Questions tagged [fortran]
Fortran is a general purpose programming language widely used by the scientific computing community.
145
questions
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59 views
How to use LAPACK function (DGELSY) in Fortran
I am trying to use Least Squares Minimization to solve a the matrix problem: b = A*x for x. The system is overdetermined, and A is a dense matrix.
In the LAPACK library, I believe the routine DGELSY ...
0
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0answers
77 views
Second derivative using Fornberg finite difference method
I have some discrete data, non-equispaced in x, y=f(x).
I want to use a numerical finite difference method to calculate the second derivatives of y, at some point.
I am using the Fornberg method, ...
1
vote
1answer
66 views
Gaussian Elimination Using Fortran [closed]
I developed the code below for performing gaussian elimination in order to evaluate the determinant of a matrix:
...
0
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1answer
35 views
Access PETSc data in totalview?
Is it possible to view the data stored in the various PETSc data types from within totalview?
Ordinarily, PETSc types are integers which act as pointers to the actual data (obviously my understanding ...
1
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1answer
134 views
LAPACK equivalent on c++ , which is the best one? [duplicate]
I am following a course of computational material physics. The professor uses fortran to code and uses lapack to solve eigenvalue problems.
So far I just know c++. There is an equivalent library that ...
2
votes
1answer
138 views
A robust algorithm to sort a non-convex polygon vertices
Let v_{0},...,v_{N-1} be N points in a Cartesian xy plane defining the vertices of closed polygon (i.e. v_{N} = v_{0}).
Let P_{0}...
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1answer
90 views
Compute outward normal and surface area for 8 noded brick element in FEA
I have a cube which is divided into 8 small cubes by bisecting each edge, I am trying to find out the surface area of each of the faces and the corresponding outward normals for them. This operation ...
1
vote
1answer
174 views
How write a integration loop in fortran, leapfrog scheme to solvind PDE (advection)?
I want to resolve numerically this equation using of difference finite method with Leapfrog Scheme
$$\frac{\partial{u}}{\partial t}+ v \frac{\partial{u}}{\partial x}= 0 $$
I'm trying to write a code ...
4
votes
2answers
107 views
Analytical testing/quality control for scientific software in professional setting
I am charged with maintaining a buildserver on Teamcity which is meant to test our in house FE software. Currently our test suite consists of a list of benchmarks which run every time a commit is made ...
3
votes
1answer
127 views
Compute bilinear form with LAPACK
I need to compute a bilinear form for a set of left and right vectors
$$ w_k = \sum_{i,j} V_{ik}^*A_{ij}U_{jk},$$
where $A_{ij}\in\mathbb{R}$ and $U_{jk}, V_{ik} \in \mathbb{C}$ (Assume that all the ...
2
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0answers
56 views
Parallel compact schemes using the Parallal Diagonal Dominant (PDD) algorithm
I would like to use the PDD algorithm developed by Sun to solve tridiagonal matrices in parallel for the following compact finite difference scheme:
$
\begin{align}
\dfrac{1}{4}f^{'}_{i-1} + f^{'}_i +...
5
votes
2answers
230 views
Recommended language/environment for large scale semi-continuous biological models
We have a fairly large (maybe 1000 equations) differential-algebraic equation model written in ACSLX, an obsolete modelling environment similar to Modelica. The model represents the evolution of a ...
0
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1answer
608 views
implementation of a simple SPH example
I am currently learning the Smoothed Particle Hydrodynamics method that I need to use later in my thesis. I have studied the mathematics behind the method and I want to code a simple example to show ...
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0answers
76 views
Dealing with non-physical negative ODE solutions using ODEPACK
Hi and thank you all again. I am solving the reaction-diffusion-advection equation as follows
$ \partial_{t} n\left(t,z\right) = -\partial_{z}\left(\Phi\left(t,z\right)\right) + p\left(t,z\right) -n\...
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3answers
240 views
Why there are people that still prefer fortran 77 over new versions?
I am reading some notes from a course in numerical analysis for physical sciences and it is my impression that there are still people that prefer Fortran 77 over new version due to the implicit ...
1
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1answer
146 views
Bulirsch-Stoer algorithm to solve simple chemistry. Spanning long time intervals after stationarity
Hi all and thank you in advance.
I am working on a time-dependent transport-chemistry model to study the composition of planetary atmospheres.
The equations are the following
$$\frac{\partial n(z,t)}...
