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+/*
+ * Copyright 2014 Ettus Research LLC
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+/*
+ * Welcome to the firmware code for the USRP Octoclock accessory product!
+ *
+ * Notes regarding this firmware:
+ * NOT in M103 compatibility mode
+ * CKOPT full rail-to-rail
+ * xtal osc
+ * 16K CK (16K clock cycles)
+ * additional delay 65ms for Crystal Oscillator
+ * slowly rising power
+ *
+ * These settings are very conservative. If a lower power oscillator is
+ * required, change CKOPT to '1' (UNPROGRAMMED).
+ *
+ * M103C = [ ]
+ * WDTON = [ ]
+ * OCDEN = [ ]
+ * JTAGEN = [X]
+ * SPIEN = [X]
+ * EESAVE = [X]
+ * BOOTSZ = 4096W_F000
+ * BOOTRST = [X]
+ * CKOPT = [X]
+ * BODLEVEL = 2V7
+ * BODEN = [ ]
+ * SUT_CKSEL = EXTHIFXTALRES_16KCK_64MS
+ *
+ * EXTENDED = 0xFF (valid)
+ * HIGH = 0x80 (valid)
+ * LOW = 0xFF (valid)
+ *
+ */
+
+#include <avr/io.h>
+
+#include <octoclock.h>
+
+void setup_atmel_io_ports(){
+/*
+ * PORT A
+ *
+ * pin# Sig Our Functional Name
+ *
+ * p51 PA0 CLK_CDCE to U205 pin 24 -- L-->H edge latches MOSI and MISO in CDCE18005
+ * p50 PA1 CE_CDCE Low = Chip Enabled for SPI comm to U205 pin 25
+ * p49 PA2 MOSI_CDCE Goes to CDCE18005 - U205 pin 23
+ * p48 PA3 MISO_CDCE Input Comes from U205 pin 22
+ * p47 PA4 PD_CDCE Low = Chip is in Power-Down state; is Hi for normal operation U205 pin 12
+ * p46 PA5 SYNC_CDCE Low = Chip is sync'd with interal dividers; Hi for normal operation U205 pin 14
+ * p45 PA6 PPS_SEL Low --> PPS_EXT selected; Hi -> PPS_GPS selected; to U203 pin 1
+ * p44 PA7 gps_lock Input Comes from M9107 - U206 pin 3
+ *
+ */
+
+// /pd_cdcd, /sync_code, /ce need to be 1 (disabled) to start
+// all bits are outputs, except PA7 (gps_lock) and PA3 (MISO_CDCE) are inputs
+PORTA = Bits_8(00110010);
+DDRA = 1<<DDA6 | 1<<DDA5 | 1<<DDA4 | 1<<DDA2 | 1<<DDA1 | 1<<DDA0;
+
+/*
+ * Port B
+ *
+ * pin# Sig Our Functional Name
+ *
+ * p10 PB0 Ethernet /SEN
+ * p11 PB1 Ethernet SCLK
+ * p12 PB2 Ethernet MOSI
+ * p13 PB3 Ethernet MISO
+ * p14 PB4 Not connected, set as output with value 0
+ * p15 PB5 Ethernet /RESET -- Set to HI for normal use, weak input
+ * p16 PB6 Ethernet /WOL --- Wake on LAN -- set, weak input
+ * p17 PB7 Not connected, set as output with value 0
+ *
+ */
+
+PORTB = Bits_8(01100001); // Initial Value is all zeros
+DDRB = 1<<DDB2 | 1<<DDB4 | 1<<DDB7; // MOSI is an output; the Not Connected pins are also outputs
+
+/*
+ * Port C
+ *
+ * pin# Sig Our Functional Name
+ *
+ * p34 PC0 Not connected, set as output with value 0
+ * p35 PC1 Reference Select Switch INPUT
+ * p36 PC2 Not connected, set as output with value 0
+ * p37 PC3 Not connected, set as output with value 0
+ * p38 PC4 Not connected, set as output with value 0
+ * p40 PC5 "Top LED" of D103 3-stack of green LEDs
+ * p41 PC6 "Middle LED"
+ * p43 PC7 "Bottom LED"
+ *
+ */
+
+PORTC = 0; // Initial Value is all zeros
+DDRC = ~( 1<<DDC1 ); // All bits are outputs, except PC1. including the 5 Not Connected bits
+
+/*
+ * Port D
+ *
+ * pin# Sig Our Functional Name
+ *
+ * p25 PD0 Ethernet /INT input
+ * p26 PD1 GPS NMEA bit, (INT1) INPUT
+ * p27 PD2 GPS Serial Out (RXD) INPUT
+ * p28 PD3 GPS Serial In (TXD) OUTPUT
+ * p29 PD4 GPS Present, INPUT hi = Present
+ * p30 PD5 Not connected, set as output with value 0
+ * p31 PD6 Not connected, set as output with value 0
+ * p32 PD7 Not connected, set as output with value 0
+ *
+ */
+
+PORTD = 0; // Initial Value is all zeros
+DDRD = 1<<DDD3;
+
+/*
+ * Port E
+ *
+ * pin# Sig Dir Our Functional Name
+ *
+ * p2 PE0 In avr_rxd (Also MOSI [PDI] when used for SPI programming of the chip)
+ * p3 PE1 Out avr_txd (Also MISO [PDO] when used for SPI programming of the chip)
+ * p4 PE2 In avr_cts
+ * p5 PE3 Out avr_rts
+ * p6 PE4 In PPS_GPS
+ * p7 PE5 In PPS_EXT_n
+ * p8 PE6 In Not Connected
+ * p9 PE7 In Not Connected
+ *
+ */
+
+PORTE = 0;
+DDRE = 1<<DDE1; // make outputs, set to zero. PE1 is usart0 TXD
+
+/*
+ * Port F
+ *
+ * Split into 2 nibbles; goes to Amp/Filter board to select ENABLE and two bits
+ * to select band one bit per nibble is not connected.
+ *
+ * pin Sig Dir Our Functional Name
+ *
+ * p61 PF0 Out J117 pin 3 (J117 pins 1 and 2 are GND)
+ * p60 PF1 Out J117 pin 4
+ * p59 PF2 Out J117 pin 5
+ * p58 PF3 Out J117 pin 6
+ * p57 PF4 Out J118 pin 3 (J118 pins 1 and 2 are GND)
+ * p56 PF5 Out J118 pin 4
+ * p55 PF6 Out J118 pin 5
+ * p54 PF7 Out J118 pin 6
+ *
+ */
+
+PORTF = 0; // Initial Value is all zeros; be sure ENABLE bits are active high!!!!
+DDRF = 0xff; // All bits are outputs
+
+}