91
Visualization / Re: Get channel and cages from zeolites in iRaspa
« Last post by David Dubbeldam on May 04, 2021, 07:50:02 PM »You should be able to add an 'ellipsoid'. See the IRMOF-1 example in the 'primitives' section of the Gallery.
Recent Posts
92
General / Problems on Compiling RASPA2
« Last post by LHZF on May 01, 2021, 10:10:58 PM »Hi, Greetings!
On trying to install RASPA on my PC an unrecorded error in the community has been reported: I encounter a problem in the file output.ac;
The problem is described as the following:
"(...)
output.c -DDLL_EXPORT -DPIC -o .libs/output.o
output.c: In function ‘ReadRestartOutput’:
output.c:7981:62:error: request for member ‘__pos’ in something not a structure or union
7981 | if(((OutputFilePtr=fopen(buffer2,"r+"))!=NULL)||(pos.__pos<0))
| ^
output.c:8005:40: error: request for member ‘__pos’ in something not a structure or union
8005 | if(feof(OutputFilePtr)||(pos.__pos>sz))
| ^
output.c:8012:99: error: request for member ‘__pos’ in something not a structure or union
8012 | fprintf(stderr,"Failed to Reposition output-file at %ld ( beyond file-length %ld)\n",pos.__pos,sz);
| ^
output.c:8024:101: error: request for member ‘__pos’ in something not a structure or union
8024 | fprintf(stderr,"Succesfully repositioned output-file of size %ld to position %ld\n",sz,pos.__pos);
| ^
I have tried to compile the software by changing the highlighted variable, deleting "__pos", although it was not a way out.
Important information:
I'm working on Windows 10 OS, using VSCode with a ZSH terminal.
Hope for instructions,
On trying to install RASPA on my PC an unrecorded error in the community has been reported: I encounter a problem in the file output.ac;
The problem is described as the following:
"(...)
output.c -DDLL_EXPORT -DPIC -o .libs/output.o
output.c: In function ‘ReadRestartOutput’:
output.c:7981:62:error: request for member ‘__pos’ in something not a structure or union
7981 | if(((OutputFilePtr=fopen(buffer2,"r+"))!=NULL)||(pos.__pos<0))
| ^
output.c:8005:40: error: request for member ‘__pos’ in something not a structure or union
8005 | if(feof(OutputFilePtr)||(pos.__pos>sz))
| ^
output.c:8012:99: error: request for member ‘__pos’ in something not a structure or union
8012 | fprintf(stderr,"Failed to Reposition output-file at %ld ( beyond file-length %ld)\n",pos.__pos,sz);
| ^
output.c:8024:101: error: request for member ‘__pos’ in something not a structure or union
8024 | fprintf(stderr,"Succesfully repositioned output-file of size %ld to position %ld\n",sz,pos.__pos);
| ^
I have tried to compile the software by changing the highlighted variable, deleting "__pos", although it was not a way out.
Important information:
I'm working on Windows 10 OS, using VSCode with a ZSH terminal.
Hope for instructions,
93
Simulation algorithms and theory / Order-N Implementation for Computing MSD
« Last post by raghuram14 on April 30, 2021, 04:14:32 PM »Hello,
I have noticed RASPA implements the order-N method to estimate the correlations and diffusion coefficients. Are you aware if there is a similar implementation available in LAMMPS ? Is it possible to implement the routine within the LAMMPS engine? The algorithm I discuss here has been detailed in the following reference:
David Dubbeldam , Denise C. Ford , Donald E. Ellis & Randall Q. Snurr (2009) A new perspective on the order-n algorithm for computing correlation functions, Molecular Simulation, 35:12-13, 1084-1097
Thank you,
Raghu
I have noticed RASPA implements the order-N method to estimate the correlations and diffusion coefficients. Are you aware if there is a similar implementation available in LAMMPS ? Is it possible to implement the routine within the LAMMPS engine? The algorithm I discuss here has been detailed in the following reference:
David Dubbeldam , Denise C. Ford , Donald E. Ellis & Randall Q. Snurr (2009) A new perspective on the order-n algorithm for computing correlation functions, Molecular Simulation, 35:12-13, 1084-1097
Thank you,
Raghu
94
Visualization / Re: Get channel and cages from zeolites in iRaspa
« Last post by cbornes on April 22, 2021, 01:19:21 PM »Hi David thanks for the answer.
I'm not quite sure how I can transform the tubes into a sphere. I've been playing around with the transformation number under Appearance --> Properties but I can not transform a tube into a sphere. I was able to do cubes, pyramids and so on.
I'm not quite sure how I can transform the tubes into a sphere. I've been playing around with the transformation number under Appearance --> Properties but I can not transform a tube into a sphere. I was able to do cubes, pyramids and so on.
95
General / Re: The difference between PMF/PT-MC and setting each MF/Temperature GCMC job
« Last post by jimmy on April 19, 2021, 05:20:03 PM »Parallel tempering (PT)
Parallel mole fraction (PMF)
Parallel mole fraction (PMF)
96
General / The difference between PMF/PT-MC and setting each MF/Temperature GCMC job
« Last post by jimmy on April 18, 2021, 07:40:01 AM »Dear all,
I am wondering what is the difference between the PMF/PT-MC simulations and we set several GCMC jobs with different Mole Fractions or Temperatures? Will PMF/PT-MC produce higher acceptance than we set individual jobs?
Thank you.
I am wondering what is the difference between the PMF/PT-MC simulations and we set several GCMC jobs with different Mole Fractions or Temperatures? Will PMF/PT-MC produce higher acceptance than we set individual jobs?
Thank you.
97
General / Re: Problems installing on Ubuntu
« Last post by heitorabreu on April 08, 2021, 09:25:16 PM »Now it is working fine.
Thank you!
Heitor
Thank you!
Heitor
98
General / Re: Problems installing on Ubuntu
« Last post by David Dubbeldam on April 08, 2021, 04:19:10 PM »Apparently, the new Ubuntu removed sysctl. I have replaced sysctl by uctsname.
Please update to v2.0.42, and check whether it now works for you on Ubuntu 20.10.
Please update to v2.0.42, and check whether it now works for you on Ubuntu 20.10.
99
Visualization / Re: Get channel and cages from zeolites in iRaspa
« Last post by David Dubbeldam on April 08, 2021, 10:00:31 AM »Drag the MFI-example to your local projects so that it is editable. Then select the channel in the 'Scene Navigator' (See help).
After that go to the detail-view called 'Appearance' on the right, and set the properties of the 'primitive' (like the color and shape/size of the cylinder primitive).
After that go to the detail-view called 'Appearance' on the right, and set the properties of the 'primitive' (like the color and shape/size of the cylinder primitive).
100
General / Problems installing on Ubuntu
« Last post by heitorabreu on April 08, 2021, 03:37:00 AM »Dear all,
I am trying to install RASPA on ubuntu 20.10 and I am having the following problem:
output.c:43:10: fatal error: sysctl.h: Arquivo ou diretório inexistente
43 | #include <sysctl.h>
Can anyone help me with this problem?
Thank you in advance.
I am trying to install RASPA on ubuntu 20.10 and I am having the following problem:
output.c:43:10: fatal error: sysctl.h: Arquivo ou diretório inexistente
43 | #include <sysctl.h>
Can anyone help me with this problem?
Thank you in advance.