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modify the chemistry scheme

L

ljdiao@gmail_com

Member
I am deleting species N2p, O2p, Np, Op, NOp, e and N2D from the default waccm_mozart chemistry scheme. So the whole Ion reactions are all gone as well as other reactions related with those species. The run time error is (shr_sys_abort) WARNING: calling shr_mpi_abort() and stopping
[0] MPI Abort by user Aborting program !
[0] Aborting program!
p0_4082:  p4_error: : 1001
Killed by signal 2.

So there is no meaningful messages here. I also tried deleting only N2p and the error is related with memory leak. So how can I delete those species? Very appreciate your help!
 
mmills

mmills

CSEG and Liaisons
Staff member
Which log files did you look at? Generally, the atm.log.* and ccsm.log.* files from the latest run (in the run directory) are the most useful. Is there nothing meaningful in either one of these? If not, have you tried to repeat the run with the same setup? Some crashes can occur due to transient system problems. Since you are making significant changes to the chemistry, it is likely that the crash is due to something else, but it is worth checking when nothing can be gathered from the log files.
 
mmills

mmills

CSEG and Liaisons
Staff member
Which log files did you look at? Generally, the atm.log.* and ccsm.log.* files from the latest run (in the run directory) are the most useful. Is there nothing meaningful in either one of these? If not, have you tried to repeat the run with the same setup? Some crashes can occur due to transient system problems. Since you are making significant changes to the chemistry, it is likely that the crash is due to something else, but it is worth checking when nothing can be gathered from the log files.
 
L

ljdiao@gmail_com

Member
Hi, Dr. Mills:I have been tried several times already and the result is the same as I said before. It is in the brand new directory to exlude possible confusion. I have attached my chem_mech.in file and error message in case you want check. What I should do next for checking or you have other suggestions? thanks,
 
L

ljdiao@gmail_com

Member
Hi, Dr. Mills:I have been tried several times already and the result is the same as I said before. It is in the brand new directory to exlude possible confusion. I have attached my chem_mech.in file and error message in case you want check. What I should do next for checking or you have other suggestions? thanks,
 
mmills

mmills

CSEG and Liaisons
Staff member
What is your motivation for removing the ion chemistry? If you are doing this for model efficiency, it seems the payoff is likely to be quite small. What science questions are you hoping to address with WACCM? If you are looking for an efficient version of the model with reduced chemistry, you should start with the specified chemistry (SC-WACCM) compset that is available.There are a number of WACCM modules, such as the ion drag module, that may assume ions are present. There are also ion sources, such as aurora, that will continue to produce ions unless you turn them off. It is unclear what will happen in your scheme where there are no species to add them to.
 
mmills

mmills

CSEG and Liaisons
Staff member
What is your motivation for removing the ion chemistry? If you are doing this for model efficiency, it seems the payoff is likely to be quite small. What science questions are you hoping to address with WACCM? If you are looking for an efficient version of the model with reduced chemistry, you should start with the specified chemistry (SC-WACCM) compset that is available.There are a number of WACCM modules, such as the ion drag module, that may assume ions are present. There are also ion sources, such as aurora, that will continue to produce ions unless you turn them off. It is unclear what will happen in your scheme where there are no species to add them to.
 
mmills

mmills

CSEG and Liaisons
Staff member
Yes. There is a lot of upper atmospheric physics that is added automatically when you use WACCM. Perhaps if you could tell me what you are trying to accomplish by running WACCM with these things turned off, I can help you assess whether it is worth the effort, or suggest a better approach.
 
mmills

mmills

CSEG and Liaisons
Staff member
Yes. There is a lot of upper atmospheric physics that is added automatically when you use WACCM. Perhaps if you could tell me what you are trying to accomplish by running WACCM with these things turned off, I can help you assess whether it is worth the effort, or suggest a better approach.
 
