct("2023-05-04 00:00:00"), as.POSIXct("2023-05-04 23:00:00"), by = "hour") )
Then, create a grid of points with a 10-minute interval using the expand.grid function:
# create grid of points with 10-minute interval x_grid <- seq(min(df$x), max(df$x), by = 1/6) y_grid <- seq(min(df$y), max(df$y), by = 1/6) grid <- expand.grid(x_grid, y_grid) names(grid) <- c("x", "y")
Next, use the gstat package to create a spatial object from the data frame:
# create spatial object coordinates(df) <- ~x+y
Then, use the idw function to interpolate the data to the grid points:
# interpolate data to grid points using IDW idw_model <- gstat::idw(value ~ 1, df) grid_interp <- gstat::predict(idw_model, newdata = grid)
Finally, plot the original data and the interpolated data using ggplot2:
# plot original data and interpolated data ggplot() + geom_tile(data = df, aes(x = x, y = y, fill = value)) + geom_point(data = grid, aes(x = x, y = y), color = "black", alpha = 0.3) + geom_raster(data = grid_interp, aes(x = x, y = y, fill = var1.pred)) + scale_fill_gradient(low = "white", high = "red") + labs(x = "Longitude", y = "Latitude", fill = "Value") + theme_bw()
This code will interpolate the hourly data to a 10-minute interval and create a plot of the original data and the interpolated data.
You can modify the code to suit your specific data and requirements.
Please recommend my reply if you find it useful .
Thank you
Aahed Alhamamy
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I want everything related to the role of Interpol in combating cyber terrorism?
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I have n=61 and t=25, and I have performed linear interpolation for missing values. Could it be the reason for insignificant GMM results? Please help.
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Yes, interpolation and extrapolation can affect the results of Gaussian Mixture Models (GMM).
Interpolation refers to predicting values within the range of the training data, while extrapolation refers to predicting values outside the range of the training data.
When GMM is used for interpolation, it assumes that the data within the range of the training data is generated from a mixture of Gaussian distributions. If this assumption is correct, then GMM can accurately predict the values within the range of the training data.
However, if the assumption is incorrect, then the predicted values may not accurately reflect the underlying distribution of the data.
Similarly, when GMM is used for extrapolation, it assumes that the data outside the range of the training data is generated from a mixture of Gaussian distributions. If this assumption is incorrect, then the predicted values may not be reliable.
Therefore, it is important to evaluate the assumptions made by GMM and carefully consider the implications of interpolation and extrapolation when interpreting the results.
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I did some thermal maps of the Girona’s atmospheric urban heat island with a method of car's mobile transect. I use the software Surfer 6.0 to do the maps, but Surfer isn’t a Geographical Information System, I think this is a throuble. Also in my transects there is a very high spatial density of observation points in the downtown of the city of Girona (15/km2) and a low density in rural areas (2/km2). I always interpolate isotherms with the kriging method. What is the best method to interpolate temperatures (Kriging, IDW, etc.) in my area of interest, Girona and it environs? Can you give me bibliographic citations?
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It is important to note that the choice of interpolation method depends on the specific characteristics of the data and the study area. However, in general, kriging is considered to be one of the most accurate methods for interpolating temperature data.
In your case, since you have a high spatial density of observation points in the downtown area and a lower density in rural areas, it might be useful to use a spatially adaptive interpolation method such as kriging with varying local means (KVL) or regression kriging (RK). These methods can account for the varying spatial patterns of temperature across the study area.
Here are some references that might be helpful:
  • Stein, A. (2012). Interpolation of Spatial Data: Some Theory for Kriging. Springer Science & Business Media.
  • Oliver, M. A., & Webster, R. (2014). A tutorial guide to geostatistics: Computing and modelling variograms and kriging. Catena, 113, 56-69.
  • Hengl, T. (2009). A practical guide to geostatistical mapping. Office for Official Publications of the European Communities.
  • Zhang, Y., & Li, W. (2014). Spatial interpolation of temperature using kriging with varying local means. International Journal of Applied Earth Observation and Geoinformation, 27, 36-44.
  • Li, X., Li, J., & Li, Y. (2019). Comparison of interpolation methods for temperature in the Yellow River Basin. International Journal of Remote Sensing, 40(8), 2961-2979.
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Hope you all are doing well!!
I am wondering if anyone can suggest how to use the If statement to give the following condition in Comsol Multiphysics:
source1(T), for time(t)= 0-2 sec,
0, for t=2-3 sec,
source(2), for t=3-5 sec,
0, for t= 5-6 sec,
source1(T), for time(t)= 6-8 sec,
0, for t=8-9 sec,
source(2), for t=9-11 sec,
0, for t= 11-12 sec, and so on till 600 sec. Please note that source1 and source2 are functions of temperature, which had been added using the interpolation function in the definition tab.
