Problem in measuring impedance at lower frequency from 10 Hz to 1k Hz using AD5933

Quite an elaborate AFE you got there... The suspect would be the circuit R8R9R10C3 that acts as a low-pass filter with a time constant (R8||R9||R10)*C3 = 1.41630901288kOhm*1μF = 1.4 ms, so operating frequencies lower than a few KHz start noticeably leaking through. The suggestion would be to increase the resistors R8, R9, R10 (and, of course, R13 to keep R13/R10 ratio the same) or C3 or all the above. And prepare for long sweep duration.

If your current number of settling cycles works for your measurements at high MCLK, there should be not need to change it at lower MCLK.

Thank you for your reply, I got this circuit from chabowski paper [1],  In this paper page num. 16 it is discussed that (ICA and ICB are for DC bias canceller. the voltage detectors are averaged on R8 and R9 and its correspond to DC bias voltage. 

I think it's not an AFE problem because now I am trying to measure lower frequencies without AFE. I have measured 20kohm resistor with RFB 10kohm, it gives correct measurement from frequency sweep (5k-100k) by using 16Mhz external clock (settling cycle 0x64) and from 1khz to 5khz by using the 4Mhz external clock (settling cycle=0x0F), but when I am connecting 2Mhz external clock it acts as I have shown in video (running infinitely). but if I change the settling cycle from 0x0x0F to 0x05 it gives the result that I have shown in the image (not correct), I have measured 20kohm with 10kohm RFB. 

1: SIMPLE WIDE FREQUENCY RANGE IMPEDANCE METER BASED ON AD5933 INTEGRATED CIRCUIT

     Konrad Chabowski, Tomasz Piasecki, Andrzej Dzierka, Karol Nitsch

     Metrology & Measurement System, Vol. XXII (2015), No. 1, pp. 13–24.

Thank you for your reply, I got this circuit from chabowski paper [1],  In this paper page num. 16 it is discussed that (ICA and ICB are for DC bias canceller. the voltage detectors are averaged on R8 and R9 and its correspond to DC bias voltage. 

I think it's not an AFE problem because now I am trying to measure lower frequencies without AFE. I have measured 20kohm resistor with RFB 10kohm, it gives correct measurement from frequency sweep (5k-100k) by using 16Mhz external clock (settling cycle 0x64) and from 1khz to 5khz by using the 4Mhz external clock (settling cycle=0x0F), but when I am connecting 2Mhz external clock it acts as I have shown in video (running infinitely). but if I change the settling cycle from 0x0x0F to 0x05 it gives the result that I have shown in the image (not correct), I have measured 20kohm with 10kohm RFB. 

1: SIMPLE WIDE FREQUENCY RANGE IMPEDANCE METER BASED ON AD5933 INTEGRATED CIRCUIT

     Konrad Chabowski, Tomasz Piasecki, Andrzej Dzierka, Karol Nitsch

     Metrology & Measurement System, Vol. XXII (2015), No. 1, pp. 13–24.

It would be helpful if you posted the circuit without the AFE, Otherwise it is difficult to comment.

You may be bumping into the artifacts of the "DFT" type the chip is performing. Those artifacts tend to show up at the lower end of the frequency sweep regardless of MCLK frequency. Basically, at Frequency Codes below about 250000 (decimal) the “DFT” errors start growing (in oscillating manner) quite substantially, so generally there is quite sizeable systematic error in the measurement unless you measure at a handful of specific Frequency Codes where this oscillating error is zero (the so-called coherent sampling, where the sampled sequence encompasses the integer number of signal periods). If you want more details, tfsoft posted reference to a paper where it is discussed.

Other people in this forum have bumped into this effect and worked around it by reducing MCLK. To see how far they reduced their MCLK to operate at low frequencies of interest, please look, for example, here: Three electrode measurement for AD5933? , posts by rvalencia .

Running sweep without end could indicate some I2C issue. Your movie also shows unchanging value in the right column, which is suspicious - the status register and Re and Im registers do not contain correct values or red incorrectly. People reported I2C errors at low MCLK, but below 100KHz - much lower than yours. As to number of selling cycles - it should not be zero, but that would be the only restriction.
Again, commenting without seeing the circuit is always a crapshoot.

I have uploaded my circuit and external oscillator output. It's working for  16Mhz or 4Mhz, but for lower frequencies, it's not working. Now I am giving 2Mhz frequency, I want to take measurement from 300 Hz to 5000 Hz.

This circuit should work fine if Vexc is set at maximum and gain is set at 1x.
Do you have control over I2C speed of your microcontroller? Something similar to, say, Arduino's Wire.setClock() function that could reduce the I2C clock below 100KHz?

Thanks for your reply, I am using Teensy3.2 and Arduino IDE for programming. yes, I can control the i2c speed, I have mentioned the function below. now I am using 400Khz. but minimum speed will be 100kHz,

Vexc = 1.98Vp-p;

gain= X1;

Wire.begin(I2C_MASTER, 0x00, I2C_PINS_18_19, I2C_PULLUP_EXT, 400000);

I have tried with Arduino UNO with 50kHz i2c frequency, but I am facing the same problem.

AFAIK with Wire library you can go as low as 31KHz if you call Wire.setClock(31000L) after Wire.begin(). Maybe that would resolve your operation issues at low MCLK.

Snorlax, I think I am doing some mistake in my code, I saw the post as you mentioned above, can you please tell what is L in the picture below that must be an integer as gennyelectro said, I am using the function for frequency code I mentioned below  

byte getFrequency(float freq, int n){
	long val = long((freq/(MCLK/4)) * pow(2,27));
	byte code;

	  switch (n) {
	    case 1:
	      code = (val & 0xFF0000) >> 0x10; 
	      break;
	    
	    case 2:
	      code = (val & 0x00FF00) >> 0x08;
	      break;

	    case 3:
	      code = (val & 0x0000FF);
	      break;

	    default: 
	      code = 0;
	  }

	return code;  
}

Your function should work just fine as long as you change your global MCLK value in accordance with the clock frequency you feed the AD5933 chip.
As to the "L" gennyelectro discussed - it is the integer number of full cycles encompassed by the 1024-long sampled sequence to eliminate the effects of the DFT artifacts. Not sure if it is directly related to your problem.

sorry for the late reply. I have solved my problem, Actually i was not waiting between reads.