0
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1answer
119 views
implicit method (crank-Nicolson) I not understand the procedure [closed]
I'm trying to understand the passage through this equation can be written for easily solved with the fortran alghorithm in particular i don't understood the meaning of L_x and L_xx ... what (-1,0,1) ...
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1answer
130 views
Parameter identification for first order ODE
I have two arrays $f(z)$ and $z$ both indexed by k and I want to solve $\frac{df}{dz}=\mu(1-f)$ to find $\mu(z)$
What would be the best numerical method to solve this equation?
3
votes
1answer
1k views
Loop optimization with f2py, Cython and Numba
I tried to used f2py, Cython and Numba to make a simple loop structure be faster in python. Python implementation:
...
1
vote
1answer
147 views
LAPACK: ZGETRF with INFO greater than zero but ZGETRI does not fail.
I am computing the inverse of a complex matrix. I execute ZGETRF but U(2,2) = 0. When I compute ZGETRI, the inverse is determined. Can I trust this inverse?
5
votes
1answer
394 views
Half precision in Fortran
To improve the time efficiency of my code, I'd like to test a lower precision for real number, using e.g. half precision (2 bytes).
However, I'm not sure if I can do that in Fortran.
After playing ...
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3answers
2k views
What is the difference between MATLAB and FORTRAN?
In our university some Ph.D students for computational methods prefer FORTRAN over MATLAB. I can't understand why? What is the difference between them when are used in computational methods like ...
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0answers
528 views
IDE for Scientific computing using Fortran [closed]
I am looking to learn Fortran for Scientific Computing, which IDE setup for this exists that supports debugging, code completion capabilities and offers granular Running time Analytics. I am ...
1
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0answers
65 views
Is MATLAB feasible for app deployment versus lower level languages [duplicate]
MATLAB/Octave is a pretty useful language for prototyping scientific computation use cases, however I would like to know if the sheer nature of being a high level language bottlenecks how fast the ...
1
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1answer
219 views
Numerical Free Fall Analysis with RK4
I am trying to calculate real speed and time in free fall of a body. I wrote a code in Fortran and I am trying to improve it by using RK4 method
x=time y=total free fall
Purple line using:
...
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vote
0answers
111 views
Computing only the $k$ biggest eigenvalues and eigenvectors with Scalapack
Given that there are eigensolvers in Scalapack that use a divide and conquer method, is there any way we can use Scalapack functions to only compute the first $k$ dominant eigenvalues and ...
1
vote
1answer
80 views
Declare variable to substitute one calculate only once
Frame of the question
I am currently editing an add-on module to an ocean/circulation model, which is written in Fortran. The code of the main model is quite optimized with respect to short run time (...
0
votes
1answer
581 views
Best books and notes for beginners in the parallel FORTRAN 90 programming
I am a PhD student and my field of study is Quantum Information and Computation in the theoretical aspect. Actually I write the computer codes/program in FORTRAN 90 which are serial codes but now I ...
1
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0answers
169 views
Mass conservation in atmospheric continuity equation numerical solution
My phd project is heavily related to numerical modeling of planetary atmospheres. In particular now I am dealing with a particular expression of the continuity equation, involving a thermodynamic flux....
0
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1answer
134 views
checksum of a distributed variable
Let say I have N computers and 2 N-by-N matrices distributed across them called A and B. Matrix A is row distributed while B is column distributed. Therefore, processor i knows
...
2
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0answers
258 views
Algorithm for face based data-structure - CFD
Good morning
I'm trying to develop an unstructured CFD code to solve Euler equations in a finite-volume (cell-centered) context (learning purposes). I was able to build from a cgns file some basic ...
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vote
2answers
212 views
derivative of an array
Hi I am trying to take a derivative of an array but am having trouble. The array is two dimensional, $x$ and $y$ directions. I would like to take a derivative along $x$ and along $y$ using central ...
0
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2answers
232 views
Using two computers to run one parallelized program with intel fortran [closed]
I have two computers, both with 4-cores and I am running some heavy computational stuff in one of them using Intel Parallel Studio Cluster edition. I am coding in fortran and making extensive use of ...
3
votes
1answer
105 views
Alternative to messy grid node indexing within multiple layers of loops
Recently,I dive into a set of somehow ancient Fortran codes and try to fully understand them. A large fraction of these codes are multiple layers of loops over many state variable dimensions, which ...