Is there any other way to give the above-mentioned conditions? Please sugeest.
Regards
Prakash Singh
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Thank you.
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I am using heat transfer in solids and fluids model in Comsol Multiphysics. I want to add a heat source term in the solid domain, which is the function of solid domain temperature.
The source term is as follows:
Q=rho*Cp(T)*Tad(T)/dt.
where rho, Cp and Tad are density, specific heat and Adiabatic temperature of the solid domain, which is the function of solid domain temperature.
I have used interpolation for defining Cp and Tad properties of materials in Comsol Multiphysics.
Please see the attached files.
Then I defined the source as, Source= (rho*Cp(T)*Tad(T))/dt in the variables node and used this Source in the Heat transfer in solids and fluids section as a source term.
I am getting very less increment in temperature after simulation(only 1.5K). It should be approx 4.5-5K.
Can anyone tell me, where I am doing wrong?
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Follow the below video for help-
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I produced three different raster layers interpolating points collected in-situ in three different months in the same area using Kriging. What is the best way to highlight the temporal changes that occurred in the test site during this time? I did the standard deviation of the images, since it permits to summarize the variations in just one image. If I did the difference between subsequent images I produce two images to represent the same results. Am I right?
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Performing change detection of interpolated datasets involves comparing two or more raster layers to identify areas where changes have occurred. Here are the general steps you can follow:
  1. Preprocessing: Preprocess the datasets to ensure that they are spatially aligned and have the same resolution and extent. You can use the resampling tools in ArcGIS or other GIS software to resample the raster layers to a common resolution and projection.
  2. Difference layer: Create a difference layer by subtracting one raster layer from another. The difference layer will show the changes that have occurred between the two datasets.
  3. Thresholding: Set a threshold value to determine what magnitude of change is significant. For example, if you are detecting changes in vegetation cover, you may choose a threshold based on the percentage change in vegetation index.
  4. Visualize and analyze the change layer: Visualize the difference layer to identify areas where significant changes have occurred. You can use GIS tools to analyze and quantify the changes, such as calculating the area of change or generating statistics on the magnitude of change.
It's important to note that change detection of interpolated datasets can be challenging because interpolation can introduce uncertainty and artifacts in the data. Therefore, it's important to use appropriate interpolation techniques and validate the interpolated datasets before performing change detection. Additionally, understanding the limitations of the data and the assumptions made during the interpolation process can help to interpret the results accurately.
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Hello everyone,
I try to do time-frequency analysis on the EEG data which are processed.
I want to average the trials together within a condition and then average the data within a group before doing the frequency treatments.
The problem is that I cannot average across participants in a group as they do not have the same channel numbers (some channels were removed during the pre-processing).
I have tried to interpolate each of my EEG structures with the interpol.m (Marco Simoes) function which takes as input an EEG structure and a chanlocs - cell array of channels specification (taken from EEG.chanlocs before removing channels) and returns as output an EEG structure with the new electrodes and respective signal added in he right places but I get this type of error: unable to perform assignement because the size of the left size is 70x45500 and the size of the right size is 61x45500.
I don't see how to solve this problem as I want all my structures to have 61 channels so that I can compare the data between participants.
Thank you very much for your help.
Best regards,
Mohamed Bouguerra
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Thanks for your responses.
I tried to complete the missing electrodes at 61 to have the same number of electrodes for each subject. Indeed I do not understand why the number 70 appears. I have the same error message with 46 channels for example.
The problem is that when I apply the Interpol.m function to an EEG structure with, for example, 50 channels (indicating a chanloc of 61 electrodes), I get a structure with more electrodes than 61.
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Hi,
I have 26 sampling locations, relatively well distributed, but not adequately enough to cover the study area. I have also a digital elevation model, from which I can extract much more locations. An important detail is that the temperature data are distributed in low elevations, but no temperature data is available at high elevations. Hence, I want to use the elevation data to sensitize the temperature interpolation process through co-kriging, which works with non collocated points. I prefer to use gstat, but I am not sure: a) what is an optimal number of elevation points that I have to use (I know that I have 26 temperature points, and that I need elevation points at high elevations) b) is there an automatic process tha provides reasonable kriging predictions, such as autokrige, for co-kriging?
