WSJT-X uses rig control to tune the rig to the standard FT8 frequency on the band you select, to control TX/RX switching (PTT), and if you are using one of the split modes ("Rig" or "Fake it"), to keep the transmit audio range between 1500 Hz and 2000 Hz regardless of where the received signal is in the waterfall (highly recommended). The simple solution is to turn rig control off in one of the programs. Can this be solved? Yes it can, once more in at least two different ways. So far so good, but what about rig control? Both WSJT-X and N1MM+ want to control the rig, but serial ports cannot be shared between two programs. OK, so there are two different ways to get contacts logged in N1MM+, each one with its own advantages and drawbacks. You also have to be careful not to use any of the N1MM+ function keys while WSJT-X is active. You will also need to turn off N1MM+'s Enter Sends Messages (ESM) mode in order to prevent N1MM+ from trying to use the sound card to transmit in one of its digital modes whenever you press the Enter key, which would interfere with the WSJT-X operation and cause QRM. It will be up to you whether you want to correct the mode in the log afterwards it makes no difference to Field Day scoring, but of course if you plan to send QSL cards or log to LotW or eQSL, you will want to get the mode logged correctly. Since all digital modes are treated as if they were a single mode in the Field Day rules, you can just put N1MM+ into a digital mode (RTTY, PSK31 or PSK63) whenever you start to use WSJT-X and log contacts that way. You will have to log the contact in one of N1MM+'s native modes (CW, SSB, RTTY, PSK31 or PSK63) and then edit the mode in the Log window afterwards. There is a gotcha with this method, too, though - N1MM+ cannot initially log the mode of such contacts correctly. That involves reading the call sign in the WSJT-X window and typing it into the N1MM+ entry window, and then reading and typing in the exchange when it is sent to you. Instead of using the automatic logging, you might actually find it easier instead to simply log contacts manually in the N1MM+ Entry window the same way as you do in SSB. Also, if you want N1MM+ to keep track of which ARRL sections you have worked, you might want to do a Tools > Rescore Current Contest operation at the end of each WSJT-X session, and possibly at intervals during the session. You can do this by selecting the contact in the Log window, double-clicking on the exchange column and entering the exchange information that the other station sent (if they sent it - the only way to send Field Day exchange data in WSJT-X is by using the 13-character free format Tx5 message, and if the other station does not do this, you will not receive the exchange from them). So if you use the automated logging method, you will have to wait until the contact has been logged in WSJT-X, at which time the data from WSJT-X is transferred into the N1MM+ log, and then edit the contact in the N1MM+ log to add the received exchange. In fact, WSJT-X has no way to record that information. Why not? Well, the information it transfers between the two programs includes signal reports and grid squares in addition to the essential date, time, frequency, mode and call sign, but it does not include the Field Day exchange information. This automated logging method works very well in VHF contests where the exchange is the grid square, but it won't work quite so well in Field Day. This is described in the manuals, and in a previous message in the archives of this user group at (written before the current general release version of WSJT-X was issued, but the procedure describes there works with the current version). It is possible to set up the two programs so that when WSJT-X logs a contact, the data is automatically entered into the N1MM+ log as well. Your question was really about rig control, but before getting to that I am going to deal with logging first. This doesn't work, because serial ports cannot be shared directly between programs. You want to be able to get the contacts logged in the N1MM+ log regardless of where they were made from, but in the process of trying to set this up you have discovered that both programs are looking to control the rig. There are really two aspects to this: logging and rig control.
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