0
votes
1answer
76 views
0 Hz (quite sharp) peak in FFT and division by 0
In a previous question, link, I asked about how I could most effectively do a Fourier Transform of a radial function given at certain values and which we knew the asymptotical behaviour of. The ...
1
vote
1answer
247 views
Does anyone have a driver for fortran DAE solver - COLDAE?
Coldae is a solver writter by U Ascher and R Spiteri, located here http://www.cs.ubc.ca/~ascher/coldae.f .
It can solve upto index-2 DAEs using collocation.
I am new to Fortran, and having a hard ...
3
votes
2answers
282 views
How to calculate efficiently and accurately the Fourier transform of a radial function in Fortran
As my question states, I want to calculate the Fourier transform $F(q)$ of a radial function $f(r)$ (defined on $[0,\infty)$ and which decays like an exponential $\exp(-Ar+b)$ at large $r$) as ...
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vote
1answer
184 views
A fast I/O file format readable by Fortran, Java, PHP?
I am writing a Fortran program that does fairly light weigt computation on fairly large data files. The output must be readable by some Java-script (that i have no insight in) and preferably also by ...
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1answer
403 views
Fortran round-off error with floating point operations
I have simple code, which flags nodes with in region enclosed by cylinder. On implementing the code, the result is mild tilt of the cylinder observed case with $\theta=90^{\circ}$.
The algorithm for ...
3
votes
1answer
2k views
How do I program periodic boundary conditions? [duplicate]
Hi I have a code below that solves non linear coupled PDE's given Dirichlet boundary conditions. However I need to implement periodic boundary conditions. The periodic boundary conditions are ...
1
vote
0answers
545 views
Generating Random Numbers in Fortran for Metropolis method
I am having a really hard time getting any kind of reliable / consistent result from my Metropolis code. I have torn it apart and am now examining just the randomness in my random number generator.
I ...
1
vote
0answers
524 views
Heat equation from implicit scheme with Neumann B.C
To solve the heat equation from implicit scheme subject to Neumann boundary condition we can write:
$$
T_i^{j+1}-T_i^{j}=\alpha (T_{i+1}^{j+1}-2T_{i}^{j+1}+T_{i-1}^{j+1})
$$
$$
\textbf{A} T^{n+1} = T^...
6
votes
1answer
160 views
How to compare runtimes of two algorithms in a reproducible way
I am solving one relatively simple problem with two different algorithm: one which uses brute force while the other is optimized. For a variety of reasons I actually cannot show the codes here but I ...
1
vote
2answers
450 views
efficient MPI collective non-blocking communication
I am facing a problem with MPI (Fortran). I have a really big matrix at each node and they differ at different nodes. At some point of my calculations, each node needs the matrix from all other nodes, ...
2
votes
2answers
168 views
what is the best way to code a formula to reduce roundoff error
I have an expression like the following (anyway to input latex?),
$$ z^{m}\left( \ln\left(\frac{z}{z-1}\right)-\sum_{k=1}^m \frac{z^{-k}}{k} \right)$$
for m integer, z complex
It seems if I code it ...
2
votes
2answers
513 views
Solve $AX=B$ where $A$ is a skyline matrix
Solve a matrix equation of the type $AX=B$, where $A$ is an $n \times n$ symmetric matrix stored in the form of symmetric skyline matrix.
With the solution given by Bill and some more research on ...
1
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1answer
929 views
Skyline solver for AX=B where A is symmetric skyline matrix
I am looking for a simple subroutine in Fortran 90 (GNU Compiler) to solve linear equation of the type $AX=B$, where $A$ is an $n\times n$ symmetric matrix stored in the form of symmetric skyline ...
5
votes
3answers
772 views
What do C, C++ and Java have that Fortran 2003 don't? [closed]
As you may know, Fortran is widely and longly (?) used in science. I've heard a lot of people saying that we natural scientists should all migrate to C++ or Java. I've seen people increasingly ...
2
votes
1answer
66 views
Is it common or to use objects for calculation of pair interactions in physics and chemistry simulations?
When simulation atoms, molecules, colloids, autc., are there programs that define each interacting unity as an object in the OOP sense?
In my own case, I've been simulating magnetic nanoparticles in ...
9
votes
2answers
582 views
Library with polylogarithm function [duplicate]
I am looking for a reliable library where I can find polylogarithm function and newton/secant method for solving non-linear equations. Basically I have something like this:
...