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You don't mention the specifics of how large your area of interest is (i.e. a 1 sq km, 10 sq km, 1000 sq km, 10000 sq km, etc.) or what exactly 'low' and 'high' mean, along with the baseline those are stating from, or where in the world it is - which would indicate the orography and general texture of the terrain relief. Perhaps extreme, but in my neighborhood, that can range from 2000 ft to 14,000 ft in 18 miles - 50 miles east that same distance has a range of about a 100ft, not 12,000 ft of elevation. Also you don't mention the chronological aspects and intervals.
Merely creating some sort of interpolated surface between your samples, depending on the above is self referential and artificial. The actual 'surface', again depending on the area of interest, is another 'DEM', grid data from the weather model of the region appropriate for the AOI which captures the general trends in the AOI.
Also, there is another correction, depending on your data source, it is not only the measured temperature on the interpolated surface, but the Density Altitude relationship correction, which will vary across the surface. Even very small variation in pressure, temperature, and altitude can have influences of a thousand feet - this life or death correction is done immediately before every airplane flight.
These aren't the only factors, and whether they matter of not depends on the extents and sampling of your area of interest, and your analytical goals.
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I’ve come across a handful of tutorials on free energy perturbation (FEP) that use a pme interpolation order of 6, like the one from mdtutorials. It sets the interpolation order value in the GROMACS .mdp file with the following:
pme-order = 6
I have found other, different types of FEP tutorials that use interpolation orders of 4, like the ones linked below:
I have a general understanding of how PME works and some familiarity with FEP simulations and alchemical transformations, but have not run FEP simulations myself.
Could someone explain to me if and/or why higher order interpolation is needed for some or all types of FEP simulations?
Thank you!
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PME interpolation order determines the number of grid points used to interpolate the long-range electrostatics in GROMACS simulations. The default value of 4 or 5 is sufficient for most systems. However, higher interpolation orders (up to 7) may be necessary for systems with larger unit cells or larger periodicity in the z-dimension, where the default values may not be accurate enough.
In terms of FEP simulations, higher interpolation orders may be useful to improve the accuracy of free energy calculations, especially for systems with a high degree of charge transfer or polarization, where the electrostatic energy plays a significant role. However, it should be noted that higher interpolation orders require more computational resources and longer simulation times. In general, it is recommended to use the default interpolation order unless it is necessary to increase it based on system-specific considerations.
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I have an Excel file (a table) containing precipitation data, I need to place that data into a map. Each of the precipitation values correspond to a point which has a latitude and longitude.
I assume that the values have to be interpolated but I am not sure how to do it.
Could you help me with that?
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Bearing in mind the above suggestions, It is simplest to plot the points on the maps. If you wish to interpolate the point data to create isohyets (lines of equal rainfall), you might wish to do some research on the best interpolation method, to give the accuracy that you need, for your circumstances. There are a number of interpolation algorithms, that will produce varying results.
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I computed the structural similarity index (SSIM) value between a ground truth mask and its corresponding predicted mask in an image segmentation task using a UNet model. Both the ground truth and predicted masks are of 1024 x 1024 resolution. I got an SSIM value of 0.9544. I resized the ground truth and predicted mask to 512 x 512 using bicubic interpolation and measured its SSIM value to be 0.9444. I repeated the process for 256 x 256, 128 x128, and 64 x 64 image resolutions and found the SSIM values as 0.9259, 0.8593, and 0.8376. I observed that the equations for luminance, structure, and contrast components in the SSIM formula appear to be normalized and does not seem to vary with image resolution. My question is for the same pair of ground truth and predicted mask, why the SSIM values keep decreasing with decreasing image resolution?
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The structural similarity index (SSIM) value is a measure of the structural similarity between two images. It compares the luminance, contrast, and structure of the images. When you decrease the image resolution, you are essentially reducing the number of pixels in the image. This can lead to a loss of information and detail, which can affect the SSIM value.
When you use bicubic interpolation to resize the image, you are essentially estimating the values of the pixels in the new resolution. These estimated values may not match the original high-resolution values exactly, leading to a decrease in the structural similarity between the two images.
Additionally, as the resolution decreases, the structural similarity will be less and less, as the change in pixel values is more pronounced for smaller images. This can also contribute to the decrease in SSIM values as the resolution decreases.
It's worth noting that SSIM is a relative measure and its value can vary depending on the image content, lighting conditions and the specific dataset. The value of 0.9544 for 1024 x 1024 resolution is considered as a high value but it does not provide a clear interpretation of the quality of the predicted mask compared to the ground truth mask.
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I want to create rectangular zone, in my modele, after that interpolate data in this zone and exported it in data file. I have done for one time step but i can't do it for all time steps.