L

ljdiao@gmail_com

Member
Hi, Dr. Mills:We are trying to prepare a simplified waccm chemistry scheme. So we are trying to delete some unwanted species. I found I have a couple of photo-ionization reactions untouched. After I delete them, there is no error then. But I am curious why it says 'QJOULE', 'UE', 'VE' don't found in FINCL. I can not imagine the relationship between QJOULE etc with ION species. Thanks, 
 
L

ljdiao@gmail_com

Member
Hi, Dr. Mills:We are trying to prepare a simplified waccm chemistry scheme. So we are trying to delete some unwanted species. I found I have a couple of photo-ionization reactions untouched. After I delete them, there is no error then. But I am curious why it says 'QJOULE', 'UE', 'VE' don't found in FINCL. I can not imagine the relationship between QJOULE etc with ION species. Thanks, 
 
mmills

mmills

CSEG and Liaisons
Staff member
I think you will find the effort required to remove the ion species and get heating rates working will be quite significant, and the cost reduction will be minimal. We do provide a simlified WACCM chemistry compset (FWSC) in which the heating rates are prescribed. Is that not suited to your needs?
 
mmills

mmills

CSEG and Liaisons
Staff member
I think you will find the effort required to remove the ion species and get heating rates working will be quite significant, and the cost reduction will be minimal. We do provide a simlified WACCM chemistry compset (FWSC) in which the heating rates are prescribed. Is that not suited to your needs?
 
L

ljdiao@gmail_com

Member
Hi, Dr. Mills:I don't understand what you was saying about the "heating rates". Can you tell me more about that, s.g. how to get the heating rate working? The FWSC only has five species, not suites our needs. Also we are required to run B compset rather than F compset. thanks, 
 
L

ljdiao@gmail_com

Member
Hi, Dr. Mills:I don't understand what you was saying about the "heating rates". Can you tell me more about that, s.g. how to get the heating rate working? The FWSC only has five species, not suites our needs. Also we are required to run B compset rather than F compset. thanks, 
 
M

marsh

Member
QJOULE is the joule heating rate which is from ion neutral collisions and is an important heat source in the thermosphere at high latitudes.  If you have commented out the code that calculates this forcing in the upper atmosphere then requesting the heating rate in the output files will cause an error.Have you profiled the code with and without these species?  They, and the associated physics, should add minimally to the cost of running the model (especially if you are running a B compset), and as Mike says it may not be worth the trouble to remove them. In addition, you will be missing NOy in the stratosphere that is transported downward from the thermosphere during polar night.   Note, you will be running a new version of the code which has not been scientifically validiated if you do this.  Typically to validate the model you will need to run ~200 years of 1850 control to make sure the model is balanced in the new configuration.  THis may wipe out any cost savings you might achieve from modifiying the released code.
 
M

marsh

Member
QJOULE is the joule heating rate which is from ion neutral collisions and is an important heat source in the thermosphere at high latitudes.  If you have commented out the code that calculates this forcing in the upper atmosphere then requesting the heating rate in the output files will cause an error.Have you profiled the code with and without these species?  They, and the associated physics, should add minimally to the cost of running the model (especially if you are running a B compset), and as Mike says it may not be worth the trouble to remove them. In addition, you will be missing NOy in the stratosphere that is transported downward from the thermosphere during polar night.   Note, you will be running a new version of the code which has not been scientifically validiated if you do this.  Typically to validate the model you will need to run ~200 years of 1850 control to make sure the model is balanced in the new configuration.  THis may wipe out any cost savings you might achieve from modifiying the released code.
 
R

Rgh

New Member
mmills said:
What is your motivation for removing the ion chemistry? If you are doing this for model efficiency, it seems the payoff is likely to be quite small. What science questions are you hoping to address with WACCM? If you are looking for an efficient version of the model with reduced chemistry, you should start with the specified chemistry (SC-WACCM) compset that is available.There are a number of WACCM modules, such as the ion drag module, that may assume ions are present. There are also ion sources, such as aurora, that will continue to produce ions unless you turn them off. It is unclear what will happen in your scheme where there are no species to add them to.
Click to expand...
Could you please guide me how I can turn off or modify ion sources like aurora? or introduce user-defined ionization profile in waccm?
 
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