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It's me
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  • I have a question about moving mesh in FLUENT, and I want to make the tube boundary move due to node pressure. I have seen other people's answers that the node pressure cannot be directly obtained, and The node pressure needs to be interpolated by the pressure on the face around the node. I would like to ask how to achieve this. Can anyone provide specific UDF?Thanks a lot~
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To get the node pressure in a user-defined function (UDF) by interpolating the pressure on the faces surrounding the node, you can follow these steps:
  1. Identify the node for which you want to calculate the pressure.
  2. Find the faces that are adjacent to the node.
  3. Retrieve the pressure values on these faces.
  4. Use an interpolation method, such as linear interpolation, to calculate the pressure at the node based on the pressure values on the surrounding faces.
Here is some example code in C that demonstrates how this could be done:
#include "udf.h"
/* define a function to interpolate the pressure at a node */
real interpolate_pressure(Node *node)
{
/* retrieve the adjacent faces */
Face *f1 = node->f[0];
Face *f2 = node->f[1];
Face *f3 = node->f[2];
/* retrieve the pressure values on the faces */
real p1 = C_P(f1, NULL);
real p2 = C_P(f2, NULL);
real p3 = C_P(f3, NULL);
/* interpolate the pressure at the node using linear interpolation */
real p_node = (p1 + p2 + p3) / 3;
return p_node;
}
DEFINE_ON_DEMAND(interpolate_pressure_udf)
{
/* retrieve the node for which we want to calculate the pressure */
Node *node = THREAD_NODE(t);
/* interpolate the pressure at the node */
real p_node = interpolate_pressure(node);
}
This example uses linear interpolation to calculate the node pressure, but you can use other interpolation methods if desired. You can also adjust the number of faces used in the interpolation depending on your specific needs.
I hope this helps! Let me know if you have any questions or need further assistance.
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Hello, I performed a spatio-temporal regression kriging (ordinary) on the residuals from a regression. I would like to know if the ST kriging predictor is an exact interpolator : That is, the values predicted at the sample data locations are equal to the observed value at the sample locations?
Thanks for your answer.
Lucas
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No, the ordinary spatio-temporal kriging predictor is not an exact interpolator. This is because the kriging model is based on the assumption that the sample data points are not perfectly representative of the underlying trend of the data. Thus, kriging will provide an estimate of the underlying trend, rather than an exact interpolation of the sample data points.
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Hi :)
I'm trying to replicate a protocol contained in the following paper: doi:10.1152/jn.00511.2016
I'd need to measure the median frequency of spontaneous oscillations of the membrane potential. To do so, I would like to calculate the discrete Fourier transform from a recording of spontaneous Vm oscillations and then the median frequency from a first-order interpolation of the cumulative probability of the power-spectral densities from 0.1 to 100 Hz.
I don't know how to perform this kind of calculations in Origin Pro software or Matlab: could you please help me with suggestions? Is there any simple code you know to start from?
Thanks,
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I would like to use the R package "gstat" for predicting and mapping the distribution of water quality parameters using tow methods (using kriging and co-kriging)
I need a guide to codes or resources to do this
Azzeddine
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So you want the code for Kriging using gstat. A simple Google search shows plenty of tutorials. You just need to apply the principles showed on these tutorials to your data.
I would advise you to start with Kriging and then move to co-Kriging.
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I used to interpolate the result to structured grid and display with 'mesh' or 'surf' functions, but sometimes the interpolated data was outside of the boundary. I have tried different interpolation method, but it doesn't help.
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Daniel Gaida hi, does DistMesh just generate mesh ? Is there any tools which can visualize the numerical results ?
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Hello,
I performed a calibration, then with the measured values I got an equation for interpolating the values.
Is it possible to calculate the uncertainty for the interpolated values?
Any references would be great!
Thanks!
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Hello,
you derived the equation from the measurement values having uncertainties. For this reason, the coefficients of your functions are also uncertain. Several approaches are known to transfer the measurement uncertainties to the coefficients, for instance, propagation of uncertainty or the Monte-Carlo simulation. Please take a look to the "Guide to the Expression of Uncertainty in Measurement" to get further information, cf. https://www.bipm.org/en/committees/jc/jcgm/publications
All the best
Michael
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Regards
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Comsol 5.5
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I was using bilinear interpolation for a PPPM (particle-particle-particle-mesh) on a FEM mesh but I think it is not valuable enough. So my question is: ¿ Do you know any algorithm for mesh point-particle interpolation on a Finite element mesh (for quadratic node elements actually).
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Ok what is the meaning of that?
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Recently, our group collect some water samples at several rainfall events. And then I tried to analyze the c-Q relationships. The question is the amount of data in the falling part is less than the rising part. Could we use extending lines to interpolate the missing data? Or do I have some other choice to solve this problem?
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Dear Dr. Li,
Technically, it requires at least five (5) data points with flow (q) and concentrations (c) to generate a C-Q hysteresis loop, including the initial data point, one in the rising limb, the peak flow, one in the falling limb, and the event ending point. The more data you have, the less uncertainties in your hysteresis analysis.
In your case, as long as you have more than two data points in your falling limb, I did not see a problem to do an interpolation for hysteresis analysis.
Best,
Wenlong
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Hi everybody,
I would like to ask you how I can get wind speed at a given location (lon, lat) and at a precise location. The attached script allows me to get wind speed at the mass point but I need to get wind speed at a given height e.g: 60m or 80m.
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I think the "wrf_interp_3d_z" function can be helpful for you. It Interpolates WRF variables to a specified pressure/height level.
Based on your NCL script, I think you need to have your output at a specific location. In WRF version 4.4, there is a new capability for printing the WRF output time series at a given location (lon, lat). You can look at the following link for more information.
Best,
Morteza Babaei
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I am doing land use classification using multiple scenes from the Landsat satellite for 12 months. In each scene, I have removed the cloudy pixels and replaced them with pixels with no data value. Now I composited the 7 bands from 12 scenes together, but most of the bands have missing values, and the classified image also has missing values from those bands used.
Is there a way I could interpolate the missing values in each band from an average of the corresponding pixel from all other bands with values? I would like to do change detection afterward.
I am doing the analysis in ArcGIS Pro.
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I have two points along a straight line path. Each of these points has associated with it weather forecast data in the form :
[forecast time, direction, speed]
I need to generate direction and speed predictions along a route between these points at regular intervals (e.g. 10m or 10s)
I have seen a lot of methods using four points for speed interpolation but these do not work well for only two points.
Any suggestions?
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So this has plagued me for a while. The short answer for anyone following this is to use linear interpolation or something like a 2-point COSINE interpolation (What we settled on).
The problem is, as intuitive as it may be, is that this assumes that the position you are interpolating will lie exactly on this line between point A and B. Secondly, interpolating wind speed might be easy but wind direction is not. A somewhat simple solution to this is to change it from direction and magnitude to just a vector and interpolate it that way.
The better interpolation method that we finally rested on was just to hit our wind server with more traffic in an effort to do 4 point interpolation.
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Dear, I am performing molecular dynamics through NAMD, and in the production stage (100ns), in my generated script, I can only get files > 80gb. How can I avoid producing a huge DCD file in the NAMD production step? Can anyone give a hint?
structure step3_input.psf
coordinates step3_input.pdb
set temp 310;
outputName step5_production; # base name for output from this run
# NAMD writes two files at the end, final coord and vel
# in the format of first-dyn.coor and first-dyn.vel
set inputname step4_equilibration;
binCoordinates $inputname.coor; # coordinates from last run (binary)
binVelocities $inputname.vel; # velocities from last run (binary)
extendedSystem $inputname.xsc; # cell dimensions from last run (binary)
dcdfreq 100;
dcdUnitCell yes; # the file will contain unit cell info in the style of
# charmm dcd files. if yes, the dcd files will contain
# unit cell information in the style of charmm DCD files.
xstFreq 100; # XSTFreq: control how often the extended systen configuration
# will be appended to the XST file
outputEnergies 100; # 5000 steps = every 10ps
# The number of timesteps between each energy output of NAMD
outputTiming 100; # The number of timesteps between each timing output shows
# time per step and time to completion
restartfreq 100; # 5000 steps = every 10ps
# Force-Field Parameters
paraTypeCharmm on; # We're using charmm type parameter file(s)
# multiple definitions may be used but only one file per definition
parameters toppar/par_all36m_prot.prm
parameters toppar/par_all36_na.prm
parameters toppar/par_all36_carb.prm
parameters toppar/par_all36_lipid.prm
parameters toppar/par_all36_cgenff.prm
parameters toppar/par_interface.prm
parameters toppar/toppar_all36_moreions.str
parameters toppar/toppar_all36_nano_lig.str
parameters toppar/toppar_all36_nano_lig_patch.str
parameters toppar/toppar_all36_synthetic_polymer.str
parameters toppar/toppar_all36_synthetic_polymer_patch.str
parameters toppar/toppar_all36_polymer_solvent.str
parameters toppar/toppar_water_ions.str
parameters toppar/toppar_dum_noble_gases.str
parameters toppar/toppar_ions_won.str
parameters toppar/toppar_all36_prot_arg0.str
parameters toppar/toppar_all36_prot_c36m_d_aminoacids.str
parameters toppar/toppar_all36_prot_fluoro_alkanes.str
parameters toppar/toppar_all36_prot_heme.str
parameters toppar/toppar_all36_prot_na_combined.str
parameters toppar/toppar_all36_prot_retinol.str
parameters toppar/toppar_all36_prot_model.str
parameters toppar/toppar_all36_prot_modify_res.str
parameters toppar/toppar_all36_na_nad_ppi.str
parameters toppar/toppar_all36_na_rna_modified.str
parameters toppar/toppar_all36_lipid_sphingo.str
parameters toppar/toppar_all36_lipid_archaeal.str
parameters toppar/toppar_all36_lipid_bacterial.str
parameters toppar/toppar_all36_lipid_cardiolipin.str
parameters toppar/toppar_all36_lipid_cholesterol.str
parameters toppar/toppar_all36_lipid_dag.str
parameters toppar/toppar_all36_lipid_inositol.str
parameters toppar/toppar_all36_lipid_lnp.str
parameters toppar/toppar_all36_lipid_lps.str
parameters toppar/toppar_all36_lipid_mycobacterial.str
parameters toppar/toppar_all36_lipid_miscellaneous.str
parameters toppar/toppar_all36_lipid_model.str
parameters toppar/toppar_all36_lipid_prot.str
parameters toppar/toppar_all36_lipid_tag.str
parameters toppar/toppar_all36_lipid_yeast.str
parameters toppar/toppar_all36_lipid_hmmm.str
parameters toppar/toppar_all36_lipid_detergent.str
parameters toppar/toppar_all36_lipid_ether.str
parameters toppar/toppar_all36_carb_glycolipid.str
parameters toppar/toppar_all36_carb_glycopeptide.str
parameters toppar/toppar_all36_carb_imlab.str
parameters toppar/toppar_all36_label_spin.str
parameters toppar/toppar_all36_label_fluorophore.str
parameters ../unk/unk.prm # Custom topology and parameter files for UNK
# Nonbonded Parameters
exclude scaled1-4 # non-bonded exclusion policy to use "none,1-2,1-3,1-4,or scaled1-4"
# 1-2: all atoms pairs that are bonded are going to be ignored
# 1-3: 3 consecutively bonded are excluded
# scaled1-4: include all the 1-3, and modified 1-4 interactions
# electrostatic scaled by 1-4scaling factor 1.0
# vdW special 1-4 parameters in charmm parameter file.
1-4scaling 1.0
switching on
vdwForceSwitching on; # New option for force-based switching of vdW
# if both switching and vdwForceSwitching are on CHARMM force
# switching is used for vdW forces.
# You have some freedom choosing the cutoff
cutoff 12.0; # may use smaller, maybe 10., with PME
switchdist 10.0; # cutoff - 2.
# switchdist - where you start to switch
# cutoff - where you stop accounting for nonbond interactions.
# correspondence in charmm:
# (cutnb,ctofnb,ctonnb = pairlistdist,cutoff,switchdist)
pairlistdist 16.0; # stores the all the pairs with in the distance it should be larger
# than cutoff( + 2.)
stepspercycle 20; # 20 redo pairlists every ten steps
pairlistsPerCycle 2; # 2 is the default
# cycle represents the number of steps between atom reassignments
# this means every 20/2=10 steps the pairlist will be updated
# Integrator Parameters
timestep 2.0; # fs/step
rigidBonds all; # Bound constraint all bonds involving H are fixed in length
nonbondedFreq 1; # nonbonded forces every step
fullElectFrequency 1; # PME every step
wrapWater on; # wrap water to central cell
wrapAll on; # wrap other molecules too
wrapNearest off; # use for non-rectangular cells (wrap to the nearest image)
# PME (for full-system periodic electrostatics)
PME yes;
PMEInterpOrder 6; # interpolation order (spline order 6 in charmm)
PMEGridSpacing 1.0; # maximum PME grid space / used to calculate grid size
# Constant Pressure Control (variable volume)
useGroupPressure yes; # use a hydrogen-group based pseudo-molecular viral to calcualte pressure and
# has less fluctuation, is needed for rigid bonds (rigidBonds/SHAKE)
useFlexibleCell no; # yes for anisotropic system like membrane
useConstantRatio no; # keeps the ratio of the unit cell in the x-y plane constant A=B
# Constant Temperature Control
langevin on; # langevin dynamics
langevinDamping 1.0; # damping coefficient of 1/ps (keep low)
langevinTemp $temp; # random noise at this level
langevinHydrogen off; # don't couple bath to hydrogens
# Constant pressure
langevinPiston on; # Nose-Hoover Langevin piston pressure control
langevinPistonTarget 1.01325; # target pressure in bar 1atm = 1.01325bar
langevinPistonPeriod 50.0; # oscillation period in fs. correspond to pgamma T=50fs=0.05ps
# f=1/T=20.0(pgamma)
langevinPistonDecay 25.0; # oscillation decay time. smaller value corresponds to larger random
# forces and increased coupling to the Langevin temp bath.
# Equal or smaller than piston period
langevinPistonTemp $temp; # coupled to heat bath
# run
numsteps 500000; # run stops when this step is reached
run 10000000; # 1ns
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Change dcdfreq 100 to dcdfreq 1000 or dcdfreq 5000
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How can we interpolate between two very distant cross sections of a river ?
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The character of the river changes as it may meander or sometimes straight sections as it flows downstream. The characteristics change with various factors as geology, substrate, sediment loading, vegetation, access to floodplain, gradient, watershed or basin size and land use patterns. The facet sequence of riffle, run, pool and glide, and whether the channel is braided (typical of too much sediment), or entrenched (lack of floodplain access) can make a difference. Many rivers adjust their pattern with time. The suggestions of Dr. Harris are helpful too. It may take some training and experience to successfully interpret between two cross sections, but this may be difficult nonetheless unless some effort in placement was made. If the river is relatively clear, green LiDAR coverage may be helpful in visualizing complex river patterns and depths. If I had to choose two measurement cross sections, I would probably choose a riffle (shoal) and a typical pool. Riffles typically are gradient controls, and pools are located at river bends, often have a pronounced point bar, which is suggestive of bankfull flow, and whether there is floodplain access. Besides geologic controls and substrate controls, many rivers have a history of hydrologic modification and upstream influences by land instability and/or accelerated erosion from land use practices, which can influence river character and adjustments. Rivers are more dynamic than we are likely to perceive. Using aerial photos (leaf off period may be best, and possibly select photos taken in dry and wet or flood periods if available, and the sequence through time may also help evaluate the river boundaries and frequency and extent of changes.
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Hello,
We use the commercial eurofins abraxis kit's for the detection of anatoxin-a (toxin produced by cyanobacteria). The test is a direct competitive ELISA based on the recognition of Anatoxin-a by a monoclonal antibody. Anatoxin-a, when present in a sample, and an Anatoxin-a-enzyme conjugate compete for the binding sites of mouse anti-Anatoxin-a antibodies in solution.
The concentrations of the samples are determined by interpolation using the standard curve constructed with each run.
The sample was containing a large concentration of cyanobacteria. So we analysed the sample pur and diluted at 1/100 and 1/200 (to be ine the linearity zone of the standard range). The sample pur was negative. However the dilutions gave positive results and I don't know why.
Thank you for helping me understand.
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When dilutions work but the neat/pure sample don't work the causes are most likely to be matrix effects or user error. Dilution decreases concentration of interfering substances in the matrix. Depedent on your isolation method there may be something in your solution that is interfering with the assay. High detergent and alchohol concentration are common examples of this.
Examples of methods to resolve this would be some chromotography approaches(immobilize on column and exchange buffer) or much cheaper dialysis into another buffer. However, it would be suprirsing to see such a dramatic matrix effect with zero change in signal without this always occuring when you run the test. Is this the first time this assay was run by your group?
Second just to confirm the pure sample had no change in signal from your 0 ng sample?
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I am working on kaolin clay as an adsorbent for wastewater treatment and also i have undergone XRD characteristics. Thus, the analyst send me two type of data. one is the scan of the sample in the ‘native’ detector resolution of 0.1313° 2Θ, the other contains the same data, but interpolated to a step size of 0.02° 2Θ. So, which one can be used for graphical analysis to interpret its diffraction pattern?
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Get your XRD data analyzed using this website!
Check out this website:
The service is not free but it's very affordable and definitely worth it.
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Hello, I am trying to run a simulation with real gas model from NIST using ch4a as working fluid. When I try to initialisate or run the simulation its not converging in Fluent,
in my simulation, inlet temp 110K, 0.02 kg/s ch4, pressure outlet 53 bar. just ıwant to see the phase change, ı try to understand the supercritical fluid, firstly ı tried to fit the curves at MATLAB, but there were wrongs with interpolations. ı reserach the rgp table from nist to CFX, ı couldnt, how do we deal with?
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The interesting thing about a Mollier chart (enthalpy vs. entropy): it's the only one with isotherms or isobars that are continuous in value and slope.
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I was wondering if there's any tutorial or scripts that can be used to directly downscale and correct the bias in a reanalysis data available as NetCDF such as those provided by CRU or GPCC?
Also, for the downscaling part, does this mean we're just interpolating to lower mesh or is there an actual algorithm used to downscale the data in CDO?
Thanks in advance!
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what Ahmed Albabily mentioned in the query looks like he is interested in downscaling the precipitation data. I seriously suggest against statistical downscaling, especially for precipitation. Though physical-based numerical models are better for downscaling, the present employed methods can not downscale the precipitation reliably.
Cheers,
Kishore
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Srtm 30m Dem data has significantly less data coverage in Nepal region; even NasaDEM modified version of SRTM is not precise in that region, I have tried a fill function by which via idw interpolation I filled the gaps of those dem in that region, but since the holes in dem data extend up to 10km it is not scientifically justified to interpolate in that large region. Even after this kind of dem gaps filling interpolation algorithm, further processing using that dem like Slope, Aspect, etc. map carry forward those errors... Can anyone suggest any solution regarding how to fill those gaps in the srtm data?
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Hi,
check the recently released Copernicus DEM (30 m and 90 m versions available; see -->https://spacedata.copernicus.eu/web/cscda/dataset-details?articleId=394198) is accessible via OpenTopography (https://portal.opentopography.org/dataCatalog?group=global).
Regards
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How could one increase data values from weekly to daily observations using mathematical algorithm for interpolation?
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Hello Nasiru,
What's the reason for wanting these values? That may have more to do with what sort of approach, if any, might make sense.
At first glance, doing this doesn't sound like a good idea to me. Among the reasons:
Any method for taking adjacent weekly values and inserting some estimate for the 6 six "missing" daily values will only bias the estimates of day-to-day variance in scores/values as well as increase the serial correlation across a lag from 1 to 6 days. As well, the presumption of a (perfectly) predictable day to day change is unlikely to be realized in actual measurements.
Good luck with your work.
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I did baseline correction by Xpert high Score Plus software with manual setting and used cubic spline interpolation for bacterial cellulose (BC). Is this baseline correction good in xrd spectrum of cellulose?
Thank you
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Thank you very much.
How should I draw the baseline?
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I want to learn about Solving Differential Equation based on Barycentric Interpolation. I want to learn this method, if someone has hand notes it would be great to share with me. I need to learn that in 2 weeks. Thanks in advance.
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we can see this:
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Suppose I got Force constants at 500K, 1000K, 1500K, and 2000K using TDEP. How do I interpolate the force constants for the temperatures in between?
I found it confusing when I first used it, so I am explaining the steps here in much detail.
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Hi everyone,
I'm trying to apply the spatial interpolation process for my NetCDF file. However, I keep getting the "segmentation fault (core dumped)" error.
The screenshot of the error and my NetCDF file are in the attachment.
I'd be so glad if you could explain what goes wrong during the interpolation process.
Thanks in advance
Best of luck
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The problem seemed to be subregional cropping while downloading the climate data from Copernicus website.
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I am setting up an experiment to estimate the accuracy of different interpolation algorithms for generating a spatially continuous rainfall data (gird) for a certain area. The data density (number of points versus the area) and the spatial arrangement of the data (i.e., random versus grid-based ), will vary for each run (attempt)
The objective is to understand how each algorithm performs under varying data density and spatial configuration.
Typically, different studies have done this using station data of varying data density and spatial configuration. In the current context, there are limited stations (just about 2)and the intent is to execute this experiment using data sampled (extracted) from existing regional rainfall grid, but varying the data density as well as the spatial configuration.
Note that I cannot generate random values because the kriging is to be implemented as a (multivariate stuff ) using some rainfall covariates....random values will mess up the relevance of such covariates.
I did a rapid test and found that, despite a wide difference in the density and configuration, there was no significant difference in the accuracy result, based on cross validation results. What's going on? It's not intuitive to me!!
Please, can you identify something potentially not correct with this design? Theoretically, is there anything about dependency that may affect the result negatively? Generally, what may not be fine with the design? how can we explain this in your view??
Thanks for your thoughts.
Sorry for many text..
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Hi Elijah,
Here are some suggestions:
If you use rainfall data you need to question what accumulation you employ. For instance, hourly accumulations have steeper gradients (are less smooth) than monthly accumulations, meaning that any prediction for hourly images is more difficult than for monthly ones, therefore what interpolation scheme and data you use matter the smaller the accumulation is.
The variability of the distances between the chosen points matters also, especially for kriging. Avoid choosing points all of which have similar distances from each other: if you do that the semivariogram is not computed correctly because this scheme exclude measurements in small distances. You need to inform the semivariogram on how the variability of the field changes in all different distances, including the short ones. Then you will catch microvariability (variability in short scales).
Choice of skill scores also matters. RMSE Bias and HK should be included. Also any measure for the scatter (in the scattergram measurements versus cross-validated